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comparative genomics

12191 relationships annotated with this phrase. Showing first 500 of 12191.
Source entity Relationship Target entity Species
genome sequencing technologies provide opportunity to generate high-quality genome assemblies
CrusView enables analysis of segmental duplications
class II peroxidase potential estimates are based on genomes matching 50 out of 195 fungal genera
31 candidate genes have orthologous genes in Arabidopsis thaliana Brassica rapa; Arabidopsis thaliana
close relatedness of Rorippa species to Arabidopsis allowed use of DNA microarrays developed for Arabidopsis model species Rorippa amphibia; Rorippa sylvestris; Arabidopsis thaliana
CrusView enables analysis of genomic macrosynteny
genes strongly differentially regulated in garden cress seed compartments were also strongly regulated in Arabidopsis in similar manner in same compartments Lepidium sativum; Arabidopsis thaliana
CrusView includes array of utilities to visualize genome synteny
core genomes of multiple introductions are highly similar each other Magnaporthe oryzae
synteny plots can be generated at scale of single gene to one chromosome
phylogenomics inferred gene families for 28 sequenced model species of the Plantae
Easyfig is used to generate synteny plots of genome segments
overcoming the redundancy barrier in functional studies could enable improving inferences about cell-type homologies across genetic backgrounds and species
CoGe's SynMap2 tool was used to assess synteny between Syntrichia ruralis and Syntrichia caninervis Syntrichia ruralis; Syntrichia caninervis
barley (Hordeum vulgare) used in comparison with fern species Ceratopteris richardii and Polypodium vulgare Hordeum vulgare; Ceratopteris richardii; Polypodium vulgare
study of wild relatives of Arabidopsis extends range of natural variation that can be studied Arabidopsis thaliana
CrusView includes array of utilities to visualize duplication events
CrusView enables analysis of gene families
CrusView is designed to facilitate comparative genomics research
collinearity was conserved between pea, M. truncatula, G. max and A. thaliana Pisum sativum; Medicago truncatula; Glycine max; Arabidopsis thaliana
15 wheat varieties with publicly available genome assemblies three present in variety panel Triticum aestivum
CoGe database allows users to perform online visual analyses of genome synteny and duplication events
PLAZA is Web-based database
VISTA is Web-based database
ChIP-seq analysis revealed high degree of conservation of (AN3, ATGIF1, GIF, GIF1, AT5G28640) target genes
homology search against pea genomic sequence data from cultivar Cameor identified two sequences similar to PALM1 Pisum sativum
CrusView enables analysis of high-frequency recombination sites
genomic resources of Brassicaceae species have opened new era of comparative genomics in Brassicaceae
CoGe is comparative genomics analysis platform
genes of interest are associated with syntenic regions
clusters of orthologs provide phylogenomic framework for in-depth and genome-wide comparative analysis
potato genome search identified StCLV2 Solanum tuberosum
2 081 674 variants were located in genic regions (27.5%) Ficus erecta; Ficus carica
discrepancy between human and Arabidopsis SNP density patterns may require another independent investigation
(ATMED14, MED14, SWP, AT3G04740) paralogues are present in animals, plants, fungi and protozoa
Ory s 23 and (CYN, AT3G23490) d 23 show amino acid identity of 37% amino acid identity with 55% positives Oryza sativa; Cynodon dactylon
CrusView karyotype feature may facilitate understanding of chromosome evolution
CrusView is more flexible than database-based comparative genomics tools in ability to analyze unpublished genomes
CrusView may be used in other organisms
barley is Poaceae genome comparison reference
CrusView may be used in other plant families
photoautotrophic eukaryotes have sequenced genomes
homologous gene pairs identified by sequence similarity Salicornia parvula; Arabidopsis thaliana
A candidate for the fig sex determinant gene is an orthologue of RESPONSIVE-TO-ANTAGONIST1 (AtHMP51, HMA7, RAN1, AT5G44790) in Arabidopsis Ficus carica; Arabidopsis thaliana
387 alpha-gliadin peptide variants includes 27 peptide variants present in both T. aestivum and A. tauschii Triticum aestivum; Aegilops tauschii
2946 OGs include proteins of Brassicaceae Aethionema arabicum; Arabidopsis thaliana; Capsella rubella; Eutrema salsugineum
89.3% of genes in OGs shared with other species in Ae. arabicum is compared to 92.4% on average in the other Brassicaceae, and only 64.9% in papaya Aethionema arabicum; Arabidopsis thaliana; Capsella rubella; Eutrema salsugineum; Carica papaya
COP data enabled characterization of genome structure of eight species Cucumis
new whole-genome comparisons enabled by improved assembly methods reveal and utilize essentially all differences between genomes independent of their size or complexity
Brachypodium distachyon is Poaceae genome comparison reference Brachypodium distachyon
N. attenuata and N. obtusifolia gene sets were included in parental origin analysis of N. benthamiana Nicotiana attenuata; Nicotiana obtusifolia
5 477 434 variants were located in intergenic regions (72.5%) Ficus erecta; Ficus carica
Acer truncatum, Camellia sinensis, Gossypium raimondii, Arabidopsis thaliana, and Acer yangbiense share 10 033 gene clusters Acer truncatum; Camellia sinensis; Gossypium raimondii; Arabidopsis thaliana; Acer yangbiense
Aethionema arabicum gene annotation is valuable resource for comparative genomics analyses Aethionema arabicum
1372 OGs include Brassicaceae except for Ae. arabicum Arabidopsis thaliana; Capsella rubella; Eutrema salsugineum
k-mer frequency ratio analysis was used to analyze 171 million Illumina 101 bp paired-end reads of Aegilops speltoides Aegilops speltoides
tandem duplicates in Ae. arabicum is significantly lower than in A. thaliana (with 10 390) Aethionema arabicum; Arabidopsis thaliana
A. tauschii lines Ent-077 and Ent-078 have peptide variant expression pattern most similar to bread wheat lines Aegilops tauschii; Triticum aestivum
13.84% of the genes were classified as both At-α ohnologs and tandem duplicates Arabidopsis thaliana; Aethionema arabicum
collinear blocks on Amaranthus hypochondriacus most have one or two homoeologous copies in Amaranthus cruentus Amaranthus cruentus; Amaranthus hypochondriacus
s01133g27051 and s01133g27052 had 40 and 72 missense mutations respectively Ficus carica
X. viscosa genome was searched for similar sequences to X. humilis (ABI3, AtABI3, SIS10, AT3G24650) Xerophyta viscosa
six diploid Nicotiana species were analyzed for homologues of genes of Nicotiana benthamiana and Nicotiana tabacum Nicotiana benthamiana; Nicotiana tabacum; six diploid Nicotiana species
18 616 gene groups include 109 single-copy gene families Acer truncatum
(LEA, AT2G21490) genes in Acer truncatum (82 genes) is more than (LEA, AT2G21490) genes in Arabidopsis thaliana (50), Camellia sinensis (72), Moringa oleifera (55), Acer yangbiense (68), Solanum lycopersicum (74) Acer truncatum; Arabidopsis thaliana; Camellia sinensis; Moringa oleifera; Acer yangbiense; Solanum lycopersicum
387 alpha-gliadin peptide variants includes 211 peptide variants unique to T. aestivum Triticum aestivum
species that diverged less time ago have more similarity in their gene composition Aethionema arabicum; Arabidopsis thaliana; Capsella rubella; Eutrema salsugineum; Carica papaya
Ae. arabicum had 5357 tandem duplicates Aethionema arabicum
rice GTs computationally identified as rice-diverged by detecting which rice GTs lack orthologs in sequenced dicots Oryza sativa; Arabidopsis thaliana; Populus trichocarpa; Medicago truncatula; Ricinus communis
five genes in O2 region and one in (OHP, OHP1, PDE335, AT5G02120) region conserved between sorghum and maize Sorghum bicolor; Zea mays
phylogenetic analysis included 12 grapevine sequences and 76 sequences from representative dicot and monocot species Vitis vinifera; Arabidopsis thaliana; Populus trichocarpa; Solanum lycopersicum; Picea abies; Pinus sitchensis; Pinus sylvestris; Citrus sinensis; Oryza sativa; Zea mays
published sulfate transporter genes from different plant species
m6A methylation patterns in plant mitochondria differ markedly from m6A patterns in bacteria Arabidopsis thaliana; Brassica oleracea var. botrytis
compare feature has power to reveal candidate sequences with increased multiplicity or uniqueness to compared WGS datasets
Venn diagram of orthogroups showed concordance with topology of the species' phylogenetic tree Aethionema arabicum; Arabidopsis thaliana; Capsella rubella; Eutrema salsugineum; Carica papaya
approach and data resources created in this study could be easily expanded to other plant systems
74.03% of the genes with more copies in A. thaliana and one copy in Ae. arabicum were classified as At-α ohnologs or tandem duplicates Arabidopsis thaliana; Aethionema arabicum
Kmasker plants compare mode analysis of barley cultivar Morex gene set using two WGS datasets of spring and winter barley Hordeum vulgare
62 A. thaliana genes could be divided into 45 orthogroups Arabidopsis thaliana; Xerophyta viscosa
comparative analysis was completed with five other plant species with annotated genomes Arabidopsis thaliana; Camellia sinensis; Moringa oleifera; Acer yangbiense; Solanum lycopersicum
phylogenetic heatmap is based on 2,617 phylogenetic trees and eight tissue RNA-sequencing datasets Oryza sativa L.
mapped F. carica contigs covered 193 530 279 bp Ficus carica
newly assembled genomes provided opportunity for identifying SVs and understanding genome evolution Oryza nivara; Oryza rufipogon; Oryza barthii; Oryza glaberrima
number of common orthogroups (OGs) decreases in accordance with divergence time of the species Aethionema arabicum; Arabidopsis thaliana; Capsella rubella; Eutrema salsugineum; Carica papaya
divergence of the genus Aethionema occurred after the 'crown group' of Brassicaceae Aethionema arabicum
three of 11 amino acids in motifs are conserved in Lhcx4 compared with Lhcx1 Phaeodactylum tricornutum
phylogenetic profiling identifies functionally linked proteins
Acer truncatum and Camellia sinensis have 396 syntenic blocks with 1:1 syntenic patterns (cscore >0.7) Acer truncatum; Camellia sinensis
33-mer peptide was not found in A. tauschii in earlier studies Aegilops tauschii
MCScanX analysis examined homologous relationships among the 17 Amaranthus cruentus pseudochromosomes Amaranthus cruentus
methods to analyze sets of assemblies are hardly available
m6A-RIP-seq data provided similar m6A patterns Arabidopsis thaliana; Brassica oleracea var. botrytis
Cross-mapping of fsQTLs between bottle gourd and relatives revealed syntenic relationship of bottle gourd fsQTLs with 12 fsQTLs in cucumber, melon or watermelon
gene manipulation tools have driven mustard species into the spotlight of comparative research
Carica papaya (Brassicales) has a higher number of exclusive genes (3559), exclusive OGs (844) and unassigned genes (6200) Carica papaya
genome sequencing provides insights into evolution and function of BAHD acyltransferases
research with Arabidopsis thaliana can be complemented by investigating other plants with larger, more complex genomes Arabidopsis thaliana
Brassicaceae species showed in 20.7% of the cases that many genes were orthologs of only one gene in Ae. arabicum Aethionema arabicum; Arabidopsis thaliana; Capsella rubella; Eutrema salsugineum
networks are becoming available for various plant species
four Lhcx protein sequences of Phaeodactylum tricornutum were aligned and searched for major differences between Lhcx1/2/3 and Lhcx4 proteins Phaeodactylum tricornutum
Cucumber Chr07 is syntenic to CM27 (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) Cucumis sativus; Cucumis metuliferus
MCScanx analysis of Amaranthus cruentus and Beta vulgaris confirmed 13 963 collinear genes Amaranthus cruentus; Beta vulgaris
metal hyperaccumulation and hypertolerance research provides highly relevant framework for comparative genomics
additional wheat varieties allow examination of copy number variation Triticum durum; Triticum aestivum
genomes of pathogenic and saprobic fungi comparison with ectomycorrhizal Laccaria genome Laccaria
Ancestral Crucifer Karyotype (ACK) and genomic blocks is robust model
clustering is explored to identify functionally equivalent genes
plant homologues (orthologues) are deduced from mammalian counterparts
OsCAS is aligned with AtCAS from Arabidopsis Oryza sativa; Arabidopsis thaliana
genome-wide atlas of conserved noncoding sequences (CNSs) illustrates power of comparative approaches
homologous gene families can be tested for functional conservation across major plant lineages
comparative analysis of multiple plant and non-plant genomes led to identification of genes specific for and conserved in cp-containing photosynthetic organisms
k-mer size upwards of k = 20 should be considered for dissimilarities between related and complex species
active QTLs-alleles in population changes were identified through direct comparisons among QTL-allele submatrices Glycine max
collinear blocks on Amaranthus hypochondriacus and Amaranthus cruentus indicate predominant 1:1 relationship with translocations of a number of collinear blocks Amaranthus cruentus; Amaranthus hypochondriacus
NBS-LRR gene number between Cucumis metuliferus CM27 and Cucumis melo L. ssp. agrestis IVF77 is significant P < 0.01 Cucumis metuliferus; Cucumis melo
Investigations of the algal relatives of land plants have strongly benefitted from recent progress in phylogenomics on plants and algae
25 genomes include seven magnoliids, eight eudicots, six monocots, two angiosperm basal group species, and two gymnosperms
Cucumis metuliferus CM27 and Cucumis melo L. ssp. agrestis IVF77 genomes contain 7,719 inversions (>1 kb) and 4,710 intra-translocations (>1 kb) Cucumis metuliferus; Cucumis melo
Cucumber Chr06 is syntenic with genomic regions of CM27 Chr03, Chr08 and (CHR11, AT3G06400) Cucumis sativus; Cucumis metuliferus
accumulating genomic information provides opportunity to perform comparative analyses
cucumber oligonucleotide (oligo) pools allowed 56 genome blocks in Cucumis to be distinguished Cucumis sativus; Cucumis
many other dioecious desert plants have been subject of genetic research
5′-UTR sequences from 22 species in Embryophyta were aligned to extract sequences in positions relevant to AUG-stop in Arabidopsis thaliana Arabidopsis thaliana; Embryophyta
genome sequencing of barley, wheat, and the diploid A and D progenitor genomes of wheat, as well as rye and diploid Th. elongatum has enabled genome-wide comparative sequence analyses of introgressive hybridization among Triticeae species
predicted protein-CDS in Amaranthus cruentus greater proportion had longer sequence compared with Amaranthus hypochondriacus Amaranthus cruentus; Amaranthus hypochondriacus
Arabidopsis thaliana (dicot) is used as model plant taxa for comparative study Arabidopsis thaliana
Cucumis melo L. ssp. agrestis IVF77 shows genomic collinearity with DHL92 melon genome Cucumis melo
large intra-chromosomal translocation on Chr05 can be detected when comparing thin-skinned melons (IVF77 and DHL92) with thick-skinned Payzawat Cucumis melo
methods to analyze sets of assemblies might change soon and open door for analyses of entire genomes of large panels of plants
low-resolution whole-chromosome painting reveal at macro level syntenic relationships of related species
Cafe software was used to identify gene families expanded or contracted across 14 genomes 14 angiosperm species
(ATBRI1, BIN1, BRI1, CBB2, DWF2, AT4G39400) ATG-stop conservation was conserved in 9 out of 22 organisms Arabidopsis thaliana; Embryophyta
plant pangenomes have expanded to encompass multiple related species at the genus level
BLASTN query with wheat nucleotide sequence resulted in single highly significant (e <10 −6 ) result at nucleotide level for Brachypodium Triticum aestivum; Brachypodium distachyon
around one-third of Y1 and Y2 insertion sequences were unique with homologues not found in other organisms Simmondsia chinensis
ATG-stops in NIP5;1 were more highly conserved among plant species than flanking regions in 5′-UTR Arabidopsis thaliana; Embryophyta
comparative genomic analyses largely rely on linear visualizations between genomes
24 792 of 27 995 contigs of F. carica genome were mapped onto F. erecta pseudomolecule sequences Ficus erecta; Ficus carica
m6A methylation patterns in plant mitochondria differ markedly from m6A patterns in nuclear-encoded mRNAs in eukaryotes Arabidopsis thaliana; Brassica oleracea var. botrytis
VvWOX1 and VvWOX6 genes are correlated in exon structure and peptide motif Vitis vinifera
genomic comparisons with phylogenetic analysis allows gene identification
relative importance of four genetic factors was evaluated through direct comparisons among QTL-allele submatrices Glycine max
most closely related sequences were from beetroot, quinoa, and spinach Simmondsia chinensis
Cucumber Chr02 is syntenic with genomic regions of CM27 Chr03, Chr05 and (CHR11, AT3G06400) Cucumis sativus; Cucumis metuliferus
first AUG-UAA in NIP5;1 was conserved in 21 out of 22 species tested Arabidopsis thaliana; Embryophyta
C. rubella has a similar number of exclusive OGs (244) Capsella rubella
A. cruentus genome assembly (371 Mb) is slightly shorter than latest A. hypochondriacus genome assembly (404 Mb) Amaranthus cruentus; Amaranthus hypochondriacus
genome sequences enabled comparative quantitative proteomic and transcriptomic analyses Arabidopsis thaliana; Oryza sativa; Populus trichocarpa; Sorghum bicolor; Zea mays
foundational resources for Oryza genus includes reference genomes and transcriptomes for all 23 Oryza species Oryza
regions on maize chromosomes 2 and 5 from second round of WGD duplications are almost 5.5 times smaller than regions on other maize chromosomes Zea mays
Inparanoid Version 2.0 used to identify rice GT orthologs in sequenced dicots Oryza sativa; Arabidopsis thaliana; Populus trichocarpa; Medicago truncatula; Ricinus communis
H. glycines parasitism genes only about 30% have database orthologues Heterodera glycines
Brachypodium genome and accompanying resources should provide more relevant model for temperate cereals Brachypodium distachyon
genome segment between 6–10Mb on rice chromosome 3 aligns with 16 rice QTLs for traits related to drought response Oryza sativa
28 OsDof genes exhibited strong consistency in ordering along the chromosomes Oryza sativa; Sorghum bicolor
entire blocks on chromosome 02A and 02B in Amaranthus cruentus share collinearity with chromosome 2 in Amaranthus hypochondriacus Amaranthus cruentus; Amaranthus hypochondriacus
isolation of genes underlying orthologous traits is the first step in conducting comparative functional studies
TB unigene set corresponded to potato and/or tomato unigene sets Solanum torvum; Solanum tuberosum; Solanum lycopersicum
VvRopGEFs were named according to their sequence similarity to AtRopGEFs from Arabidopsis thaliana Vitis vinifera; Arabidopsis thaliana
maize myosins average size much larger than rice myosins Zea mays; Oryza sativa
functional genomic data are not easily integrated for comparison between and within different rice GT families Oryza sativa
naphthoate synthase (NS/ (DHNS, ECHID, AT1G60550) ) is single orthologue of cyanobacterial MenB Arabidopsis thaliana; cyanobacteria
Arabidopsis thaliana is studied in comparative analysis with Capsella rubella and Cardamine hirsuta Arabidopsis thaliana; Capsella rubella; Cardamine hirsuta
region containing O2 on maize chromosome 7S is twice the size of region containing (OHP, OHP1, PDE335, AT5G02120) on maize chromosome 1 Zea mays
large intra-chromosomal translocation on Chr05 cannot be detected when comparing IVF77 with DHL92 Cucumis melo
Cucumber Chr05 is syntenic with genomic regions of CM27 Chr09 and (ASG3, CHR10, AT2G44980) Cucumis sativus; Cucumis metuliferus
evolution at chromosome level of A. hypochondriacus compared with quinoa and sugar beet Amaranthus hypochondriacus; Chenopodium quinoa; Beta vulgaris
454 388 genes from 14 genomes 78.8% could be assigned to orthogroups (21 039 orthogroups) 14 angiosperm species
genome duplications cause orthology issues
phylogenetic trees provide context to compare properties of gene family members
2944 pOGs comprise 34% of 8714 total pOGs Solanum tuberosum; Arabidopsis thaliana
GDIs from Citrus sinensis, Malus × domestica, and Solanum lycopersicum were generally the most abundant series in these species Citrus sinensis; Malus × domestica; Solanum lycopersicum
histone H4 and BdGLO2 have more than one homologue Brachypodium distachyon
A. thaliana genes in many-to-one OGs were found to be ohnologs (homeologs) derived from the At-α WGD in 38.87% of the cases Arabidopsis thaliana
genes, proteins and metabolites are similarly affected across different resurrection plant species
OBF-BINDING PROTEIN 3 ( (OBP3, AT3G55370) ) had relatively high ATG-stop conservation ratios Arabidopsis thaliana; Embryophyta
intragenomic duplications can be integrated with intergenomic colinearity data
papaya lcy-β2 amino acid sequences was aligned with tomato and arabidopsis lycopene β- and ϵ-cyclases Carica papaya; Solanum lycopersicum; Arabidopsis thaliana
cross-species microarray hybridization can be used for applying model organism genomics in related species for which few functional genomics resources are available
naphthoate synthase (NS) is orthologous to MenB from cyanobacteria, chlorobi, and red algae Arabidopsis thaliana; cyanobacteria; chlorobi; red algae
BLASTN survey of wheat endosperm- and cell type-specific genes against Brachypodium genome revealed generally lower levels of sequence similarity in grouping expressed in aleurone layers Triticum aestivum; Brachypodium distachyon
BdGLO2 is member of family of genes related to 12S globulins of oat Brachypodium distachyon; Avena sativa
Carica papaya (Brassicales) is sister to Brassicaceae Carica papaya
Brassicaceae species showed in 5.8% of the cases that a single gene corresponds to many in Ae. arabicum Aethionema arabicum; Arabidopsis thaliana; Capsella rubella; Eutrema salsugineum
critical gaps in the land plant tree of life have been filled recent publications of genomes of liverworts, ferns and hornworts
predicted protein-CDS in Amaranthus cruentus and Amaranthus hypochondriacus vast majority were the same length in both species Amaranthus cruentus; Amaranthus hypochondriacus
MCScanX analysis found 4561 collinear genes Amaranthus cruentus
MCScanx analysis of Amaranthus cruentus and Amaranthus hypochondriacus identified 35 242 collinear genes representing 74% and 71% of the Amaranthus hypochondriacus and Amaranthus cruentus gene complements, respectively Amaranthus cruentus; Amaranthus hypochondriacus
moss genome sequencing enabled inference of ancestral land plant states
229 genes showed high degree of homology to corresponding Arabidopsis gene products at amino acid sequence level Gossypium hirsutum; Arabidopsis thaliana
proximity of (bHLH, AT5G51780) genes more distantly related to OsRHL1 to the 5AL locus may simply be coincidental
Inparanoid is automated method for finding orthologs and in-paralogs from two species
three different proteins orthologous to (ATWOX13, HB-4, WOX13, AT4G35550) were identified in grapevine Vitis vinifera
detailed comparisons with extremophile ARMS should reveal active functional sites within C-terminus of (ATNHX7, ATSOS1, SOS1, AT2G01980) halophytes
monocots only one in (ATXIK, XI-17, XI-K, XIK, AT5G20490) and XI-E Zea mays; Oryza sativa; Sorghum bicolor
scripts in DiagHunter/GenoPix2D distribution produce finished images and predictions of synteny blocks
BLAST searches of the Brachypodium genomic sequence identified corresponding interval of 198 kb on Brachypodium chromosome 2 Brachypodium distachyon
genomic sequences of salt cress and Thellungiella parvula will enhance identification of genes responsible for salt tolerance Thellungiella salsuginea; Thellungiella parvula
MUMmer is used for identifying regions of homology between genomes
parsed BLAST data generation includes underlying BLAST analysis
RFLP probes mapped to the HvNax4 region identified related genomic region on the long arm of rice chromosome 5 Hordeum vulgare; Oryza sativa
barley orthologues of metal homeostasis genes obtained by BLAST search against TIGR Barley Gene Indices Hordeum vulgare
8714 pOGs include 18,420 S. tuberosum ESTs and 14,647 A. thaliana protein-coding genes Solanum tuberosum; Arabidopsis thaliana
phylogenetic distance of transformable C4 species from A. thaliana means that direct comparison with most widely studied model plant Arabidopsis thaliana
combining high-throughput sequencing and microarray technologies will serve as basis for future comparative functional genomic analyses using syntenic orthologues Populus euphratica; Populus trichocarpa
OrthoMCL requires assumptions about similarities
BR2/ZmABCB1 locus lies in a region syntenous to OsABCB22 Zea mays; Oryza sativa
OsCAS is aligned with BpCAS from birch Oryza sativa; Betula pendula
Arabidopsis; salt cress displayed high DNA sequence identity of 90–95% for majority of transcripts Arabidopsis thaliana; Thellungiella salsuginea
VvWOX13B and VvWOX13C have very similar sequences with 94% nucleotide identity Vitis vinifera
O2 region aligned with orthologous region in sorghum Oryza sativa; Sorghum bicolor
(OHP, OHP1, PDE335, AT5G02120) region aligned with orthologous region in sorghum Oryza sativa; Sorghum bicolor
homeodomain sequences aligned using MUSCLE algorithm Physcomitrium patens; Marchantia polymorpha; Selaginella moellendorffii; Ceratopteris richardii; Salvinia cucullata; Azolla filiculoides; Sequoiadendron giganteum; Oryza sativa; Populus trichocarpa; Arabidopsis thaliana
KOGs reports size of the conserved core of eukaryotic genes
gene set could be used successfully to identify syntenic blocks with sequenced rosid species Beta vulgaris
CrusView is designed for visualized analyses of comparative genomics data
self-defined genomic information can be integrated with genomic synteny maps
CrusView enables analysis of chromosomal rearrangements
sequence variations in C-terminal region of (ATNHX7, ATSOS1, SOS1, AT2G01980) are much more pronounced than variations in N-terminus Arabidopsis thaliana; halophytes
number of full-length (TPL, WSIP1, AT1G15750) genes in tomato fell in the range found in other plant genomes Solanum lycopersicon
phyletic pattern is a central notion introduced in the context of the COG analysis
study included in analysis (CBP1, MEE14, AT2G15890) from silkworm Bombyx mori Bombyx mori
Ceratodon purpureus has U and V sex chromosomes that share no obviously syntenic regions with each other Ceratodon purpureus
genoPlotR is used to generate synteny plots of genome segments
92,668 genes of 'ZS11' (91%) could be clustered into OrthoMCL gene families Brassica napus
maize myosin genes number comparable to rice myosin genes Zea mays; Oryza sativa
59 LTR-RTs and 145 DNA (ATNACK2, NACK2, TES, AT3G43210) present in assembled Brassica oleracea sequences were found as intact or truncated elements in assembled Brassica rapa sequences Brassica rapa; Brassica oleracea
some (ATNACK2, NACK2, TES, AT3G43210) shared by the two genomes may not be detected based on comparison of assembled sequences Brassica rapa; Brassica oleracea
whole-genome bisulfite sequencing (WGBS) and RNA sequencing were used to evaluate DNA methylation and gene expression differences in poplar and the fungus Populus spp.; Laccaria bicolor
of the 931 attdf1 downregulated genes only 99 genes were also only downregulated in HvTDF1 Arabidopsis thaliana; Hordeum vulgare
melon family members of six cloned tomato QTLs were identified in melon genome sequence Cucumis melo
229 cotton ESTs (expressed sequence tags) correspond to 232 Arabidopsis candidate genes Gossypium hirsutum; Arabidopsis thaliana
genes in BrSIO2 region have 243 homologues in A. thaliana Brassica rapa; Arabidopsis thaliana
large difference in genome size, structure, and dynamics between Arabidopsis thaliana and most crop species may be a challenge for transferring knowledge from Arabidopsis to crop species Arabidopsis thaliana
this review highlights convergence or differences existing with crops
programs designed to work with nucleotide data may not work with peptide data
Panicum hallii transcripts compared with Setaria italica gene models Panicum hallii; Setaria italica
synteny among species of the Triticeae tribe and whole Poaceae family makes genomic mapping and sequence information highly transferable across species
substantial colinearity evident from comparing group 7 wheat versus Th. ponticum genetic maps supports reasonable hypothesis of the existence of multiple yield-contributing loci along the 7L arms of both species Triticum aestivum; Thinopyrum ponticum
121 annotated genes in BrSIO1 have 103 homologues in Arabidopsis thaliana Brassica rapa; Arabidopsis thaliana
positions of the homologues identified from the BLAST search were compared with positions of markers in the region of the QTL
contigs containing OsRHL1 homologues were located near markers
Sonnhammer and co-workers applied the methodology to the sequenced eukaryotic genomes
genome-scale comparisons of internal duplications in the Arabidopsis thaliana genome depended on custom bioinformatics efforts and extensive pre- and post-processing tailored to the Arabidopsis genome Arabidopsis thaliana
TC141300 showed 48% amino acid identity and 68% similarity to (CYP82C2, AT4G31970) Gossypium hirsutum; Arabidopsis thaliana
substantial colinearity emerged from wheat 7AL versus Th. ponticum 7AgL genetic map comparison Triticum aestivum; Thinopyrum ponticum
maize myosin genes number less than Arabidopsis myosin genes Zea mays; Arabidopsis thaliana
chromosome-to-chromosome synteny relationships enabled production of partial wheat gene-based physical map (syntenome) with 17,317 COS Triticum aestivum; Oryza sativa; Sorghum bicolor; Brachypodium distachyon; Zea mays
Physcomitrella patens expression data enables cross-species comparisons of gene expression among photosynthetically active species Physcomitrella patens
genes in 'ZS11' were homologous to genes in Brassica rapa (Ar), Brassica oleracea (Co), Brassica napus 'Darmor-bzh', and Arabidopsis thaliana (97.35%) Brassica napus; Brassica rapa; Brassica oleracea; Arabidopsis thaliana
FISH in cucumber has been used successfully for comparative mapping with melon Cucumis sativus
25 genes are collinear between two genomes Oryza sativa; Brachypodium distachyon
de novo assembly of BSA derived RenSeq data used as genotype-specific reference
five pairwise tBLASTn comparisons performed between pennycress and each of five Brassicaceae species Thlaspi arvense; Arabidopsis thaliana; Arabidopsis lyrata; Brassica rapa; Capsella rubella; Thellungiella halophila
ps-2 locus region shows synteny with Arabidopsis thaliana Solanum lycopersicum; Arabidopsis thaliana
transcriptome and metabolome analysis revealed differences in transcripts and metabolites between Regent and Trincadeira Vitis vinifera
genes identified in Arabidopsis following infection with three pathogens were used to isolate homologues genes in cotton Gossypium hirsutum
Perennial ryegrass (Lolium perenne L.) shares significant synteny with other grass species Lolium perenne L.
Poaceae species exhibit high synteny at macro level genome organization
markers in region associated with LG4 QTL in perennial ryegrass (pps0040 and lpssr006) were aligned by in silico comparative analysis to genome segment between 6–10Mb on rice chromosome 3 Oryza sativa
sequence identity profiles and phylogenic relationships grouped chromosome blocks into two distinct clusters Aegilops markgrafii
single member of CrRLK1L family in M. polymorpha is more similar to AtTHE than to any other A. thaliana protein in this family Marchantia polymorpha; Arabidopsis thaliana
matrices of collinear genes and rearrangements were constructed from homology search results Aegilops tauschii; Triticum turgidum subsp. dicoccoides; Brachypodium distachyon; Sorghum bicolor; Oryza sativa
uncertainty about which orthologue retains the same function as the corresponding gene in the model species is a consequence of presence of multiple orthologues
A. lyrata and A. thaliana genomes could be easily aligned each other Arabidopsis lyrata; Arabidopsis thaliana
A. thaliana chromosome 4 centromere corresponds to syntenic region in A. lyrata chromosome 4 centromere Arabidopsis thaliana; Arabidopsis lyrata
Thellungiella parvula contigs aligned with chromosome A3 of Brassica rapa Thellungiella parvula; Brassica rapa
9,119 genes comprised genus-wide alignments for 25 Mb of genome Arabidopsis thaliana
this study compared genomes of three potato species Solanum chacoense; Solanum tuberosum; Solanum commersonii
M. polymorpha PTI protein is sister to group of six A. thaliana PTI proteins that includes MARIS Marchantia polymorpha; Arabidopsis thaliana
ortholog and phylogenetic analyses were conducted and yielded results consistent with previous studies Prunus persica
DiagHunter assigns numbers synteny blocks
scripts in DiagHunter/GenoPix2D distribution allow processing of The Institute for Genomic Research (TIGR) pseudochromosome assemblies
high-throughput technologies facilitate comparative analyses across species
GeneChip microarray studies demonstrated potentials in studies of closely related species Arabidopsis thaliana; Arabidopsis halleri
DiagHunter identifies very large-scale synteny blocks on the order of many megabases
chromosomes of the four target species thoroughly analyzed in previous studies Arabidopsis thaliana; Populus trichocarpa; Theobroma cacao; Vitis vinifera
DiagHunter makes genome-scale comparisons
GenoPix2D provides interactive viewing, querying, and plotting
genome sequences that represent the rosid or asterid lineage are available, or are in progress
understanding molecular processes and gene regulatory networks allows rapid utilization of this information into other plant species
KNOX protein sequences were downloaded from Genome Database for Rosaceae, TAIR, Sol Genomics Network and NCBI Fragaria vesca; Fragaria × ananassa; Arabidopsis thaliana; Solanum lycopersicum; Zea mays
highly repetitive heterochromatic DNA present particular challenges
three target genomes under consideration confirmed each other Vitis vinifera; Populus trichocarpa; Theobroma cacao
this work is the first systematic, genome-wide examination of the sets of orthologous genes in eukaryotes
DiagHunter can operate on marker data
10 families differed in gene number between 'ZS11' and 'Darmor-bzh' (P < 0.01) Brassica napus
GenoPix2D allows highlighting of groups of genes
SALAD homolog genes were identified in Arabidopsis thaliana and Solanum lycopersicum Arabidopsis thaliana; Solanum lycopersicum
protein sequences were aligned using Clustal Omega program Arabidopsis thaliana; Solanum lycopersicum; Fragaria vesca; Zea mays
GenoPix2D can view any other two-way genomic similarity comparisons
similar sequences of CaLUR transcription site were also found in other solanaceous species such as potato and tomato
core angiosperm genes were significantly enriched in PAE in all samples Solanum tuberosum
Cytogenetic approach provided a basis for comparative sequence analysis of discrete parts of the genome
all variants called on the T. urartu genome were projected onto genome of wild emmer wheat (Triticum turgidum spp. dicoccoides) Triticum urartu; Triticum turgidum spp. dicoccoides
Zea mays has more than 10-times larger genome Zea mays
A. lyrata and A. thaliana genomes have remained syntenic approximately 90% of the two genomes Arabidopsis lyrata; Arabidopsis thaliana
32,986 distinct gene families are 40% appearing to be dispensable Arabidopsis thaliana
longer and high quality reads at high coverage are believed to be very important to address evolutionary questions at whole-genome level
grape syntenic blocks 85.84% contain two regions of synteny with sacred lotus gene set sacred lotus; Vitis vinifera
research on the heterozygosity of sweet orange contributes to comprehensive understanding of the genetic diversity of citrus or closely related species Citrus sinensis; Citrus
genome sequences of higher plants permits cross-species comparisons
sequence comparisons of prokaryotic and eukaryotic IPMDH suggest substitution of one active site residue may lead to altered substrate specificity and metabolic function Arabidopsis thaliana
Profilin query sequences are used to identify extended profilin homologs
~53.6-kb genomic variation contains one gene (Ppe_1-Hap2G0054500) from (GCS1, HAP2, AT4G11720) Prunus persica
PatternHunter is used for identifying regions of homology between genomes
programs designed to identify homologous regions by sequence alignments may not excel at piecing together and reporting larger genomic-scale homologies
GenoPix2D provides interactive querying function
genes annotated in Aegilops tauschii pseudomolecules searched for homology with genes annotated in sorghum pseudomolecules Aegilops tauschii; Sorghum bicolor
four Spirodela syntenic blocks found between Amborella and Apostasia Spirodela polyrhiza; Amborella trichopoda; Apostasia shenzhenica
conservative approach will enhance accuracy of comparative analysis
studies of accelerated organelle genome evolution in plants have been limited to close relatives within just two groups (Geraniaceae and Silene) Geraniaceae; Silene
proteins of the four large clusters are homologous to annotated Phytophthora infestans RXLRs Plasmopara halstedii; Phytophthora infestans
21,523 Thellungiella parvula ORFs of very similar lengths (80–120%) to putative Arabidopsis thaliana homologs Thellungiella parvula; Arabidopsis thaliana
programs designed to work with nucleotide data may not work with raw positional information such as marker positions
DiagHunter appears to out-perform PipMaker, MUMmer, FORRepeats, REPuter, BLASTZ and PatternHunter
extensive molecular resources for sugar beet enable cross-referencing to regions sequenced in other plant species Beta vulgaris
region of approximately 10 Mb in pseudomolecule 2 appeared to be inverted translocation from syntenic region of G. max chromosome 8 Glycine latifolia; Glycine max
phylogenetic distribution of putative and functionally characterized UGTs has been analyzed in 27 plant genera with fully sequenced genomes Chlamydomonas reinhardtii; Physcomitrella patens; Selaginella moellendorffii
collinear gene pairs confirmed that intergenic regions in A. lyrata are longer than counterparts in A. thaliana Arabidopsis lyrata; Arabidopsis thaliana
phylogenetic analysis was conducted to assign putative functions and identify related genes in Arabidopsis thaliana Marchantia polymorpha; Arabidopsis thaliana
homology analysis identified 25,849 genes from (GCS1, HAP2, AT4G11720) with homologous genes in (HAP1, MAGO, MEE63, AT1G02140) Prunus persica
allele-specific sequences at the GPA-resistant locus demonstrated ~53.6-kb variation Prunus persica
inclusion of newly sequenced genomes should proceed at faster rate once KOG system is established
predicted flax genes aligned with Arabidopsis genes Linum usitatissimum
comparative analysis method is applicable for studying divergence of k-mer profiles between genomic datasets of closely related species
4CL ligases from monocots and dicots have been characterized based on sequence identities to Arabidopsis 4CLs
Kmasker plants enables comparative studies between different cultivars or closely related species
three clustered genes (KCS_Maole_016461.T1, KCS_Maole_016463.T1, KCS_Maole_016467.T1) are closely related to three Arabidopsis thaliana KCS genes ( (KCS11, AT2G26640) (DAISY, KCS2, AT1G04220) (KCS20, AT5G43760) ) Moringa oleifera; Arabidopsis thaliana
F. vesca KNOXI genes were identified by blast against F. vesca genome Fragaria vesca
inclusion of newly sequenced genomes and other genomes will enable further, deeper studies into the functional and evolutionary patterns of eukaryotic life
regions of synteny between sugar beet and rosid species involves 1400–2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao Beta vulgaris; Arabidopsis thaliana; Populus trichocarpa; Vitis vinifera; Theobroma cacao
93 450 predicted genes in F. erecta genome were clustered with genes of fig, mulberry, jujube, and sweet cherry Ficus erecta; Ficus carica; Morus species; Ziziphus jujuba; Prunus avium
genes annotated in rice pseudomolecules searched for homology with genes annotated in other grass pseudomolecules Oryza sativa
TaMs5-A, TaMs5-B and TaMs5-D are homoeologs Triticum aestivum
candidate UGTs were identified from genomes using stringent criteria
124 RXLRs are found only in Plasmopara halstedii and Plasmopara viticola Plasmopara halstedii; Plasmopara viticola
1:1:1 orthologs limits number of genes that could be assessed
analyses of gene families flanking the eight representative genomes of green plants provide in-depth insights into evolutionary genomics about green plants
junction sites of 102 LTR-RTs and 456 DNA (ATNACK2, NACK2, TES, AT3G43210) present in assembled Brassica oleracea sequences were found in Brassica rapa NGS read dataset Brassica rapa; Brassica oleracea
sweet orange reference genome may provide a resource for study of ancient genome traits of the mandarin and pummelo ancestors of sweet orange Citrus sinensis
CrusView enables analysis of tandem duplications
CrusView is developed using SWI/Swing graphics libraries
multiple alignment throughout all members of the ALMT family in Arabidopsis identified several conserved or partially conserved amino acids within the transmembrane domain Arabidopsis thaliana
CrusView allows users to integrate self-defined genomic information
CrusView allows users to upload self-defined genomic information
CrusView is designed to give users higher flexibility in analyzing currently unpublished genome data
whole genome sequencing data of Rorippa aquatica enables rapid identification of orthologs of Arabidopsis thaliana developmental regulatory genes Rorippa aquatica; Arabidopsis thaliana
homology analysis identified 24,745 homologous genes in (HAP1, MAGO, MEE63, AT1G02140) Prunus persica
orthologs of Acer truncatum and 14 other sequenced plant species were clustered into 18 616 gene groups Acer truncatum
pairwise comparison of Syntrichia ruralis and Syntrichia caninervis uncovered chromosome rearrangement between Syntrichia ruralis Chr. 11 and Syntrichia caninervis chromosomes 2 and 8 Syntrichia ruralis; Syntrichia caninervis
three-way genome-wide synteny comparisons with McScan inferred directionality of chromosomal rearrangement between Syntrichia species Syntrichia ruralis; Syntrichia caninervis; Ceratodon purpureus; Physcomitrella patens
CrusView is developed using SQLite databases
CrusView incorporates genomic karyotype information
af-flanking markers from the pea consensus genetic map and synteny relationships with close species used to mine candidate genes for Af Pisum sativum
synteny blocks on G. max chromosome 11 contains thirty-two genes Glycine max
Medtr5g014400 has conserved orthologues in G. max and A. thaliana Medicago truncatula; Glycine max; Arabidopsis thaliana
Arabidopsis thaliana used in comparison with fern species Ceratopteris richardii and Polypodium vulgare Arabidopsis thaliana; Ceratopteris richardii; Polypodium vulgare
limitation of de novo assembly makes difficult genomic macrosynteny analyses
CrusView is applicable to Brassicaceae species
CrusView performs visual comparison of Arabidopsis and E. salsugineum genomes Arabidopsis thaliana; Eutrema salsugineum
CrusView allows integration of self-defined genomic information
CrusView karyotype feature may facilitate understanding of karyotype evolution
CrusView karyotype feature may facilitate understanding of genome evolution
CrusView includes array of utilities to map list of genes of interest
chimeric assembly of the BAC contig or rearrangements between wheat and the other grass species in this region might suggest Triticum aestivum; Oryza sativa; Brachypodium distachyon
number of reads mapped to barley assembly decreased with phylogenetic distance Hordeum vulgare; Hordeum spontaneum; Hordeum bulbosum; Hordeum pubiflorum; Triticum aestivum
draft transcriptome shows high degree of conservation in comparative analysis versus other Brassicaceae species
comparative chromosome map of this region was constructed between cucumber and melon Cucumis sativus; Cucumis melo
39 genes in Aegilops tauschii region most were non-syntenic genes only present in Aegilops tauschii Aegilops tauschii
this work describes analyses of two genome-wide datasets obtained for all diploid species of Aegilops, Amblyopyrum, and Triticum, and always multiple individuals per taxon Aegilops; Amblyopyrum; Triticum
235 exclusive OGs in Ae. arabicum include 1205 species-specific genes and 1268 genes not assigned to orthogroups Aethionema arabicum
other species-specific genes were annotated as cytochrome P450 (27), cysteine/histidine-rich C1 (32), domain of unknown function (DUF) (76), glycoside hydrolase (22), NAC domains (14), peptidases (40), protein kinases (15), WRKY (15), and zinc finger proteins (35) Aethionema arabicum
Aethionema arabicum has lower number of genes than other Brassicaceae Aethionema arabicum
CrusView may be used to perform karyotype-assisted genome synteny analysis
most analyses have focused on small number of plant genomes
barley and wheat orthologous gene sequences were used to compare discrete parts of Ae. markgrafii genome involved in rearrangements Aegilops markgrafii
orthologs detected with OrthoFinder (version 2.1.2) Arabidopsis thaliana; Capsella rubella; Glycine max; Zea mays; Oryza sativa; Solanum lycopersicum
PipMaker is used for identifying regions of homology between genomes
DiagHunter can operate on protein data
DiagHunter identifies synteny blocks despite high levels of background noise in comparisons
all chromosomes in one or more genomes can be run in batch process
draft genome sequence of chickpea and its analysis has provided rich information on similarity and diversity of structural and organizational components in relation to other sequenced legume genomes Cicer arietinum
orthologous genes in rice and Brachypodium are in same chromosomal regions Oryza sativa; Brachypodium distachyon
target regions from Morex assembly projected onto H. pubiflorum assembly Hordeum pubiflorum
Maximum-Likelihood phylogenetic trees were constructed with protein sequences predicted from M. polymorpha transcriptome assembly and published A. thaliana genome Marchantia polymorpha; Arabidopsis thaliana
DiagHunter can operate on nucleotide data
DiagHunter can carry out comparable predictions of segmental duplications in Arabidopsis Arabidopsis thaliana
COS markers provide access to robust links with sequence genomes and precise orthologous candidate genes Triticum aestivum
one-third of the N. tabacum (Hicks Broadleaf) WGP tags are not present or are undetectable in N. sylvestris or N. tomentosiformis Nicotiana tabacum; Nicotiana sylvestris; Nicotiana tomentosiformis
orthologous region of M. guttatus genome lies in 484-kbp interval (2325–2809 kbp) on scaffold 4 Mimulus guttatus
60S ribosomal protein gene was shared between Brachypodium and Aegilops tauschii Brachypodium; Aegilops tauschii
other grass genomes contain single copies of GLR gene Brachypodium; Oryza sativa; Sorghum bicolor
putative differentially fractionated genes were aligned to annotated genes present on scaffolds or contigs
synteny blocks between G. latifolia and G. max reproduced results from previous comparative analysis using shared SNP-containing sequences Glycine latifolia; Glycine max
assembly could still identify near complete synteny between (ATCAD7, CAD7, CHR, ELI3, ELI3-1, AT4G37980) 2 and 13 Linum usitatissimum
intragenomic, whole-genome analyses for synteny identified almost three times more syntenic relationships Spirodela polyrhiza
wild-type Cys residue is completely conserved across orthologous sequences Triticum aestivum; Triticum turgidum; Aegilops tauschii; Aegilops speltoides; Hordeum vulgare; Brachypodium distachyon; Oryza sativa; Zea mays
assembled translated pennycress transcriptome compared to peptide database from sequenced genomes Thlaspi arvense; Arabidopsis thaliana; Arabidopsis lyrata; Capsella rubella; Brassica rapa; Thellungiella halophila
limited overlaps of expressologs and enriched gene functions (ontologies) reflects lower similarity between endodermis/QC, vasculature, and meristematic cortex Arabidopsis thaliana; Solanum lycopersicum; Oryza sativa
Taxus wallichiana genes had one-to-one syntenic orthologs in Sequoiadendron giganteum Taxus wallichiana; Sequoiadendron giganteum
almost three times more syntenic relationships compared with similar analysis with previous Sp5909v3 assembly Spirodela polyrhiza
(PPR4, AT5G04810) and (EMB2654, AT2G41720) orthologs extracted from nuclear genome sequences from 14 phylogenetically diverse species
very small insertions and deletions do not correspond to sequences only found in A. lyrata Arabidopsis lyrata; Arabidopsis thaliana
T. salsuginea; L. virginicum; D. pinnata; T. parvula were selected for further analysis in comparison to Arabidopsis (glycophyte) and T. salsuginea (halophyte) Thellungiella salsuginea; Lepidium virginicum; Diplotaxis pinnata; Thellungiella parvula; Arabidopsis thaliana
research to elucidate function of rice genes would benefit greatly from direct integration and parallel comparison of information on orthologous genes in Arabidopsis Oryza sativa; Arabidopsis thaliana
plant families of microtubule-associated proteins (MAPs) examined through recently sequenced genomes Arabidopsis thaliana; Oryza sativa; Selaginella moellendorffii; Physcomitrella patens; Volvox carteri; Chlamydomonas reinhardtii
Cardamine hirsuta is experimental system for comparative studies Cardamine hirsuta; Arabidopsis thaliana
micro-synteny between Arabidopsis and B. rapa genomes exploited to identify candidate genes for QTL Arabidopsis thaliana; Brassica rapa
genome structure of Cardamine hirsuta with eight chromosomes and 24 conserved genomic blocks is similar to ACK and extant genomes of Arabidopsis lyrata and Capsella rubella Cardamine hirsuta; Arabidopsis lyrata; Capsella rubella
Syntrichia caninervis U and Syntrichia ruralis V sex chromosomes have significantly fewer syntenic blocks between homologous autosomes of these species Syntrichia ruralis; Syntrichia caninervis
study of wild relatives of Arabidopsis allows the use of molecular tools developed for Arabidopsis model Arabidopsis thaliana
503 gene families were expanded in Amaranthus cruentus compared with the other 13 genomes Amaranthus cruentus
orthologous genes in rice and Brachypodium are separated by 52 and 41 protein-coding genes in the two species, respectively Oryza sativa; Brachypodium distachyon
likelihood method implemented in cafe version 2.0 has been used in rhesus macaque genome Macaca mulatta
Cardamine hirsuta is genetic system for comparative studies Cardamine hirsuta
Arabidopsis AtGenExpress data were used following conversion of Arabidopsis genes into soybean orthologs Arabidopsis thaliana; Glycine max
21 039 orthogroups <4% (773 orthogroups) are species-specific 14 angiosperm species
Ancestral Crucifer Karyotype (ACK) defines 24 conserved genomic blocks
sequencing technologies have driven mustard species into the spotlight of comparative research
gene01 and Os01g37800 and Bradi2g41180 share 94 and 97% amino acid identities, respectively Triticum aestivum; Oryza sativa; Brachypodium distachyon
RT-directed Hidden Markov Model (HMM) serves to create cross-species profile of LINE RTs in plant genomes
78.6% of Tnt1-flanking sequences matched coding sequence in Medicago truncatula Medicago truncatula
genes identified using multi-trait multi-SNP approach show syntenic conservation Zea mays
Qfs.zaas-6 was syntenic to cucumber fd5.2
integration of species phylogeny enables exploration of functional relationships between omics data types
Collinearity of genes between the tetraploids and the reference genome DM was higher than that observed between the diploid (DAG1, AT3G61850) and RH Solanum tuberosum
DM was used as reference genome Solanum tuberosum
Collinear Blocks module table lists collinear blocks with detailed information
breakpoints of chromosomal translocation were determined by microcolinearity analysis of D. villosum and Ae. tauschii Dasypyrum villosum; Aegilops tauschii
synteny blocks on M. truncatula chromosome 5 contains fifty-two genes Medicago truncatula
144 small ubiquitin-related modifier (SUMO) members identified in 28 plant genomes
Nelumbo nucifera can be used as model for comparative and evolutionary genomics studies in angiosperms Nelumbo nucifera
uncertainty about whether ancestral functions have been partitioned between orthologues is a consequence of presence of multiple orthologues
PME and PMEI transcripts in garden cress CAP and RAD were compared with homologs in Arabidopsis Lepidium sativum; Arabidopsis thaliana
Darwin Tree of Life project allows examination of intra and interspecific centromere diversity
Zambian strain mini-chromosome was similar to B71 mini-chromosome Magnaporthe oryzae
3891 collinear genes represent 13.75% of 28 290 genes Acer truncatum
analysis of over 600 pennycress ESTs revealed close relationship between pennycress and Arabidopsis
M02_1500K marker ortholog maps to M. guttatus scaffold 89 at position 201 kbp Mimulus guttatus
70 single-copy orthologous gene sets identified among 25 genomes Chimonanthus praecox; Cassytha filiformis; Cinnamomum kanehirae; Persea americana; Litsea cubeba; Lindera benzoin; Sassafras albidum; Gomortega keule; Peumus boldus; Litsea chinense; Piper nigrum; Macleaya cordata; Vitis vinifera; Amborella trichopoda; Ginkgo biloba
PAV SPE genes showed average proportion categorized as syntenic (16%) Zea mays
eFP browser has been used for other species
comparative transcriptomics application in studying plant morphological diversity addresses challenges including identifying homologous gene pairs
large-scale comparative genomic approaches represent the only meaningful way of exploring the vast amount of available genomic data
Collinear Blocks module shows circle map with genes located in collinear blocks
28 248 genes were unassigned to any cluster Solanum tuberosum
CPBD includes orthologous genes between 23 genomes
Gli-V2 on 6VS was collinear with homologous locus Gli-2 in CS Dasypyrum villosum; Triticum aestivum
locus on 4VL was specific to D. villosum Dasypyrum villosum
Plant T-2-T genomes ensure unified coordinate system for cross-comparison
genome-wide synteny analysis revealed evolutionary relationships among chromosomes Linum usitatissimum
262882 genes assigned to 23261 orthogroups Capsicum annum; Nicotiana benthamiana; Solanum chacoense; Solanum commersonii; Solanum lycopersicum; Solanum melongena; Solanum tuberosum
Plasmopara halstedii pathotype 710 genome assembly is significantly less fragmented and more syntenic to Plasmopara viticola genome assemblies Plasmopara halstedii; Plasmopara viticola
genomic regions in Thellungiella parvula contigs c2 and c3 matched distinct ancestral karyotype blocks Thellungiella parvula
lack of phylogenetic linkage between resurrection plants means that studies cannot be simply integrated comparative studies across resurrection plant species
Annotation of the A. cruentus assembly indicated gene number similar to A. hypochondriacus and closely related B. vulgaris Amaranthus cruentus; Amaranthus hypochondriacus; Beta vulgaris
multiple grass species can be employed as single genomic system
Plasmopara halstedii (CRN, SOL2, AT5G13290) effectors are conserved in at least 12 oomycete species Plasmopara halstedii
4 core effectors (PhRXLR-C14, -C20, -C22 and -C29) having no homologs in the published Plasmopara halstedii sequence Plasmopara halstedii
pan-genome analyses uncovered 32,986 distinct gene families Arabidopsis thaliana
Medicago truncatula and Glycine max were considered for candidate gene identification Pisum sativum; Medicago truncatula; Glycine max
reciprocal best hits (RBHs) from alignments between G. latifolia and G. max primary protein sequences were utilized as putative orthologous pairs for synteny block prediction Glycine latifolia; Glycine max
Camelina genes have homologs in Arabidopsis thaliana genes Camelina sativa; Arabidopsis thaliana
TaMs5 and TaMs1 have protein sequence similarity of less than 30% Triticum aestivum
putative (PPR4, AT5G04810) and (EMB2654, AT2G41720) binding sites extracted from respective chloroplast genomes
largest Thellungiella parvula contig c1 (13.08 Mb) aligned with entire length of one arm of Arabidopsis thaliana chromosome 1 Thellungiella parvula; Arabidopsis thaliana
contig c3 shared similarity with genes from three Arabidopsis thaliana chromosomes Thellungiella parvula; Arabidopsis thaliana
3,118 predicted ORFs had no BLASTn hits to Arabidopsis thaliana cDNAs Thellungiella parvula; Arabidopsis thaliana
gene03 is orthologous and syntenic with rice chromosome 1 and Brachypodium chromosome 2 Triticum aestivum; Oryza sativa; Brachypodium distachyon
targets not covered in related species may not be captured or reads could not map due to excessive sequence divergence Hordeum pubiflorum
'ZS11' genome identified 35,337 gene pairs orthologous between An and Ar Brassica napus; Brassica rapa
99 genes downregulated in both attdf1 and hvtdf1 included (AMS, AT2G16910) (ACOS5, AT1G62940) (FAR2, MS2, AT3G11980) (LAP5, PKSB, AT4G34850) /6, (AtMYB103, ATMYB80, MS188, MYB103, MYB80, AT5G56110) (KCS7, AT1G71160) /21, and (SHT, AT2G19070) Arabidopsis thaliana; Hordeum vulgare
TaMs5 is divergent to TaMs1 Triticum aestivum
putative differentially fractionated genes were aligned to expected syntenic position in opposite genotype
E169 and F242 in GhPGIP1 are corresponding residues from PvPGIP2
annotation LiftOver procedures identified 70, 256 and 219 genes with no hits in the other two assemblies for Lee, Wm82v4, and G. soja, respectively Glycine max; Glycine soja
Thellungiella parvula predicted ORFs primary matches to Arabidopsis thaliana coding regions (29%) Thellungiella parvula; Arabidopsis thaliana
comparative genomics analysis performed to uncover associations between key traits and gene families Cichorium intybus
pairwise comparison of Syntrichia ruralis and Syntrichia caninervis uncovered smaller inversion events along Syntrichia ruralis Chrs. 1, 2, 9, and 10 Syntrichia ruralis; Syntrichia caninervis
SynMap was used to identify blocks of syntenic genes
Kolukisaoglu and his co-workers identified 10 OsCBLs and 30 OsCIPKs in rice Oryza sativa L.
orthologous groups containing genes involved in sesquiterpene synthase showed increased gene occupancy in tuber-bearing species Solanum chacoense; Solanum commersonii; Solanum tuberosum
orthology analysis revealed core set of 158367 Solanaceae genes Capsicum annum; Nicotiana benthamiana; Solanum chacoense; Solanum commersonii; Solanum lycopersicum; Solanum melongena; Solanum tuberosum
(MS5, TDM1, AT4G20900) and (MS1, AT5G22260) are distinct to other members of wheat (LTP, LTP7, AT2G15050) super-family Triticum aestivum
assembled sequences surrounding the GPA-resistant locus were compared between (HAP1, MAGO, MEE63, AT1G02140) and (GCS1, HAP2, AT4G11720) genomes Prunus persica
Wang et al. computationally compared derived protein clusters with established gene families in budding yeast Arabidopsis thaliana; Saccharomyces cerevisiae
the COGs have been used for genome-wide evolutionary studies
REPuter is used for identifying regions of homology between genomes
BLAST alignments used to validate and identify missed syntenic assignments
G. latifolia pseudomolecule 2 contained 10-Mb region colinear with syntenic G. max chromosome 19 Glycine latifolia; Glycine max
Saccharomyces cerevisiae has very small genome (~12.2 Mbp/1C) Saccharomyces cerevisiae
Ms5-A shows 76.5% amino acid identity with B. distachyon Triticum aestivum; Brachypodium distachyon
differences in gene numbers may arise from greater completeness of Wm82v4 assembly or true gene presence/absence variation Glycine max; Glycine soja
introns behave similarly intergenic regions Arabidopsis lyrata; Arabidopsis thaliana
raw SynMap analysis identified 20,446 genes in PH207 with syntenic orthologs in sorghum
syntenic identification software has limitations that may underestimate number of syntenic genes identified
genes with high protein sequence similarities indicative of close/similar biological functions
ortholog clustering analysis using protein sequences identified 9700 gene families among selected dicotyledonous plant species Glycine latifolia; Glycine max; Arabidopsis thaliana; Populus trichocarpa; Vitis vinifera