Notice: Database construction is still in progress. Certain features may be incomplete, slower than usual, or temporarily unavailable while we re-ingest the knowledge graph with citation data. Thank you for your patience.
← All pathways

genome evolution

22894 relationships annotated with this phrase. Showing first 500 of 22894.
Source entity Relationship Target entity Species
Alu elements evolved from 7SL RNA
mini-chromosomes from closely related isolates show high-speed creation of genetic variability Magnaporthe oryzae
19 pairs of chromosomes in Nicotiana benthamiana is result of diploidization and chromosomal rearrangements Nicotiana benthamiana
observed large-scale duplications play a major role in origin and evolution of accessory regions in Fusarium Fusarium
self-defined genomic information includes groups of orthologs/paralogs
CrusView facilitates genome evolution studies
recent segmental duplications in accessory chromosomes cause expansion of accessory regions Fusarium oxysporum
Quercus dentata lacks independent WGD (whole genome duplication) in its evolutionary history Quercus dentata
accessory regions are likely more tolerant to structural variation Fusarium oxysporum
expansion of E3 encoding genes suggests high degree of functional specialization
accessory regions are similar within individual Fusarium oxysporum lineages Fusarium oxysporum
karyotype of a species can assist in identifying major duplication events
Ks values of 0.06 to 0.39 correspond to 13-million year genome duplication Glycine max
translocation events have been identified in diploid wheat (7Sl/4Sl) and tetraploid/hexaploid wheat (4A/5A/7B) Triticum aestivum
DNA duplication, loss, and rearrangements can serve as accelerator for fungal genome evolution Magnaporthe oryzae
tomato (PSY1, AT5G58650) and PSY2 pair was generated by Solanum-specific whole-genome triplication Solanum lycopersicum
Value-directed Evolutionary Genomics Initiative project aims to understand genome evolution of Brassicaceae species
TE mobility can expand the gene space through DNA duplication, interruption or induction of effector gene deletion Plasmopara viticola
genome size (GS) will be strongly influenced by evolutionary history
single peak of insertion time at c. 0.1 Ma suggests recent burst of LTR RTs in the genome Alopecurus myosuroides
retrotransposon families shaped epigenomic characteristics Cichorium intybus
plasticity of prominent protein isoforms in plants represents manifestation of remarkable variability of plant genomes
heterogeneity in composition provides a window into molecular and population processes impacting the genome
chromosomal duplication, together with breakage and fusion shapes evolutionary dynamics of accessory regions Zymoseptoria tritici
Quercus dentata lacks recent whole-genome duplication events Quercus dentata
Marchantia polymorpha did not undergo ancient whole-genome duplications Marchantia polymorpha
BGCs among different species had large differences even for closely related species
cytochrome p450 genes in maize were tandemly duplicated in maize
loss of Avr9B is anticipated to be facilitated through structural variations in the Fulvia fulva genome induced by repetitive elements Fulvia fulva
Quercus species did not undergo WGD (whole genome duplication) events since the gamma triploidization Quercus robur; Quercus suber; Quercus lobata; Quercus dentata
Gypsy, Copia and unclassified RTs exhibit single peak of insertion time at c. 0.1 Ma Alopecurus myosuroides
chicory genome experienced whole-genome triplication (WGT) event Cichorium intybus
18,845 orthologous gene pairs between A and Sl genomes were identified as homoeologous gene pairs in Sl Sl AA Triticum aestivum; Aegilops longissima; Triticum urartu
karyotype of a species can assist in identifying chromosomal rearrangements
centromere DNA and protein variation is common phenomenon in plants
range of deletion sizes observed at avrRpv3.1 locus Plasmopara viticola
most examples of copy number variation are linked to copy number changes in core genome
transposable elements link to mutation rate variability
accessory regions and effector profiles of Fusarium oxysporum strains infecting the same host are typically remarkably similar similarity despite genetic diversity Fusarium oxysporum
abundant intrachromosomal homology serves as reservoir for DNA duplication, loss, and rearrangements Magnaporthe oryzae
whole-genome duplications occurs across angiosperms
(retro)transposons influenced dynamics of genome evolution in chicory
TR4 strains are genetically highly similar genetic similarity Fusarium oxysporum
genome size (GS) is strongly shaped by evolutionary history
chromosome collinearity analysis between Quercus dentata and other Quercus and Fagus species showed 1:1 syntenic patterns Quercus dentata; Quercus robur; Quercus suber; Quercus lobata; Quercus variabilis; Quercus acutissima; Quercus mongolica; Fagus sylvatica
high-quality reference genome of Quercus dentata provided resources for studying evolution and diversity in Quercus Quercus dentata
accessory regions and effector profile of R1 strains show extensive variation Fusarium oxysporum
accessory contig in strain II5 underwent recent copy number change Fusarium oxysporum
polyploidization and diploidization events gave rise to duplicated or multiplicated large DNA segments or whole chromosomes
self-defined genomic information includes chromosomal break points
karyotype of a species can assist in identifying genomic synteny
mtDNA in angiosperms are notably larger in size (168 up to 11,000 kb) and much more complex in structure than mtDNA in mammals or humans Angiosperms; Homo sapiens; Mammalia
OsPIN1c and OsPIN1d have high similarity of sequence Oryza sativa
four Quercus species and Vitis vinifera present the same signature of Ks peaks only at c. 0.15 Quercus robur; Quercus suber; Quercus lobata; Quercus dentata; Vitis vinifera
pan-genomic framework together with global panel of 69 strains used to gain insights into evolution of ARs in genetically diverse Fusarium oxysporum strains Fusarium oxysporum
nuclear genomes substantially changed due to genome duplication
locus colinear to SpAVP1;2 has been replaced by transposable elements or deleted Arabidopsis thaliana
Ycf2 is absent in grasses
gene cluster on the short arm of chromosome 8 is characterized by gene duplications, deletions, rearrangements, and conversion
genes involved in external stimulus responses tend to experience lineage-specific duplication
within-species genome duplications occur in eudicot genomes
OsPIN5a and OsPIN5b share small duplication block between chromosomes 1 and 8 Oryza sativa
divergence level of duplicated segments depends on how advanced postpolyploid diploidization has become and how exposed the duplicated segment is to selection pressures
conserved patterns of chromosomal rearrangements are based on syntenic genomic blocks
more than 20,000 gene fragments in (B73, CHL6, CNX, CNX1, SIR4, AT5G20990) genome are transduplicated and reshuffled due to Helitron activities Zea mays
results of inter- and intraspecies comparisons suggest that lifespan of soybean lincRNA can exceed 15 million years but is unlikely to extend over 60 million years Glycine max
ten duplicated blocks account for 45% of rice genome sequences Oryza sativa
maize underwent genome duplication event approximately 11.4 million years ago Zea mays
one-third of XTH genes occur as clusters resulting from genome duplication Arabidopsis thaliana
Tourist-like and Stowaway elements are abundant and preferentially inserted into genes
several AtWAKLs found on other Arabidopsis thaliana chromosomes do not appear to be represented by intact genes in B. napus Arabidopsis thaliana; Brassica napus
low sequence variability of Ory s 23 suggests very short evolutionary history or strict sequence conservation mechanism Oryza sativa
tandem duplication (TD) of (ATHKT1, HKT1, HKT1;1, AT4G10310) was also observed in Eutrema salsugineum Eutrema salsugineum
random loss of genes generated great diversity in the derived inbreds and landraces Zea mays
recent duplication is special for rice Oryza sativa
preferential elimination of genes from one maize chromosome is suggested by higher frequency of gene deletions on one homoeologous region Zea mays
Acer truncatum has only ancient γ event Acer truncatum
cyanobacteria that have acquired stress-inducible D1 copy have lost flv4-2 operon
α-genome duplication in Arabidopsis occurred approximately 50 million years ago Arabidopsis thaliana
genes involved in external stimulus responses tend to pseudogenize at higher rate
four members of (ATPIN1, PIN1, AT1G73590) sub-family originated from two rounds of duplications Oryza sativa
other species of cereals should have three (ATPIN1, PIN1, AT1G73590) genes Oryza sativa; Triticum aestivum
each of two maize genomic regions experienced reciprocal deletion of one ancestral paralog Zea mays
F-box and protein kinase families differ greatly in loss rates Arabidopsis thaliana
272 manually annotated Helitrons 94% carry captured sequences from 376 genes Zea mays
relatively small divergence time between Arabidopsis and Salicornia parvula results in macrosyntenic regions evident throughout the two genomes Arabidopsis thaliana; Salicornia parvula
significant overrepresentation of Argonaute pseudogenes may be product of viral defense genes no longer useful Zea mays
genome size differences between Arabidopsis and Arabidopsis lyrata is due to extensive DNA loss Arabidopsis thaliana; Arabidopsis lyrata
pseudogenes may have been generated or retained at greater rate in maize lineage Zea mays
two rounds of duplications include one ancient and one more recent duplication Oryza sativa
gene deletions are more frequent in maize Zea mays
both duplications could have resulted from whole genome duplication within the Brassicaceae lineage Arabidopsis thaliana
syntenic genomic blocks are basic units of chromosomal breakage and fusion events
immediate 5′ upstream region including the promoter of SpBOR5 was found with insertion of about 15 kb Schrenkiella parvula
vast majority of Ks values of protein-coding gene pairs flanking homeologous lincRNA loci suggests more recent origin resulting from soybean-lineage-specific paleotetraploidization Glycine max
oldest Nicotiana polyploids are in advanced stage of long-term genome diploidization
information on most likely pair of parents for N. benthamiana is used to separate its subgenomes Nicotiana benthamiana
organelle-to-nucleus DNA transfers have contributed to generation of de novo genes during genome evolution Oryza sativa
Arabidopsis and Salicornia parvula accumulated similar numbers of duplications and other structural variations Arabidopsis thaliana; Salicornia parvula
higher retention rates among plant transcription factor duplicates particularly apply to duplicates derived from whole-genome duplications
most mitochondrial introns in angiosperms have lost cognate maturase-ORFs Angiosperms
copy number change in contig 12 in TR4 strain II5 is abundant and recent segmental duplication Fusarium oxysporum
ancient hybridization has reshaped genomes of many extant species
organelle-to-nucleus DNA transfers also contributed to genome structural variations and promoted the differentiation of rice subspecies and species genomes Oryza sativa
dense clusters of WAKL homologues and abundant tandem duplications on Arabidopsis thaliana chromosome 1 are evidence of higher rate of gene expansion Arabidopsis thaliana
putative transposons and tandemly duplicated copies of (ATCBL10, CBL10, SCABP8, AT4G33000) homologs were inserted near tandemly duplicated SpHKT1;1 and SpHKT1;2 Schrenkiella parvula
SpAVP1;1 (Sp1g13990) and (AtAVP1, ATAVP3, AtVHP1;1, AVP-3, AVP1, FUGU5, VHP1, AT1G15690) showed extensive colinearity with no significant differences between colinear homologous gene pairs Schrenkiella parvula; Arabidopsis thaliana
nuclear genomes substantially changed due to gene gain and loss
Physcomitrella patens genome had rapid proliferation of transposable elements Physcomitrella patens
ancestral D-genome became extinct sometime later after introgression Aegilops; Triticum
long-read sequencing technologies and updated algorithms enhances understanding of contribution of structural variants (SVs) to genome evolution
TE insertion occurred in Moringa oleifera genome about 4–5 Mya Moringa oleifera
duplication and insertion events leading to increase in genome size
LTR/Gypsy superfamily have played important roles in shaping rice genome divergence Oryza sativa
organelle-to-nucleus DNA transfers participate in genome divergence and environmental adaptation in rice Oryza sativa
gene family evolution analysis indicated 262 gene families expanded in Acer truncatum Acer truncatum
LTR insertion time of Euscaphis japonica showed amplification of LTR-RTs occurred largely between 0.1 and 0.25 Mya Euscaphis japonica
evolutionary stable chromosomes identified versus chromosomes prone to chromosome rearrangements (CRs)
present study aimed to characterize repeatomes of investigated Thlaspideae genomes
number of repetitive sequences and size of inbred populations are factors that could affect rate of chromosome rearrangements (CRs)
ancient whole-genome duplication (WGD) event is shared by Laurales Chimonanthus praecox
short-term responses of genome to allopolyploidy for recently formed BBCC polyploid Oryza sativa
Micro-synteny of genic regions was largely maintained across the genus, including polyploids and diploids Oryza spp.
structural diversity is mediated by Helitron transposable elements Zea mays
knowledge of haplotypes in elite varieties should help identify structural rearrangements
transposable elements (TEs) have relationship with host genomes
genome structure of M. polymorpha is different from genome structure of Physcomitrella patens Marchantia polymorpha; Physcomitrella patens
duplicated genes in Arabidopsis thaliana one-third remain conserved after 40 million years Arabidopsis thaliana
genome downsizing in some Nicotiana hybrids mostly affects paternally derived subgenome
Acer truncatum genome lacks recent whole-genome duplication events Acer truncatum
evolution of KCS gene family is essentially history of gene duplications
ancestral duplication of the whole genome results in each of the 16 chromosomes is a mosaic of ancestral genomes Saccharomyces cerevisiae
essential component of the respiratory apparatus was translocated into nuclear genome Amoebophrya ceratii
gene family evolution analysis indicated 513 gene families contracted in Acer truncatum Acer truncatum
difference in genomic distribution and characteristics of genes prone to gene body methylation could be consequence of divergent mating systems Marchantia polymorpha; Physcomitrella patens
Physcomitrella patens and Marchantia polymorpha independently retained different set of collinear regions Physcomitrella patens; Marchantia polymorpha
Acer truncatum genome underwent ancient triplication Acer truncatum
inversions have been investigated in Drosophila Drosophila
wintersweet genome appears to have undergone two whole-genome duplication (WGD) events Chimonanthus praecox
diploidization after WGD includes gene expression alteration
genomic shock leads to variety of genomic responses
smaller size of MITEs could make MITE insertions less deleterious and more easily tolerated Oryza sativa
comparative mapping to Brassica identified genomic blocks maintained since divergence of Arabidopsis and Brassica lineages Arabidopsis thaliana; Brassica
mutations is genome-scale process occurring during evolution
genomic regions showing collinearity only between Marchantia polymorpha and Physcomitrella patens were found some genomic regions Marchantia polymorpha; Physcomitrella patens
genomic variations are basis for genetic diversity
22 WAKLs characterised in Arabidopsis thaliana contrasts with 19 intact WAKL genes predicted within B. napus Darmor sequence Arabidopsis thaliana; Brassica napus
KCS genes in A. yangbiense are closely related to (KCS11, AT2G26640) (DAISY, KCS2, AT1G04220) and (KCS20, AT5G43760) from A. thaliana Acer yangbiense; Arabidopsis thaliana
Asian Cucumis species have highly shuffled genomes Cucumis melo; Cucumis hystrix; Cucumis sativus
common ancestral karyotype BDK originated from ancestral karyotype of lineage II (AKII) through three paracentric inversions on AKII8 Cucumis
results of phylogenetic analysis support inferred ancestral Cucumis karyotype (ACK) evolved into present-day Cucumis species via genome shuffling and polyploidization Cucumis
WGD common to all gymnosperms remains contentious gymnosperm phylogeny
rice GTs involved in tandem and segmental duplication events Oryza sativa
genome hybridization is one of genome shocks Zea mays
syntenic genomic blocks are result of WGDs or segmental chromosomal duplications
GO analyses of genes located in collinear blocks suggested that functional significance may have facilitated retention
high genetic turnover in some Nicotiana hybrids involves intense mobilization of retrotransposons
Strobilanthes cusia genome has not undergone lineage-specific whole-genome duplication compared with Acanthus paniculata; Mimulus guttatus; Sesamum indicum Strobilanthes cusia; Acanthus paniculata; Mimulus guttatus; Sesamum indicum
12 WAKL genes on Arabidopsis thaliana chromosome 1 are only partially represented within each of the B. napus A and C genomes as homologues Arabidopsis thaliana; Brassica napus
genomic rearrangements lead to phenotypic diversification
genome of C. anguria experienced five minor species-specific inversions in fragile regions and one ~2.5-Mb paracentric inversion in non-fragile regions Cucumis anguria
inferred HCK originated from ancestral karyotype of lineage I (AKI) by 12 inversions in fragile regions and two inversions in non-fragile regions Cucumis
fragile regions containing ancestral centromeres played essential role in shaping karyotype diversity within genus Cucumis
gene duplication is a frequent event in most plant genomes
predominant cytoplasmic type in present domestic soybean originated from a rare type of wild soybean Glycine max; Glycine soja
BAC-based CCP used to analyze evolution of chromosome alterations in Thlaspideae
cytogenetic analyses identified structurally most stable chromosomes within Thlaspideae genomes
CCP (Comparative Chromosome Painting) detected synapomorphic inversions within Graellsia and Peltariopsis genera
pericentric inversions in Thlaspideae were main type of chromosome rearrangements (CRs) in Thlaspideae
inversions have been investigated in Anopheles Anopheles
inversions have been investigated in Helianthus Helianthus
commonly lost genes between Gastrodia elata and Cuscuta australis function enrichment indicated photosynthesis, nutrient uptake, and external stimuli response as most significant Gastrodia elata; Cuscuta australis
G. elata exhibits largest extent of gene family contraction Gastrodia elata
Contrasting patterns observed when examining genomic sequence evolution in recent BBCC/CCDD and older HHJJ/HHKK polyploids Oryza spp.
mutualistic biotrophic fungi share expansion of genome size through transposon proliferation
pluralistic framework for genome evolution will use biophysics
nucleotide substitutions is one of three independent mutational mechanisms generating yellow-fleshed peach genotypes Prunus persica
time influences impacts of (ATNACK2, NACK2, TES, AT3G43210) on the genome
extensive rearrangements occurred since divergence of bryophytes and vascular plants Marchantia polymorpha; Physcomitrella patens; vascular plants
very limited collinearity between bryophyte and vascular plant genomes implies that deep divergence since common ancestor has eroded conserved ancestral gene blocks
inferred ancestral Cucumis karyotype (ACK) allowed reconstruction of evolutionary trajectories of both diploid and tetraploid wild Cucumis species from both Asian and African clades Cucumis
differences in ORF numbers between Wm82 and AGH mtDNAs mainly result from SNPs, Indels, specific regions and sequence rearrangements Glycine max
WSs and ASs are likely maintained at various patterns in mitogenomes undergoing different evolutionary paths Glycine max
Thlaspideae chromosome rearrangement rate (5.22 CRs per million years) is lower than grass lineage chromosome rearrangement rate (up to 35.7 CRs per million year)
orchids show gene family contraction in conserved gene families Orchidaceae
quantitative differences in genomic rearrangement mechanisms lead to species with very different levels of genomic instability
transposable elements (TEs) and DNA repair machinery can generate small-scale structural variation
genome collinearity between bryophyte genomes and vascular plants is limited Marchantia polymorpha; Physcomitrella patens; vascular plants
fewer than n = 24 chromosomes in many members of section Suaveolentes is less than sum of the chromosomes of their parents (n = 12)
chromosomes (B2, BCH2, BETA-OHASE 2, CHY2, AT5G52570) and Chy8 of C. hystrix originated from reciprocal translocation involving blocks from HCK2 and HCK8 Cucumis hystrix
chromosome Chy7 of C. hystrix was created by two paracentric inversions on HCK7 Cucumis hystrix
G5 type of mitogenomes evolve differently from G1–G3 types of mtDNAs Glycine max
inversions have been investigated in Boechera Boechera
natural systems consisting of multiple allopolyploidy events with different origin times provide opportunity to decipher underlying mechanisms
retrotransposon activity was suggested in ancestral species
most sequenced seed plants have undergone one or two WGD events during their evolution
Cucumis metuliferus CM27 genome contains eight NBS-LRR pseudogenes Cucumis metuliferus
pangenomes illustrate how transposable elements and non-coding sequences contribute to genome diversity and adaptation
ancestral Cucumis karyotype evolution driven by hybridizations Cucumis
karyotype variation placed in evolutionary framework can characterize evolutionary fates of fragile regions and centromeres during ancestral karyotype evolution Cucumis
orchid ancestor experienced contraction in 616 gene families Orchidaceae
Amaranthus cruentus genome assembly demonstrates shared whole genome duplication with Amaranthus hypochondriacus Amaranthus cruentus; Amaranthus hypochondriacus
illegitimate recombination is active in all plant species investigated
horizontal transfer of genomes is genome-scale process occurring during evolution
Phytophthora infestans accumulated presence-absence variation in many genes encoded by gene-sparse compartments Phytophthora infestans
transition from saprotrophy to biotrophy is associated with loss of ligninolytic and cellulolytic enzymes
gene duplication events explain the existence of gene families in Arabidopsis thaliana Arabidopsis thaliana
tandemly arrayed genes can subsequently be affected by local rearrangements
chromosome Cu4 originated from translocation between HCK5 and HCK8, followed by stitching of shattered HCK8 and HCK7 and final two inversions Cucumis sativus
large genomic SVs have increasing evidence pointing to importance Manihot esculenta
jojoba genome lacks recent duplications Simmondsia chinensis
cruciferous tribe Thlaspideae is used as model for role of large-scale chromosome alterations in genome evolution
Proto-Calepineae Karyotype (PCK) has been introduced as ancestral genome of lineage II
genomic responses to allopolyploidy can be viewed from short-term and long-term responses
young allopolyploids undergo epigenetic repatterning
magnitude of gene loss and expression alterations varied substantially across recently formed species
ancestral clade homologues are absent in gymnosperm genomes
particular changes in genome structure should be investigated for relationships with organismal function or fitness
PSY3 has origin more ancient evolutionary event Solanum tuberosum; Solanum lycopersicum
transposons play a role in host genome adaptation
gene and genome duplications have been shown to be particularly prominent in plant genomes plants
complex evolutionary histories include diploidization
genome of cultivated melon types could have originated from ancestral karyotype of lineage I (AKI) via 15 large-scale inversions, gain and loss of one NOR, and four centromere repositioning events Cucumis melo
chromothripsis could be regarded as credible mechanism for rapid and profound genome reorganization
CCP data showed that genome of Pse. szowitsii is significantly different from Pe. planisiliqua Pseudocamelina szowitsii; Peltaria planisiliqua
synteny analysis showed Liriodendron experienced WGD event after differentiation Liriodendron
C. praecox genome has two rounds of WGD Chimonanthus praecox
introns smaller than 200 bp remained in orchid introns Orchidaceae
Cuscuta australis showed approximately 10% gene loss (1,012 lost orthogroups / 9.89%) Cuscuta australis
ancestral angiosperms contained no more than 12,000–14,000 genes
in silico paleogenomic data provide insight into genome organisation
high-quality genomes and pan-genome projects enable comparative analysis of structural variation process contributions across plant lineages
phylogenomic-based evolutionary framework was constructed incorporating inferred ancestral karyotypes and eight species karyotypes Cucumis
ancestral karyotype of lineage II (AKII) originated by six paracentric inversions and one pericentric inversion involving chromosomes ACK4, ACK6, ACK9 and ACK10 Cucumis
ancestral centromeres were not observed in predetermined genome blocks (GBs) Cucumis sativus
ancestors of Euscaphis japonica and Vitis vinifera shared ancient polyploidization event before their differentiation Euscaphis japonica; Vitis vinifera
structural heteroplasmy and complexity of soybean mtDNA creates genetic variations for the structural evolution of soybean mtDNA Glycine max
jojoba genome shows evidence of ancient whole genome triplication Simmondsia chinensis
non-dysploidal chromosome rearrangements (CRs) probably represent main genome-diversifying driver in the tribe
chromosomes Thl2, Thl3 and Thl5 have least number of rearrangements in studied Thlaspideae species
synteny analysis between C. praecox and C. kanehirae, L. chinense, V. vinifera, and A. trichopoda supported two WGD events in C. praecox Chimonanthus praecox; Cinnamomum kanehirae; Litsea chinense; Vitis vinifera; Amborella trichopoda
paleotetraploidy in cassava genome explains partial conserved synteny between chromosomes 14 and 16 with chromosomes 6 and 17 Manihot esculenta
young allopolyploids undergo rapid homoeologous exchanges
creation of new genes from transposable element-acquired gene fragments potentially contributes to genome diversification
loss of DNA sequences is genome-scale process occurring during evolution
plants enhance gene repertoire
plant genomes are shaped by structural variation
monocots, Caryophyllales, and Lamiales have no or reduced TNL sets
inverted genome blocks (GBs) were deduced based on minimum number of rearrangement events concerning present-day Cucumis genome structures Cucumis
centromere-proximal regions of ancestral chromosomes (1, 3, 4, 6, 8, 10 and 11) frequently underwent inversions or breakages during origin of species karyotypes Cucumis
most plant species have smaller genomes than expected given incidence of polyploidy
G5 and GSe share many mtDNA features not observed in other groups Glycine max; Glycine soja
ancestral genome of tribe Thlaspideae was derived from PCK (Proto-Calepineae Karyotype)
whole genome duplication (WGD) is often followed by genomic downsizing
genome merger and doubling of divergent genomes would make newly formed allopolyploids undergo genomic shock
genus-level ancestral karyotype allowed elucidation of evolutionary events accounting for origin of diverse genomes Cucumis
chromosomes 4, 6, 8, 9 and 10 in AKI, AKII and C. metuliferus were shuffled through different inversions Cucumis
12 centromeres of melon were subsequently invaded by pericentromeric heterochromatin Cucumis melo
C. hystrix genome originated from HCK via five inversions, one reciprocal translocation, and NOR gain Cucumis hystrix
C. praecox genome showed two peaks with whole-genome duplication (WGD) events Chimonanthus praecox
Gastrodia elata displayed highest level of gene loss in all categories Gastrodia elata
long-term sequence elimination leads to genome fractionation
61.36-kb indel in NBS-LRR cluster on Chr09 resulted in deletion of five NBS-LRR genes in IVF77 compared with CM27 Cucumis metuliferus; Cucumis melo
ancestral clade homologues are absent in Amborella trichopoda Amborella trichopoda
effector catalogs evolve via different mechanisms
transition from saprotrophy to biotrophy is associated with diversification of novel genes
Tourist-like and Stowaway elements appear to play essential role in gene and genome evolution
Aegilops tauschii (D) is assumed to be A-, B-, and D-genome ancestors Aegilops tauschii
organelle-to-nucleus DNA transfers are involved in genome divergence within and between species and subspecies Oryza sativa
disproportionate evolution of WAKL genes may be due to functional redundancy Brassica napus
phenotypic diversification drives genome evolution
inferred structure of ancestral Cucumis karyotype (ACK10) is likely the result of two inversions on Bhi7, one inversion on AKI10, one inversion on Cmt10, and three inversions on AKII10 Benincasa hispida; Cucumis
paleo-centromere damage may actively participate in massive genomic reorganization in Cucumis through triggering chromothripsis-like rearrangements Cucumis
In rice no such segmental or tandem duplication events have been found GS genes Oryza sativa
structural rearrangements cause some genes exhibit copy number variations between two genomes Glycine max
chromosome rearrangements (CRs) play key role in driving diversification and evolution of plant lineages
inversions have been investigated in Rhagoletis Rhagoletis
Apostasia shenzhenica exhibited 463 lost orthogroups (4.52% of conserved orthogroups) Apostasia shenzhenica
30 rice-independent linkage groups represent ancestral cereal genome structure
gene loss or differentiation following gene duplication contributes to genome diversification
absolute dosage varies over time duplicate gene evolution
highly reshuffled regions near centromeres on chromosomes 4, 6, 8 and 10 are exceptions to conservative chromosome structures Cucumis
4001 gene families in Euscaphis japonica expanded in Euscaphis japonica Euscaphis japonica
present study aimed to identify key mechanisms shaping structure of Thlaspideae genomes
CR-prone chromosomes (Thl4 and Thl6) represent Thlaspideae-specific genome-diversifying drivers
recent whole-genome duplication (WGD) event is independent event specific to Calycanthaceae Chimonanthus praecox
introns smaller than 200 bp in non-orchid monocots mostly did not expand in orchids Orchidaceae
Cuscuta australis compared with Gastrodia elata, fewer genes were lost in plastome (22%) Cuscuta australis; Gastrodia elata
intron gain and loss might be correlated with transposable element activity
A and C genomes have undergone independent evolution for 3.75 million years Brassica rapa; Brassica oleracea
Chromosome 1 in Amaranthus cruentus has very little collinearity to any other pseudochromosome Amaranthus cruentus
loss of chromosome 5 homoeologue occurred before speciation of Amaranthus cruentus and Amaranthus hypochondriacus Amaranthus cruentus; Amaranthus hypochondriacus
whole-genome sequences reveal large-scale duplication events
Transposable elements (TEs) generate genomic novelty and diversity
transposable elements have overlapping contributions to gene duplications and gene fusions
most clusters identified as LTR retrotransposons and DNA transposons are shared by majority or even all Thlaspideae species
two similar peaks at Ks values detected in five Calycanthaceae species Chimonanthus salicifolius; Cinnamomum chinensis; Chimonanthus floridus; Chimonanthus occidentalis; Idiospermum australiense
Calycanthaceae, Lauraceae, Gomortega keule, and Peumus bolds experienced a specific WGD event not shared with other magnoliid lineages Chimonanthus praecox
expansion of introns in orchids speculated to be due to accumulation of different types of transposons over time Orchidaceae
chromosomal loss and fusion events are common to Amaranthus cruentus and Amaranthus hypochondriacus Amaranthus cruentus; Amaranthus hypochondriacus
recombinational mapping or orthologous clone sequence comparisons originally observed genomic rearrangement
polyploids leave substantial legacy in plant genomes
dosage effects represent one aspect of pluralistic framework for genome evolution
transposable elements (TE) are major drivers of plant genome evolution
somatic and germline mobility shapes diversity of transposons in plant genomes
C. subsericeus B-subgenome, C. dipsaceus, C. zeyheri and C. anguria originated from common ancestral karyotype, named BDK Cucumis subsericeus; Cucumis dipsaceus; Cucumis zeyheri; Cucumis anguria
melon chromosome Cme8 could have been derived from AKI through two pericentric inversions and one paracentric inversion involving ~18-Mb fragile region and NOR loss Cucumis melo
six centromeres in cucumber were detected at fusion points of shattered genome blocks (GBs) Cucumis sativus
cytoplasmic genomes of G1–G3 are not derived from wild accessions in GSa–GSe Glycine max; Glycine soja
P. turkmena has karyotype resembling ancestral genome of Thlaspideae Petriella turkmena
synteny analysis showed C. salicifolius experienced two WGD events shared with C. praecox Chimonanthus praecox; Chimonanthus salicifolius
lost genes in complete heterotrophs G. elata and C. australis show large overlap of 35.60 and 42.59% common genes Gastrodia elata; Cassytha australis
pseudogenization contributed to deviation from strict micro-synteny Oryza spp.
genome of Physcomitrella patens has undergone at least two WGD events Physcomitrella patens
55.37-kb deletion in NBS-LRR gene cluster on cucumber (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) resulted in loss of five NBS-LRR genes in cucumber compared with IVF77 Cucumis sativus; Cucumis melo
amaranth lineage whole-genome duplication (WGD) event was followed by substantial chromosomal rearrangements Amaranthus cruentus; Amaranthus hypochondriacus
polyploidy and segmental duplication followed by gene loss occur in grasses
rearrangement of chromosomes is genome-scale process occurring during evolution
Solanaceae has had ancient whole genome duplications (WGDs)
Short Read Sequencing (SRS) technologies is applied to characterization of genome evolution
specific transposable element elements can be dominant within a lineage
transposable elements (TEs) are responsible for genomic variation in plants
ancestral karyotype of lineage II (AKII) evolved into C. dipsaceus, C. zeyheri and C. anguria through inversions Cucumis dipsaceus; Cucumis zeyheri; Cucumis anguria
melon genome evolution suggests melon genome evolved independently from other species Cucumis melo
origin of Cu5 involves three inversions, followed by round of shattering-stitching between HCK9 and HCK10 Cucumis sativus
chromothripsis-like rearrangement is mechanism to rapidly remodel genomes
A ( (AGL8, FUL, AT5G60910) /AP), B (Bs/ (AP3, ATAP3, AT3G54340) /PI), and SEP subfamilies have been duplicated in Euscaphis japonica Euscaphis japonica
cassava genes exist in one syntenic block reciprocally in either genome Manihot esculenta
sub-stoichiometric shift (SSS) process alternates mitochondrial genotype (mitotype)
mitogenome of GSe has a close relationship to mtDNA of G5's maternal donor Glycine max; Glycine soja
ancestral Thlaspideae genome has seven chromosome pairs
this study represents most comprehensive cytogenomic study so far performed within monophyletic plant clade
no chromosome rearrangements on chromosomes Thl4 and Thl6 were identified in analyzed species of tribes Isatideae, Sisymbrieae and Eutremeae
Vanilla planifolia exhibited 528 lost orthogroups (5.16% of conserved orthogroups) Vanilla planifolia
parasitic plants show strong contraction in plastomes
evolutionary shifts from conventional endoreplication (CE) to partial endoreplication (PE) (and vice versa) has adaptive potential for evolution of genome size and GC content variation in orchids
substantial homology of five pseudochromosomes indicates additional rearrangements Amaranthus cruentus
2:1 orthologous relationship between Amaranthus cruentus and Beta vulgaris results from the WGD event in the Amaranthus cruentus lineage that is not shared with Beta vulgaris Amaranthus cruentus; Beta vulgaris
chromosome loss, fusion and fission after the whole-genome duplication (WGD) appears to be prevalent in Amaranthus genus Amaranthus
whole genome duplication in salicoid clade resulted in large fraction of paralogous gene pairs Populus species
comparative analyses decipher evolutionary process in leguminous plants
small insertions is one of three independent mutational mechanisms generating yellow-fleshed peach genotypes Prunus persica
non-allelic homologous recombination can arise from additional variation
karyotype variation placed in evolutionary framework Cucumis
polyploidization event corresponding to Ks2 of Euscaphis japonica is likely the same as polyploidization event experienced by Vitis vinifera Euscaphis japonica; Vitis vinifera
rearrangement breakpoints are mostly associated with micro-repeats (MRs) (MR9a, MR16, MR9b) Glycine max
two WGD events shared by all Calycanthaceae species Chimonanthus praecox; Chimonanthus salicifolius; Cinnamomum chinensis; Chimonanthus floridus; Chimonanthus occidentalis; Idiospermum australiense
Ks analyses in accordance with synteny analysis results
large introns are not a genome feature related to heterotrophy
fission of chromosome 2 occurs in Amaranthus cruentus Amaranthus cruentus
ancestral clade homologues are absent in 11 basal genomes
small rearrangements are caused by illegitimate recombination
illegitimate recombination has relative aggressiveness that differs dramatically in different plant lineages
four melon chromosomes (Cme1, Cme3, Cme6 and Cme8) experienced centromere repositioning through centromere seeding Cucumis melo
sublimons can increase rapidly through sub-stoichiometric shift (SSS) process
transposable elements (TEs) can mediate chromosome rearrangements (CRs)
lost genes in S. asiatica and A. shenzhenica show limited overlap of 17.62 and 15.98% common genes Striga asiatica; Apostasia shenzhenica
diploidization after WGD includes chromosomal rearrangements and reduction in number
syntenic gene loss contributed to deviation from strict micro-synteny Oryza spp.
collinearity pattern of Chromosome 1 in Amaranthus cruentus indicates likely fusion of the original subgenome homeologues Amaranthus cruentus
shuffled region of Cmt10 probably differs from Bhi7 by just two inversions Benincasa hispida; Cucumis metuliferus
chromosome Cu3 formation resulted from six inversions, single end-to-end fusion event and pericentric inversion Cucumis sativus
short repeat (SR)-mediated recombination is a major driving force of soybean mtDNA evolution Glycine max
Chromosome 1 in Amaranthus cruentus has 496 collinear genes that showed collinearity to the other half of chromosome 1 Amaranthus cruentus
retrotransposons (short interspersed nuclear elements, SINEs) is RNAPIII-transcribed RNA in plants Plantae
amplification and elimination of (ATNACK2, NACK2, TES, AT3G43210) are highly dynamic processes in plant genome evolution
genome evolution complexity varies to lineage-specific extents
accumulation of transposable elements is generally suggested to contribute to increased genome sizes in ferns
large genomes of pines may experience irreversible increase in genome size
minimal genome hypothesis could explain wide span of genome sizes in G. aurea populations Genlisea aurea
lineage-specific polyploidy in gnetophytes occurs in Ephedra Ephedra
ancestral genomes of lineage I (AKI) and lineage II (AKII) have been inferred based on three premises about ancestral chromosome number, chromosome structure conservation, and inversion deduction Cucumis
highly shuffled regions of ancestral Cucumis karyotype (ACK) can therefore be inferred based on wax gourd karyotype Benincasa hispida
centromere-proximal regions of ancestral chromosomes could be defined as 'fragile' genomic structures Cucumis
evolution of soybean mtDNA should involve configuration conversion from one master circle to two discrete circles or vice versa Glycine max
specific regions in Wm82_mtDNA and AGH_mtDNA infer that two genomes have experienced different sequence gain-and-loss events after they diverged Glycine max
recent whole-genome duplication (WGD) event has Ks value of 0.6 Chimonanthus praecox
lost orthogroups in all other heterotrophic species approximately 65–80% found to be lost in Scaphosepalum himalayana
genome size variation is linked to amount of repetitive DNA
Chromosome 5 in Amaranthus cruentus has just one collinear block with chr02B Amaranthus cruentus
fission of chromosome 2 into 02A and 02B in Amaranthus cruentus occurred subsequent to the chromosome 5 copy loss and chromosome 1 fusion shared with Amaranthus hypochondriacus Amaranthus cruentus; Amaranthus hypochondriacus
fission of chromosome 2 into 02A and 02B in Amaranthus cruentus produced n = 17 Amaranthus cruentus
complex orthologous relationships between Bvchr5 and multiple Amaranthus cruentus chromosomes presumably due to multiple chromosomal rearrangements Amaranthus cruentus; Beta vulgaris
fusion of chromosomes is genome-scale process occurring during evolution
hybridisation is process involving horizontal transfer of genes or genomes
transposable elements (TEs) dominate plant genomes
analysis of this region in Brachypodium confirms rapid evolution of the same region in rice Brachypodium distachyon; Oryza sativa
pangenomics enables understanding of transposable element dynamics
WGD in gnetophytes was less conclusively demonstrated in Gnetum Gnetum
massive chromosomal rearrangements and gene fractionation during diploidization possibly caused extremely fragmented synteny in Gnetum genome Gnetum
satellite repeats often evolve rapidly in eukaryotic genomes
polyploidy correlates with life history trait evolution
C. metuliferus maintains most ancestral chromosome structures Cucumis metuliferus
karyotype reconstruction of Thlaspideae species detected genus- and species-specific chromosome rearrangements (CRs)
Ks value between C. praecox and L. chinense larger than L. chinense WGD event Chimonanthus praecox; Litsea chinense
gene space in IWGSC RefSeq v2.1 pseudomolecules more faithfully reflects divergence of wheat subgenomes from common ancestral genome
DNA sequence information combined with informatic tools and experimental approaches enables linking genome behaviour with its consequences
plant (ATNACK2, NACK2, TES, AT3G43210) and DNA repair machinery often work together and can produce similar SV outcomes
two large gene families exhibit extreme levels of copy-number and structural variation
ectomycorrhizal lifestyle is associated with convergent genomic expansions
most chromosomes in given lineages retain conservative structures resembling ancestral chromosomes Cucumis
C. dipsaceus chromosome Cdi7 experienced single ~6-Mb pericentric inversion in non-fragile areas Cucumis dipsaceus
C. zeyheri genome further shows two minor species-specific inversions in fragile regions of Cze8 and Cze10 Cucumis zeyheri
melon chromosomes Cme2 and Cme10 can be explained by two inversions on AKI2 and AKI10 respectively Cucumis melo
sub-stoichiometric shift (SSS) process drives mtDNA evolution
intergenic regions in plant mitogenomes are extremely divergent sequence divergence
ancestral genome of Thlaspideae should resemble proto-Calepineae Karyotype (PCK)
present study aimed to reconstruct ancestral genome of Thlaspideae
inversions have been investigated in Prospero Prospero
Gastrodia elata exhibited largest contraction of 1,440 gene families Gastrodia elata
syntenic analysis in Amaranthus hypochondriacus indicated chromosome number reduction was likely due to the loss of one homoeologue of chromosome 5 and the fusion of the two homoeologues of chromosome 1 Amaranthus hypochondriacus
biosynthetic gene inversions and variation in the exact biosynthetic gene number is seen in several orthologous clusters demonstrating genome rearrangements that are specific to each Amaranthus species Amaranthus cruentus; Amaranthus hypochondriacus
paleo-duplications and intergenomic colinearity data enable proposal of model for the evolution of the grass genomes from a common ancestor
Brassicaceae has had ancient whole genome duplications (WGDs)
dynamic genome compartments is important for accelerated gene evolution
pluralistic framework for genome evolution will broaden view of how genomes evolve
selection and drift will be important mechanisms to eliminate TE copies
paralogous gene copies indicate continuous dynamic process of chromosomal changes in gene content Zea mays; Oryza sativa; Sorghum bicolor
identity between LaSCR1 and LaSCR2 intronic and exonic sequences may reflect genome duplication some 56 million years ago followed by divergence Lupinus albus
genomic democratization will serve as foundation for understanding genome dynamics and role of WGD
characterizing transposable elements (TE) across species using pangenomics can help us better understand how SVs originate and how TE dynamics contribute to gene neofunctionalization
large gene families such as RLKs are usually exception in genome evolution
smallest haploid angiosperm genomes are less than one-half that of Arabidopsis Utricularia; Genlisea; Arabidopsis thaliana
whole-genome analysis of B. rapa revealed high rate of gene loss, from 30% to 64% depending on the degree of fractionation Brassica rapa
long-arm Chy12 of C. hystrix gained nucleolar organizer region (NOR) without apparent chromosomal rearrangement Cucumis hystrix
1403 gene families in Euscaphis japonica contracted in Euscaphis japonica Euscaphis japonica
Triticum urartu is A genome donor of common wheat Triticum urartu; Triticum aestivum
Ks analysis showed evidence of two whole genome duplication events Simmondsia chinensis
inversions have been investigated in Noccaea Noccaea
genome dominance has been observed in some polyploids
genome sequences of red and green algae showed that introns were genome-wide abundant introns prior to origin of land plants red algae; green algae
genome size variation is linked to number of chromosomes
genomes of Asian Cucumis species (C. metuliferus) and Africa Cucumis species (melon) underwent tremendous changes after divergence genome structure Cucumis metuliferus; Cucumis melo
different types of (ATNACK2, NACK2, TES, AT3G43210) show different dynamics in rice Oryza sativa
A. cruentus genome contains gene families that contracted and expanded Amaranthus cruentus
Chenopodium quinoa has retained haploid chromosome number of n = 18 during the 3.3–6.3 million years since genome duplication Chenopodium quinoa
some species of Utricularia and Genlisea possess smallest haploid angiosperm genomes known, at c . 60 megabases (Mb) Utricularia; Genlisea
polyploidy can influence dynamics of plant genomes
gene and genome duplications have greatly influenced genomes organization and evolution plants
expansion of introns is generally suggested to contribute to increased genome sizes in ferns
coding and regulatory sequences were essentially conserved after whole-genome duplication (WGD) and diploidization events Brassica napus
localization study could provide a new basis for comparison of the evolution of this gene family Arabidopsis thaliana; Brassica napus
Utricularia and Genlisea are prime candidates for further research on evolution of minimal plant genome Utricularia; Genlisea
some populations of bladderworts have smaller than 60 Mb genomes Utricularia
minimal genome hypothesis could provide platform to understand evolution and specialization of genome structure in relation to nutrient acquisition Utricularia; Genlisea
three regions of AKI and Cmt retain ancestral structure in ancestral Cucumis karyotype (ACK6, ACK8, ACK9) Cucumis metuliferus
remaining four chromosomes of HCK are conserved at level of resolution of this study Cucumis
observations of Csh and Csa genome differences suggest genome of Csh retains more ancestral structure of cucumber Cucumis sativus
identification and detailed characterization of chromosome shattering and stitching events contributes significantly to understanding evolutionary plasticity of genomes
Wm82 mitogenome was evaluated for recombination behavior Glycine max
cytoplasmic genomes of G1–G3 are likely evolved from the same lineage Glycine max
chromosome rearrangement (CR) rate estimated for Thlaspideae tribe
ancestral genome of tribe Thlaspideae underwent reciprocal translocation between chromosomes (AK2, CARAB-AK-LYS, AT5G14060) and AK5/8/6
conserved gene families in all orchids approximately 75% have sizes below average gene family size of all species examined Orchidaceae
gene loss events in partial heterotrophic plants mostly lineage-specific
orthologous genomic sequences and published sequences were used to investigate divergence of two subgenomes in Oryza polyploids Oryza sativa
fission of chromosome 2 in Amaranthus cruentus gives rise to haploid chromosome number of 17 Amaranthus cruentus
ten of the other 15 pseudochromosomes in Amaranthus cruentus have clearly identifiable one-to-one homoeologous relationships Amaranthus cruentus
whole-genome duplication impacts plant trait evolution
transition from saprotrophy to biotrophy is associated with co-option of ancestral genes
heterosporous fern genomes are some of the smallest in the fern lineage
model clade dataset could be used to address causes for differences in genome dynamics and diploidization rates across lineages
one of the two paralogues of MEK2 may have been deleted from genomes of Nicotiana spp. Nicotiana spp.
S genome is most similar to B genome of wheat
polyploidy plays role in shaping genome dynamics
polyploidy is significant for genome evolution in angiosperms
earlier inferences of independent WGDs in the two conifer lineages likely represent other types of gene duplications
allotetraploidization resulted in drastic changes in homoeologous regions of maize Zea mays
Utricularia and Genlisea exhibit dynamic evolution of genome size Utricularia; Genlisea
B genome might be derived from Aegilops speltoides Triticum aestivum; Aegilops speltoides
melon chromosome Cme4 was created by ~8-Mb paracentric inversion and NOR gain at boundary between blocks Cucumis melo
further exploration of gene hemizygosity in cassava will be interesting from genome evolution standpoint Manihot esculenta
pericentric inversions are mostly genus- and species-specific chromosome rearrangements (CRs)
variation in genome size, GC content, and genome-wide proliferation of (particular families of) repeat elements exhibits strong phylogenetic dependence
pan-genomic analysis of 77 different isolates of Pezicula neosporulosa revealed balancing selection of PCWMEs Pezisula neosporulosa
frequent restructuring of accessory regions leads to rapid gain or loss of effectors Fusarium oxysporum; Verticillium dahliae
lineage-specific polyploidy in gymnosperms occurs in gnetophytes and cupressid conifers
Triticum monococcum L. (AA) is probable donor of the A genome of modern wheat (AABBDD)
chromosomal rearrangements in cucumber evolution include chromothripsis-like events, nested and end-to-end fusions, 21 inversions, two reciprocal translocations, and seven new centromere formations Cucumis sativus
(GLN1;4, AT5G16570) share a segmented duplicate region with GS gene of Carica papaya Arabidopsis thaliana; Carica papaya
WSs and ASs are ancient sequences mutually retained in Wm82 and AGH mtDNAs Glycine max
integrated viral sequences may contribute to evolution of the genome acting as sources of novel genetic material
repetitive sequences can be associated with chromosome rearrangements (CRs) such as inversion, deletion, duplication and translocations
Ks value between C. praecox and L. chinense slightly smaller than C. praecox ancient WGD event Chimonanthus praecox; Litsea chinense
introns bigger than 200 bp in non-orchid monocots tended to lengthen in orchids Orchidaceae
whole genome duplication (WGD) is followed by genomic downsizing
contraction of gene families in Amaranthus cruentus reason for is not clear Amaranthus cruentus
recent research focused on extent of colinearity at the DNA-sequence level
pathogenic biotrophic fungi share expansion of genome size through transposon proliferation
sequence-based methods identify point of coalescence of ancestral genomes
(NIP1, AT2G17750) effector gene shows gene deletion and copy number variation across populations Rhynchosporium commune
transposable elements (TEs) interact with plant genomes
two B genome loci in hexaploid wheat (T. aestivum, 2 n =6 x =42) dominate the much-reduced A and D genome loci Triticum aestivum
myosins were subjected to gene loss and redistribution within specific lineage
segmental duplicates identified 1357 collinearity events among 1547 PK genes Glycine max
Ks value of 0.40–0.80 used to differentiate 59-Mya WGD events from 13-Mya WGD events Glycine max
476 collinearity events arranged at 59-Mya WGD regions Glycine max
MHA1L arose as part of whole-genome duplication Arabidopsis thaliana
whole genome duplications (WGD) have played prominent roles in evolution of eukaryotic species
three genes including the O2 gene are inverted on maize chromosome 7 Zea mays