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molecular evolution

18897 relationships annotated with this phrase. Showing first 500 of 18897.
Source entity Relationship Target entity Species
TEM genes have greater Dn : Ds Arabidopsis thaliana
(AT-POX, ATPDH, ATPOX, ERD5, PDH1, PRO1, PRODH, AT3G30775) orthologous genes revealed specific origin of (AT-POX, ATPDH, ATPOX, ERD5, PDH1, PRO1, PRODH, AT3G30775) for pod dehiscence
credible shift set contained 31–58 shifts
gbM genes exhibit lower Dn : Ds ratios Arabidopsis thaliana
two prominent peaks in Ks plots occur for every species, including outgroups
group II introns are evolutionarily related to spliceosomal RNAs, non-LTR retrotransposons, or telomerases
MoPhzF was acquired through horizontal gene transfer (HGT) Magnaporthe oryzae
barley and Brachypodium have a much closer evolutionary relationship than barley and rice Hordeum vulgare; Brachypodium distachyon; Oryza sativa
in the family Poaceae all PPCKs are grouped together but within this clade the subdivision is driven by the high similarity of (ATPPCK1, PPCK1, AT1G08650) proteins Zea mays; Sorghum bicolor; Setaria italica; Oryza sativa
VEF-L36 and (FIE2, FIS2, AT2G35670) were derived from VRN2-like ancestral sequence in Arabidopsis and possibly in other angiosperms Arabidopsis thaliana
Physcomitrella patens Trxs m isoforms are clustering together in cluster III Physcomitrella patens
MoPHZC/D/E/G genes were not likely acquired through an ancient horizontal gene transfer (HGT) event Magnaporthe oryzae
putative xyloglucan (XyG) arabinofuranosyltransferases evolutionary history was investigated using phylogenetics Solanum lycopersicum
larger effective population sizes for nuclear loci may lead to deeper coalescence times
horizontal gene transfer (HGT) allows organisms to acquire novel traits and exploit unexplored resources
(AtcPT1, cPT1, CPT3, AT2G17570) sequences from S. habrochaites group into two major clades Solanum habrochaites
Anabaena sp. PCC 7120 (ATMSRB1, MSRB1, AT1G53670) is in second subgroup of 1-Cys MSRBs Anabaena sp. PCC 7120
TEM genes showed higher Dn : Ds ratios compared to unM and gbM genes Arabidopsis thaliana
AhMYB2 clusters with betalain regulator BvMYB1 next to anthocyanin MYBs (S6) Amaranthus hypochondriacus; Beta vulgaris
effectors with antimicrobial activity may have ancient evolutionary origins
understanding of the links between varied molecular evolutionary phenomena within Ericales and striking evolutionary novelties is limited current knowledge
shifts out of tropical climates in Ericales are associated with whole genome duplications (WGDs) and gene-tree conflict
constitutive housekeeping expression states consistent with lower Dn : Ds ratio Arabidopsis thaliana
credible shift set contained 59–89 shifts
antifungal effector AMP3 likely evolved from ancient antimicrobial proteins of terrestrial fungal ancestors Verticillium dahliae
intra and interspecific centromere diversity will be integral to enhance understanding of evolutionary dynamics of repeat regions and associated chromatin
cowpea isomiRs of miR4407 may be functionally diverged Vigna unguiculata
evolutionary events might have had an effect on (RLK, AT5G67280) subfamily expression profiles
4 (RLK, AT5G67280) subfamilies (LRR VII, LysM, RLCK IV, and RLCK X) registered negative correlation between divergence time and expression divergence
VEF-L36 and (FIE2, FIS2, AT2G35670) were derived from VRN2-like ancestral sequence Arabidopsis thaliana
synonymous (Ds) and nonsynonymous (Dn) substitution divergence from Arabidopsis lyrata used to calculate Dn : Ds ratios Arabidopsis thaliana; Arabidopsis lyrata
251 of the 604 (RLK, AT5G67280) genes (42%) show association between sequence evolution and expression divergence Arabidopsis thaliana
clear distribution into two groups suggests distinct origin for two types of MSRB genes
TEM genes showed higher Dn : Ds ratios Arabidopsis thaliana
hints of positive selection may indicate recent selective adaptation Albugo candida
antimicrobial effectors with antimicrobial activity may have evolved from antimicrobial proteins that originally functioned in microbial competition
phylogenetic analyses indicated that g162, g164, g165, g166 and g169 formed well-supported group Plasmopara viticola
(RLK, AT5G67280) subfamilies demonstrate signs of differential evolution of sequence and expression
intragenic sequence duplication, deletion/insertion, and intergenic exon shuffling could account for structural and functional diversification of the VEF genes from an EMF2-like ancestor Arabidopsis thaliana
1-Cys MSRB1s could be defined in three other subgroups photosynthetic organisms
Synechococcus sp. CC9311 MSRB1.2 is in first subgroup of 1-Cys MSRBs Synechococcus sp. CC9311
Trx m3 orthologs are forming independent clad
six of the (RLK, AT5G67280) subfamilies (16%) display inverse association between sequence divergence and expression divergence Arabidopsis thaliana
Ka/Ks ratios suggest relaxation of purifying selection for (ACC2, AT1G36180) Arabidopsis thaliana
six of the (RLK, AT5G67280) subfamilies display inverse association between selective pressure and expression divergence Arabidopsis thaliana
TmXET6.3 (Tropaeolum majus xyloglucan endotransglycosylase 6.3) clustered independently on phylogenetic tree HvXET3 and HvXET4 Tropaeolum majus; Hordeum vulgare
Group D follows Group C Striga hermonthica
molecular properties of myosin XI are conserved between bryophytes and angiosperms Marchantia polymorpha; Arabidopsis thaliana
about a third of the (RLK, AT5G67280) subfamilies display association between selective pressure and expression divergence Arabidopsis thaliana
VEF genes may be the result of historic gene duplication event followed by diversification Arabidopsis thaliana
eukaryotic 2-Cys MSRBs could be subdivided in two subgroups eukaryotes
first subgroup of eukaryotic 2-Cys MSRBs contains higher plants 2-Cys MSRBs higher plants
within the systematics groups further organization driven by PPCK isoform Flaveria pringlei; Flaveria robusta; Flaveria ramosissima; Flaveria trinervia; Flaveria bidentis; Flaveria chloraefolia; Flaveria pubescens; Flaveria anomala; Flaveria brownii; Lotus spp.; Soja spp.; Arabidopsis thaliana; Cleome gynandra
strength of purifying selection varies among (RLK, AT5G67280) subfamilies Arabidopsis thaliana
similarity in domain structure and amino acid composition could be the result of convergent evolution
high recombination rates and foreign DNA integration in plant mitochondrial DNA explains difficulty of retracing evolutionary story of group II introns
PPCK isoforms and ppcA PEPC from C4 photosynthesis species are found on branches marking longest evolutionary distance Flaveria
PpTrxm5 and PpTrxm6 are more closely related with lower percent identity (59%) Physcomitrella patens
other CslA group members formed separate clade each for rice and Arabidopsis Oryza sativa; Arabidopsis thaliana
M subunit shows by far the lowest level of sequence identity of all cyt-bf subunits between M. laminosus and Synechocystis sp. PCC 6803
(ACC2, AT1G36180) structure, function, and retention differ widely throughout Brassicaceae
plant and microbial PALs and TALs are part of superfamily of enzymes from plants, fungi, and bacteria
similarity of Class III (Plsp2B, TPP, AT2G30440) genes to proteobacterial sequences suggests Class III (Plsp2B, TPP, AT2G30440) genes may have been recruited by horizontal gene transfer from endosymbiotic ancestor of mitochondria Arabidopsis thaliana
DkBG proteins clustered into three clades Diospyros kaki; Arabidopsis thaliana; Solanum lycopersicum; Oryza sativa
EMB15 UDP-GlcNAc pyrophosphorylase domain originated in fungi
PPCKs cluster primarily based on systematic relationships rather than photosynthetic type or PPCK isoform
different evolutionary forces might be related to divergence of expression patterns within (RLK, AT5G67280) subfamilies
gene families may be the result of gene duplication and subsequent diversification from ancestral sequences
MSRBs of photosynthetic organisms are divided into two main groups photosynthetic organisms
(RLK, AT5G67280) sequence evolution linked to expression divergence
trans-splicing introns in plant mitochondria have arisen via genomic recombination of monopartite introns vascular plants
conserved changes found in both C3 species (F. robusta and F. pringlei) on one side and both C4 species (F. bidentis and F. trinervia) on the other defined as amino acid exchanges of interest Flaveria pringlei; Flaveria robusta; Flaveria trinervia; Flaveria bidentis
evolutionary time increases toward sequence form of the C4 species Flaveria trinervia; Flaveria bidentis
degree of selective pressure tested for relationship to amount of expression divergence within each (RLK, AT5G67280) subfamily
(RLK, AT5G67280) subfamilies appear to be under purifying selection Arabidopsis thaliana
CrMSRB1 is in first subgroup of 1-Cys MSRBs Chlamydomonas reinhardtii
Ostreococcus MSRB1.1s are in third subgroup of 1-Cys MSRBs Ostreococcus lucimarinus; Ostreococcus tauri
phylogenetic analyses of PEPC isoforms in Flaveria spp. are similar to results of PPCK phylogenetic analysis Flaveria pringlei; Flaveria robusta; Flaveria ramosissima; Flaveria trinervia; Flaveria bidentis; Flaveria chloraefolia; Flaveria pubescens; Flaveria anomala; Flaveria brownii
Kelch motif is ancient and has dispersed widely during evolution
(AtEMF2, CYR1, EMF2, VEF2, AT5G51230) may have acted as prototype in the generation of the VEF gene family Arabidopsis thaliana
multiple independent green algal (PRK, AT1G32060) gene origins is alternative explanation
CrMSRB1.2 cannot be clearly attached to a subgroup Chlamydomonas reinhardtii
phylogenetic analysis reveals three well supported clades of CSLCs in flowering plants
Group 3 (HKL, HLP1, AT1G66080) proteins are identified as relatively basal evolutionary clades
Group 5 proteins have many amino acid substitutions
reduced variability in plant mitochondrial transit peptides could be indicative of higher selective pressure due to the presence of chloroplasts as a second potential target organelle
transposable element activity provides opportunities for genesis of pollen-specific miRs
ancestral cis-arranged introns are found for all trans-splicing introns in ferns, fern allies, or hornworts
31 (RLK, AT5G67280) genes (5%) show inverse association between sequence divergence and expression divergence Arabidopsis thaliana
genes of the shikimate pathway do not originate from single prokaryotic ancestor single prokaryotic ancestor of cyanobacterial origin
RhNUDX1, RcNUDX1-1a, RcNUDX1-1b, and RwNUDX1-1 are closely grouped together in phylogenetic tree Rosa x hybrida; Rosa chinensis; Rosa x wichurana
duplicate paired genes encoding NF-Y proteins exhibit asymmetry in amino acid substitution rates Oryza sativa
poor conservation of rhythmic lincRNAs between distantly related diatom species suggests strong divergence in primary nucleotide sequence Skeletonema robusta
enzyme family traverses all possible lineages
ARGONAUTE proteins (AGOs) can be classified into four evolutionary classes
HYL1-like protein was present in last common ancestor of plants and animals
transfer of a partial, inverted T-DNA repeat from Agrobacterium to an N. otophora ancestor was accompanied by structural and functional divergence of the TE-6b genes Nicotiana otophora
different characteristics of PDATs from green algae and land plants strongly suggest functional divergence in the evolutionary history of PDATs from Viridiplantae
subsequent duplication to TE-1 and TE-2 was accompanied by structural and functional divergence of the TE-6b genes Nicotiana otophora
Plant RALF peptides have diverged into four major clades
CO-like proteins (COLs) have function conserved throughout the phylogenetic tree of green plants Chlamydomonas reinhardtii; Physcomitrella patens; Arabidopsis thaliana
phylogenetic computation of genomic variations at E1009 locus presents evolutionary relationship network of Striga hermonthica groups Striga hermonthica
rice PHPs and Arabidopsis (AHP6, HP6, AT1G80100) proteins are likely not orthologous Oryza sativa; Arabidopsis thaliana
phylogenetic tree shows clades related by common descent
indel occurs as conserved, extended connecting element
cyanobacterial Psb32 homologs clustered together phylogenetic tree
conserved interrelation between algae and plant homologs shows probable conservation and importance of this interaction among photosynthetic eukaryotes Chlamydomonas reinhardtii; Arabidopsis thaliana
PM3A is evolutionary young Triticum aestivum
unequal distribution of SAPs allows hypothesis that Rpi-chc1 alleles evolved through insertion of DNA stretch into LRR domain Solanum chacoense; Solanum berthaultii; Solanum tarijense; Solanum tuberosum
mitochondrial and chloroplast transit peptides suggest common evolutionary origin
loss of the right-hand part of the TE-2 repeat was accompanied by structural and functional divergence of the TE-6b genes Nicotiana otophora
HvXET3 and HvXET4 isoforms are monophyletic evolutionary clade Hordeum vulgare
nuclear calcium (Ca 2+)-signaling system may have originated from prokaryotes prokaryotes
P. patens and S. mollendorffii have most ancestral sequences Physcomitrella patens; Selaginella mollendorffii
Arabidopsis lyrata is 5,000,000 years apart from Arabidopsis thaliana Arabidopsis lyrata; Arabidopsis thaliana
nucleotide substitution rates in Utricularia and Genlisea are radically sped up relative to sister group, the carnivorous butterworts (Pinguicula) Utricularia; Genlisea; Pinguicula
phylogenetically unrelated alleles share motifs up to 19 residues long from polymorphic regions of Prunus S-RNases Prunus
N. ventricosa is nested within different lineage in cpDNA phylogeny Nepenthes ventricosa
(CYP98A8, AT1G74540) and (CYP98A9, AT1G74550) evolved rapidly via retroposition and positive Darwinian selection Arabidopsis thaliana
evolutionary path of calcium (Ca 2+) to becoming second messenger particularly concerns possible role of calcium (Ca 2+) as second messenger in prokaryotes
plant and green algal Psb32 homologs clustered together phylogenetic tree
HvXET6 (Hordeum vulgare xyloglucan endotransglycosylase 6) clustered in independent position on phylogenetic tree HvXET3 and HvXET4 Hordeum vulgare
evolutionary analysis suggests Arabidopsis (EFR, AT5G20480) and rice XA21 are phylogenetically related
(ANAC059, ATNAC3, NAC3, ORS1, AT3G29035) ortholog promoters suggest lower selective pressure for conservation Arabidopsis thaliana; Arabidopsis arenosa; Brassica oleracea; Capsella rubella; Raphanus sativus
rates of AA substitution in Dof domains during the most recent 50-million-year period were profoundly low Oryza sativa; Sorghum bicolor
DR and duplicate lost (DL) genes showed no overall significant difference in rates Oryza sativa; Sorghum bicolor
22 AA changes is an average of 1.1 AA change per million years during that time interval Oryza sativa; Sorghum bicolor
Dof lineage SF06 exhibits dramatic asymmetry in evolutionary rate over 20-million-year interval
genome sequencing has begun to shed light on origin and evolution of dual functions of strigolactones (SLs)
genes encoding Fe-containing proteins in Arabidopsis was acquired very early during evolution Arabidopsis thaliana
Cys2-His2 zinc-finger genes show rapid evolution making orthology assessment difficult
genes following 24-h period were associated with older phylostrata than genes following 12-h period Skeletonema robusta
(TOD1, AT5G46220) paralogs from Arabidopsis and rice are clustered together phylogenetic tree Arabidopsis thaliana; Oryza sativa
relationship between structure and function explains protein structure is often more conserved than amino acid sequence
evolutionary relationship of (ATCAND1, CAND1, ETA2, HVE, TIP120, AT2G02560) and OsCAND1 supports differential essentiality of (ATCAND1, CAND1, ETA2, HVE, TIP120, AT2G02560) between species Arabidopsis thaliana; Oryza sativa
DkBG1 is closer to LOC_Os04g39880 of rice Diospyros kaki; Oryza sativa
young age of Nicotiana tabacum did not allow for many transversions to accumulate in genome Nicotiana tabacum
sequence conservation between bi-chromosomal Wm82_mtDNA and mono-chromosomal AGH_mtDNA suggests that bi-chromosomal Wm82_mtDNA and mono-chromosomal AGH_mtDNA are derived from a common ancestor Glycine max
one AA substitution is projected to have occurred in the 97–70 MYA interval Oryza sativa; Sorghum bicolor; Kobresia littledalei
amino acid substitution rates in the Dof domain are some of the lowest known for proteins
the same type of exchange was observed in the C4 species in Amaranthaceae
OsERS1 and its homologs divided into two clades: eukaryote-specific GluRSs (clade I) and prokaryote-originated GluRSs (clade II)
positive association between selective pressure and expression divergence may reflect relaxed purifying selection allowing greater divergence in expression to evolve Arabidopsis thaliana
(AtEMF2, CYR1, EMF2, VEF2, AT5G51230) is most plesiomorphic form of the gene Arabidopsis thaliana
necessity to fine-tune levels of germline-specific transcripts provides opportunities for genesis of pollen-specific miRs
centromeric histone 3 (CENH3, HTR12, AT1G01370) undergoes rapid evolution (CENH3, HTR12, AT1G01370) protein sequence
protein sub-cellular localization and undetermined functions suggest possible co-evolution of protein function and localization
S335 is under positive selection evolutionary pressure Pseudomonas syringae
divergence time of F. erecta from fig clade was 14.0 Ma Ficus erecta; Ficus carica
HvXET3 and HvXET6 did not share monophyletic origin Hordeum vulgare
HvXET3 and HvXET4 shared monophyletic origin Hordeum vulgare
HvXET5 (Hordeum vulgare xyloglucan endotransglycosylase 5) clustered independently on phylogenetic tree HvXET3 and HvXET4 Hordeum vulgare
HvXET6 branched early in clade of HvXET3 and HvXET4 Hordeum vulgare
distinct regions/motifs in (ATPDAT, PDAT, PDAT1, AT5G13640) sequences from green algae and land plants strongly suggest functional divergence in the evolutionary history of PDATs from Viridiplantae
average Ka/year of all rice Dof gene Dof domains over the last 50 MY is on par with ferredoxin protein in animals
closest homology for MATEs in cassava is in line with results of MATE protein alignment Manihot esculenta
gene body methylation (gbM) has evolutionary origin
(AtDRB1, DRB1, HYL1, AT1G09700) homologs in sponges and cnidarians proposes potential for common evolutionary origin between plants and animals
Zt6/Ribo1 is pair of orthologs
Utricularia and Genlisea exhibit highly increased rates of nucleotide substitution Utricularia; Genlisea
protein encoded by cDNA clusters with other plant (ATCCD1, ATNCED1, CCD1, NCED1, AT3G63520) enzymes Osmanthus fragrans
well characterized fructan exohydrolases (FEHs) evolved from cell wall invertases (cwINVs)
HvPPO1 and HvPPO2 were closely related to wheat PPOs on 2AL, 2BL, and 2DL Hordeum vulgare; Triticum aestivum
animal, fungal, and plant SCO proteins form separate clusters
NOMT genes from low-sakuranetin-accumulating cultivars formed at least two clusters in dendrogram Oryza sativa
short tandem duplication occurred during evolution of Brassicaceae lineages Arabidopsis thaliana
22 AA changes in the TPL-binding, GI-binding, and FKF1-binding domains occurred from 70 to 50 MYA in the SF02 and SF04 lineages Oryza sativa; Sorghum bicolor
long generation times causes slow molecular evolution at neutral sites
selective pressures on virulence effectors leave footprints in extant allelic variation
phylostratigraphic analysis revealed rhythmic protein-coding genes were enriched in eukaryote and stramenopile age Skeletonema robusta
groups I, II and III may represent the original genes of the CcCIPK family Cajanus cajan
signals of positive selection can be searched for in whole transcriptomes
(UGT73C7, AT3G53160) is recently emerged gene specific for Brassicaceae and closely related family Arabidopsis thaliana
genetic structure of bacterial virulence effectors may contribute to rapid generation and turnover of virulence effectors
VdAve1/VdAve1L2 is pair of orthologs
epimutEvo clock substitution rate exceeds DNA or protein clock rates by 4–5 orders of magnitude
quantitative data on substrate specificity and transport rates are important in understanding transporter evolution
discovery of (AtDRB1, DRB1, HYL1, AT1G09700) homologs in sponges and cnidarians challenges notion of convergent evolution
mutation that causes the P130T amino acid substitution in Kasalath NOMT was detected in other Oryza sativa cultivars and an Oryza rufipogon strain that cluster together with Kasalath NOMT Oryza sativa; Oryza rufipogon
Brassica ZEPs likely evolved rapidly after whole-genome duplication and triplication Brassica napus
absence of (AtDRB1, DRB1, HYL1, AT1G09700) homologs in bilaterian animals led to belief that (AtDRB1, DRB1, HYL1, AT1G09700) evolved independently in plants and animals
amino acid variances between AOC and MPO enzymes imply evolutionary replication event
low evolutionary rate of protein genes in plant mitogenomes is consistent with only two SNPs identified in protein coding sequences between Wm82 and AGH mtDNAs Glycine max
duplicated gene copies are more likely to escape selective constraints
NC no statistically significant differences (ANOVA, P >0.01) in ggps, (TAT, TAT3, AT2G24850) tyra, and (APG1, E37, IEP37, VTE3, AT3G63410) paralogues Solanum lycopersicum; Solanum pennellii
glutathione S-transferase (ATGSTU24, GST, GSTU24, AT1G17170) genes cluster into two sub-clades Actinidia deliciosa
insertion of DNA stretch into LRR domain may happen through unequal crossing-over with paralog sequences Solanum chacoense; Solanum berthaultii; Solanum tarijense; Solanum tuberosum
directional selection has driven evolutionary divergence of indica and japonica OsTTG1 alleles Oryza sativa
seed number differences among (TOD1, AT5G46220) orthologs are consistent with evolutionary relationships Solanum lycopersicum; Nelumbo nucifera; Nymphaea colorata; Oryza sativa; Arabidopsis thaliana
ancestral clade should be renamed as group-IV (floral) clade
phylogenetic relationships of cyclases that generate nonsteroidal triterpene alcohols might indicate recent and rapid catalytic evolution
lower Ka/Ks value (<1) in Arabidopsis suggests occurrence of purifying action in duplication events influenced by natural selection Arabidopsis thaliana
SF06A lineage had one amino acid substitution in the Dof domain Oryza sativa; Sorghum bicolor
(TOD1, AT5G46220) orthologs are clustered together phylogenetic tree Solanum lycopersicum; Nelumbo nucifera; Nymphaea colorata; Ginkgo biloba; Pinus taeda
plant endoglucanases (EG16) evolved to true XTHs
differences in miRNA biogenesis between animals and plants led to belief that (AtDRB1, DRB1, HYL1, AT1G09700) evolved independently in plants and animals
ancestral group shows divergence from group-I/II XTHs and group-III/EG16 sequences
D14L is older paralogue to (D14, AT3G03990)
effector structural conservation occurs within and across diverse taxa
polymorphic sites in sequences encoding LRR domain of Mla alleles are under positive selection Hordeum vulgare
differences in primary sequence might be proxy for functional divergence
phylogenetic analysis revealed papaya lcy-β2 was most similar to chromoplast-specific lycopene β-cyclase from tomato Carica papaya; Solanum lycopersicum
predicted amino acid sequences of (PPO, TOPP2, AT5G59160) genes from six grass species were used for phylogenetic analysis Hordeum vulgare; Triticum aestivum; Oryza sativa; Zea mays; Sorghum bicolor; Brachypodium distachyon
HvPPO1 and HvPPO2 were compared with deduced (PPO, TOPP2, AT5G59160) amino acid sequences of five other species Hordeum vulgare; Triticum aestivum; Oryza sativa; Zea mays; Sorghum bicolor; Brachypodium distachyon
AtXTH11 is member of group-IV (floral) clade Arabidopsis thaliana
protein structure is often more conserved than amino acid sequence
14 duplicated gene pairs in O2 and (OHP, OHP1, PDE335, AT5G02120) regions averaged Ks value of 0.448 Zea mays
nucleotide substitution rates in Utricularia and Genlisea occur across genomes of mitochondrial, plastid, and nuclear compartments Utricularia; Genlisea
cytoplasmic invertases (cytINVs) cluster shows only distant relationship to sequences mentioned above
Ks value of Os 03–Os 07 falls into two groups with average values of 0.30 and 0.60 Oryza sativa
LRR-Extensin gene pair has Ks values of 0.245±0.031 (Os 03–Os 07), 0.417±0.045 (Sb 01–Sb 02), 0.317±0.033 (Zm 01–Zm 07), 0.37±0.035 (Zm 02–Zm 05) Oryza sativa; Sorghum bicolor; Zea mays
enhanced speciation rates among bladderworts was attributed to systemic effect of accelerated nucleotide substitution rates Utricularia
KCHs from Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera, Ricinus communis, and Physcomitrella patens cluster into four different clades Oryza sativa; Arabidopsis thaliana; Populus trichocarpa; Vitis vinifera; Ricinus communis; Physcomitrella patens
monocotyl and dicotyl plants lack recent common ancestor of anther-specific cwINVs
(TOD1, AT5G46220) ortholog members from angiosperms are clustered together (TOD1, AT5G46220) ortholog clade Solanum lycopersicum; Nelumbo nucifera; Nymphaea colorata; Oryza sativa; Arabidopsis thaliana
AtXTH11 is member of ancestral clade Arabidopsis thaliana
Auxin gene pair has Ks values of 0.561±0.072 (Os 03–Os 07), 0.321±0.049 (Sb 01–Sb 02), 0.307±0.046 (Zm 01–Zm 07) Oryza sativa; Sorghum bicolor; Zea mays
VvRabGAPs and VvRabGDIs were from distinct clades Vitis vinifera
KCHs from Physcomitrella forming a separate branch indicates a possible higher evolutionary divergence of these proteins Physcomitrella patens
dicot-A and monocot-A clusters are only distantly related to each other
RNase Phy3 and RNase Phy4 are very different from canonical S-RNases found in Petunia hybrida Petunia hybrida
third lineage of Nepenthes endochitinases contains N. hybrid 'Mizuho' and monophyly of N. gracilis and N. singalana Nepenthes hybrid 'Mizuho'; Nepenthes gracilis; Nepenthes singalana
higher ω ratios in green algal branch means evolution was more relaxed in the algal group
higher non-synonymous (KA) than synonymous (KS) substitution rate is indication of positive selection
(GEX3, AT5G16020) shows high levels of sequence conservation
TaIVR3 from wheat is located in cluster monocot-C Triticum aestivum
first lineage of Nepenthes endochitinases consists of N. ventricosa and N. mirabilis Nepenthes ventricosa; Nepenthes mirabilis
19 genes M1a displayed the best fit, indicating that even when a proportion of codons are evolving neutrally, there is no support for positive selection Arabidopsis thaliana; Solanum lycopersicum; Solanum pennellii
460 small GTPase sequences were phyletically analysed to shed light on evolution and functional characteristics of legume-specific homologues Medicago truncatula; Lotus japonicus; Arabidopsis thaliana; Homo sapiens; Saccharomyces cerevisiae
MATE protein alignment displays highest homology between MATE genes on chromosome 16 and chromosome 17 Manihot esculenta
30 AA changes in these three domains have occurred from 50 MYA to the present, which is an average of 0.6 AA changes per million years during that time interval Oryza sativa; Sorghum bicolor
evolution of integrated domains in R genes has been postulated to be caused by unknown recombination- or transposon-independent translocation mechanism
putative rice-diverged GTs may also be grass-diverged Oryza sativa
UN1 gene pair has Ks values of 0.747±0.082 (Os 03–Os 07), 1.089±0.147 (Sb 01–Sb 02), 0.620±0.073 (Zm 01–Zm 07), 0.596±0.070 (Zm 02–Zm 05) Oryza sativa; Sorghum bicolor; Zea mays
DNA met gene pair has Ks values of 0.595±0.031 (Os 03–Os 07), 0.456±0.026 (Sb 01–Sb 02) Oryza sativa; Sorghum bicolor
vacINVs from both Arabidopsis and tobacco comprise cluster dicot-D Arabidopsis thaliana; Nicotiana tabacum
S-RNases of the Prunoideae and Maloideae form two separate clades Prunoideae; Maloideae
additional intron in Prunus S-RNases is autapomorphy Prunus
rice chromosome 1 (PPO, TOPP2, AT5G59160) (Os01PPO) formed different major clade (group B) Oryza sativa
evolutionary divergence between different organisms causes inability to identify homologues in Arabidopsis
anther-specific invertases of monocotyledenous plants cluster within phylogenic group monocot-A
monocot-A and dicot-A clusters can be clearly distinguished from each other each other
bootstrap analysis with 100 trees was performed with Protdist with Dayhoff's PAM matrix
difference in resolution between cpDNA data and present phylogenetic reconstruction strongly indicates crucial effect of marker employed for phylogenetic analyses Nepenthes
(EFO1, RUP1, AT5G52250) (EFO2, RUP2, AT5G23730) (ATCOP1, COP1, DET340, EMB168, FUS1, AT2G32950) and SPA WD domains may have descended from common ancestor Arabidopsis thaliana; Chlamydomonas reinhardtii
OsCIN3 and TaIVR1 group in cluster monocot-A Oryza sativa; Triticum aestivum
(HCC1, AT3G08950) and (HCC2, AT4G39740) proteins may have resulted from earlier duplication followed by loss of (HCC2, AT4G39740) in mosses plants; Physcomitrella patens
previous molecular study based on chloroplast (TRNA LYS, TRNK, TRNK-UUU, ATCG00030) intron sequence data divided genus Nepenthes into three major evolutionary lineages Nepenthes
amino-acid residues in enzymes encoded by ppc-aL1b and nadpme-IV have indeed changed between common ancestor of Sartidia and Stipagrostis and extant species of Stipagrostis Sartidia; Stipagrostis
phylogenetic analysis revealed two main ppc lineages in flowering plants
SF06B lineage had six amino acid substitutions in the Dof domain Oryza sativa; Sorghum bicolor
incorporation of demographic processes into models of molecular evolution and association genetics approaches has improved statistical power to detect deviations from neutral-equilibrium expectations
collection of structures contains examples of natural selection at atomic resolution
centromeric sequences undergo rapid evolution centromeric sequence composition
epimutEvo clock substitution rate exceeds that of DNA or protein clock substitution rates
Utricularia shares with sister genus Genlisea anomalous molecular evolutionary features Utricularia
VvRopGAP had distinct origin Vitis vinifera
five phenol reaction-negative accessions (types I–V) occupied unique positions separated from three phenol reaction-positive accessions Hordeum vulgare
anthranilate synthase α-subunit (AMT1, ASA1, JDL1, TRP5, WEI2, AT5G05730) nucleotide sequences reveal high degree of sequence homology Oryza sativa; Arabidopsis thaliana; Ruta graveolens; Nicotiana tabacum
Bayesian consensus tree has topology corresponding to bootstrap 50% majority rule consensus tree Nepenthes ventricosa; Nepenthes mirabilis; Nepenthes thorelii; Nepenthes ampullaria; Nepenthes hybrid 'Mizuho'; Nepenthes gracilis; Nepenthes singalana; Nepenthes rafflesiana
average Ks values of maize is 0.487 and 0.548 Zea mays
anther-specific invertases of dicotyledenous plants cluster within phylogenic group dicot-A
Ks values were calculated for Rice 3–Rice 7 (Os 03–Os 07) gene pair Oryza sativa
seven copies of KCH in Arabidopsis thaliana and Oryza sativa have presumably emerged through gene duplication during plant evolution Arabidopsis thaliana; Oryza sativa
AtTPR-like gene (RWD40, AT2G25420) could not establish clear relationship with SlTPL6 Arabidopsis thaliana; Solanum lycopersicum
adaptive changes are detectable in other protein-encoding sequences of Arabidopsis lyrata and Arabidopsis thaliana Arabidopsis lyrata; Arabidopsis thaliana
r60S gene pair has Ks values of 0.357±0.036 (Os 03–Os 07), 0.469±0.047 (Sb 01–Sb 02), 0.466±0.047 (Zm 01–Zm 07), 0.580±0.056 (Zm 02–Zm 05) Oryza sativa; Sorghum bicolor; Zea mays
DgCCD8s are placed in a well-supported clade with petunia (ATCCD8, CCD8, MAX4, AT4G32810) proteins Dendranthema grandiflorum; Petunia hybrida
distantly related isoenzyme (ATSUC2, SUC2, SUT1, AT1G22710) of yeast (Saccharomyces cerevisiae) has low sequence homology with plant antisense invertase and plant invertase inhibitor
cluster dicot-A contains additional cwINVs with other expression profiles
Ks value of the IGL–TSA gene pair in Sb 01–Sb 02 was excluded from analysis Sorghum bicolor
O2 is an old gene
rice cwINVs form one main cluster Oryza sativa
OsCIN4(Ji)_pseudo, OsCIN3 and TaIVR1 group in cluster monocot-A Oryza sativa; Triticum aestivum
I677 and U004 are distantly related Hordeum vulgare
changing environmental conditions caused diversification of function of Fe
protein sequence alignment and phylogenetic analysis resulted in phylogenetic tree divided into group I, group II, group IIIA, group IIIB, group IV (floral/ancestral group) and XTH-precursor EG16 group Arabidopsis thaliana; Brachypodium distachyon; Oryza sativa; Populus trichocarpa; Triticum aestivum
bacterial Paenibacillus macerans licheninase (PmLicheninase) is closest to EG16 members in evolutionary distance Paenibacillus macerans
(AtXTH3, XTH3, AT3G25050) is member of ancestral clade Arabidopsis thaliana
knowledge of genes involved in specialized metabolite production enables investigation of evolution of genes among closely related and divergent plant lineages
UbiA prenyltransferase protein family has undergone convergent evolution during taxon-specific molecular evolution
OsKCH1 clustering into the most expanded branch is together with two other closely related rice KCH family members Oryza sativa
both monocotyledenous and dicotyledenous plants have FEH evolution from cwINVs
changes in donor substrate and/or the acceptor substrate gave remaining forms of fructosyltransferases
coding sequence of truncated invertase OsCIN4(Ji)_pseudo shows close relationship to OsCIN3 and TaIVR1 Oryza sativa
two sorghum PPOs (Sb06PPO1 and Sb06PPO2) are sister to barley and wheat clade Sorghum bicolor; Hordeum vulgare; Triticum aestivum
duplication and divergence of FT-like proteins reveals increased complexity of function in certain taxonomic groups
(HCC1, AT3G08950) and (HCC2, AT4G39740) proteins form separate clusters within plant lineage plants
agronomic-related genes have evolutionary history
different gene pairs differ greatly in divergence rates Oryza sativa; Sorghum bicolor; Zea mays
Phylogenic analysis of plant invertases (β-fructofuranosidases) and related genes was carried out in different species Arabidopsis thaliana; Nicotiana tabacum; Solanum lycopersicum; Solanum tuberosum; Daucus carota; Oryza sativa; Triticum aestivum
remaining cwINVs group in additional clusters dicot-B and -C
gene conversion may have played a role in determining allelic diversity of RNase-based incompatibility systems Rosaceae
alignment of eukaryotic SCO protein sequences was used to construct phylogenetic tree with PHYLIP group of programs
dS and dN values varied greatly between genes Solanum lycopersicum; Solanum pennellii
ADR1s (ACTIVATED DISEASE RESISTANCE 1) demonstrate remarkable conservation
ancient duplication event timing is slightly more than divergence of the rice and sorghum/maize lineages of 50 mya Oryza sativa; Sorghum bicolor; Zea mays
cytoplasmic invertases (cytINVs) cluster was designated cytINVs (monocot+dicot)
further evolution had changes in donor substrate and/or the acceptor substrate
Protdist analysis was followed by Neighbor
ggps(2) and (ATSDX1, VTE1, AT4G32770) displayed lower significance levels Arabidopsis thaliana; Solanum lycopersicum; Solanum pennellii
rates of amino acid substitution in the critical Dof domain region were over twofold higher during 20-million-year period following the WGD Oryza sativa; Sorghum bicolor
same mechanism may be active in LRR exchange to evolve recognition of non-integrated domains Solanum chacoense; Solanum berthaultii; Solanum tarijense; Solanum tuberosum
candidate secreted effector proteins can be highly divergent even among related species
effectors potentially evolve new functions
subsequent positive selection and diversifying evolution allow relaxed selection of duplicated metabolic genes
(AtDRB1, DRB1, HYL1, AT1G09700) homologs in sponges and cnidarians introduce intriguing evolutionary connection between plants and cnidarians
Ks values were calculated for Zm 05–Zm 02 gene pair Zea mays
anther-specific invertases of different species were aligned with related genes coding for fructan-building enzymes (FBEs)
phylogenic analysis of anther-specific cwINV genes aims to provide insights into whether there is co-evolution in different plant species
cluster dicot-A contains no fructan exohydrolases (FEHs)
structure of VTE metabolic pathway could have influenced protein evolution rates Solanum lycopersicum; Solanum pennellii
divergence time between Cucumis metuliferus and Cucumis melo is 17.8 million years ago Cucumis metuliferus; Cucumis melo
DOF family rapidly expanded in vascular plants
Pgl (ATPGIP1, PGIP1, AT5G06860) has phylogenetic position among known PGIPs Pennisetum glaucum
Pgl (ATPGIP1, PGIP1, AT5G06860) was placed among monocot PGIPs Pennisetum glaucum
phylogenetic analysis is consistent with genome alignment data of orthologous sequences
stem lineages leading to Pinguicula are quite comparable to stem lineages leading to Utricularia and Genlisea Pinguicula; Utricularia; Genlisea
phylogenic analysis of anther-specific cwINV genes aims to provide insights into whether cwINVs with anther-specific expression are closely related
Cell wall invertases with anther-specific expression in dicotyl species show a kind of co-evolution
(HEMG2, MEE61, PPO2, AT5G14220) gene showed ambiguous separation of phenol reaction-positive and reaction-negative accessions Hordeum vulgare
phylogenetic tree analysis illustrated that BnHO1 belongs to the (ATHO1, GUN2, HO1, HY1, HY6, TED4, AT2G26670) family Brassica napus
genes of MEP, post-chorismate SK, and tocopherol biosynthesis core pathways displayed values similar to or lower than average dN/dS Solanum lycopersicum; Solanum pennellii
this study will assist in furthering understanding of evolutionary history of small GTPases in legume species Medicago truncatula; Lotus japonicus
Ks values of all gene pairs differ between 0.106 and 1.089 range
IGL-TSA gene pair has Ks values of 0.613±0.069 (Os 03–Os 07) Oryza sativa
cytoplasmic invertases (cytINVs) of Arabidopsis and rice form common cluster Arabidopsis thaliana; Oryza sativa
cluster monocot-A can be clearly distinguished from cluster with the anther-specific cwINVs of dicotyl plants
RNase Phy3 and RNase Phy4 seem to be closer to RNases found in the Rosaceae Petunia hybrida; Rosaceae
BjCET3 and BjCET4 genes strongly indicates that they are functional and evolutionary orthologues with similar protein functions Brassica juncea
most proteins have functional difference often the result of positive selection at only a few sites
rare variants in Arabidopsis lyrata Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) will include deleterious nonsynonymous mutations Arabidopsis lyrata
G variant is ancestral state Brassicaceae
ggps(2) and (ATSDX1, VTE1, AT4G32770) showed a higher proportion of codons evolving under positive selection (~25%) than ggps(4) (0.8%) Arabidopsis thaliana; Solanum lycopersicum; Solanum pennellii
increased efficiency and accessibility of sequencing permits application of advances in molecular evolution theory to detect effects of artificial selection on genes and gene systems
effective number of codons (Nc) was calculated for each gene and species Solanum pennellii; Solanum lycopersicum
three TPS-e/f subfamily members residing at single locus on chromosome 8 may represent orthologous loci Solanum lycopersicum; Solanum pennellii; Solanum habrochaites
CCD family is ancient
(HPD, HPPD, PDS1, AT1G06570) pair a significant Nc bias was observed (ANOVA, P <0.01) codon usage bias Solanum lycopersicum; Solanum pennellii
protein sequences from eukaryotic host are monophyletic
(GEX3, AT5G16020) KA/KS ratio is lower than 1, especially at N-terminus, suggesting evolved under purifying selection Arabidopsis thaliana; Arabidopsis lyrata; Cardamine hirsuta; Capsella rubella
z1 gene pair has Ks values of 0.218±0.035 (Os 03–Os 07) Oryza sativa
enzymes from Cichorium intybus and Triticum aestivum group in clusters dicot-D and monocot-D respectively Cichorium intybus; Triticum aestivum
neighbor-joining tree included proteins belonging to three RNase T2 classes
ppc sequences from algal species Chlamydomonas fragilis are sister to ppc sequences from gymnosperms and angiosperms Chlamydomonas fragilis
(ATIPT9, IPT9, AT5G20040) to which PpIPT1 is orthologue Arabidopsis thaliana; Physcomitrella patens
second branch is absent in Arabidopsis Arabidopsis thaliana
Dsi-1 VOC gene family probably evolved from ancestral eubacteria
QrSUT1 forms group with JrSUT1 from Juglans regia (Juglandaceae) Quercus robur; Juglans regia
SlTPL6 homologues form distinct clade Solanum lycopersicon; Solanum tuberosum; Nicotiana benthamiana; Mimulus guttatus
protein sequences from cyanobiont are monophyletic
absence of orthologue in parasitic nematodes suggests that C. elegans genes might not be conserved or may be rapidly evolving parasitic nematodes; Caenorhabditis elegans
second branch contained SlTPL2, rice (AGD7, ASP1, AT2G37550) protein, and moss or lycophyte TPL-like proteins Solanum lycopersicon; Oryza sativa; Physcomitrella patens; Selaginella moellendorffii
(AtcathB1, AT1G02300) has orthologous genes in Brassicaceae species Arabidopsis thaliana; Arabidopsis lyrata; Capsella rubella; Arabis alpina; Eutrema salsugineum; Brassica rapa
M1a model proposes that a proportion of codons is under purifying selection while the remainder have neutral evolution
two complementary repeat classes in tRNA Leu (UAA) intron have unknown evolutionary origin
genetic material for nodulation was recruited following gene duplication
rice-diverged GTs hypothesized to have significantly different primary sequences compared to dicots Oryza sativa; Arabidopsis thaliana; Populus trichocarpa
anther-specific invertases of different species were aligned with fructan exohydrolases (FEHs)
cwINVs and fructan exohydrolases (FEHs) evolved from each other rather than from different ancestors
OsCIN4 in the present broader phylogenic analysis groups in cluster monocot-C Oryza sativa
N. ampullaria, N. gracilis, N. mirabilis, N. rafflesiana, and N. thorelii were found to be members of same lineage in cpDNA phylogeny Nepenthes ampullaria; Nepenthes gracilis; Nepenthes mirabilis; Nepenthes rafflesiana; Nepenthes thorelii
dN/dS values for different ggps, (TAT, TAT3, AT2G24850) tyra, (APG1, E37, IEP37, VTE3, AT3G63410) and (HPD, HPPD, PDS1, AT1G06570) paralogues varied by 3.5, 2.1, 7.6, 3.4, and 1.9 times respectively Solanum lycopersicum; Solanum pennellii
candidate genes of related pathways: apt, chl, and lycb displayed higher dN/dS values than the mean Solanum lycopersicum; Solanum pennellii
OVULE PECTIN MODIFIER 1 (OPM1) is restricted to the Triticeae tribe Hordeum vulgare
Ka/Ks substitution rate of CsMATE1 is much higher than Ka/Ks of CmMATE1 and ClMATE1 Cucumis sativus; Cucumis melo; Citrullus lanatus
barley and Brachypodium genomes show similar synonymous substitution rates on coding genes compared with rice genome Hordeum vulgare; Brachypodium distachyon; Oryza sativa
Candida parapsilosis acquired PhzF homologs from bacteria via horizontal gene transfer (HGT) Candida parapsilosis
OVULE PECTIN MODIFIER 2 (OPM2) is relatively conserved in cereal crops Hordeum vulgare
non-demographic processes potentially contribute to compositional change
AtTPR3 and (AtTPR2, TPR2, AT1G04130) are closely related to SlTPL3 Arabidopsis thaliana; Solanum lycopersicum
phylogenetic analysis suggested that cotton MATEs were grouped into the same group with other species, including Arabidopsis TT12- and TT12-like MATE transporters Gossypium hirsutum; Arabidopsis thaliana
metazoan sequences are significantly more divergent plant and protozoan FU sequences
clade E includes accessions from groups I, III, and IV Solanum habrochaites
evolutionary pattern among candidate genes and their paralogues was investigated by estimating pairwise synonymous (dS), non-synonymous (dN), and dN/dS divergence Solanum lycopersicum; Solanum pennellii
coding and non-coding sequences in plants evolve faster
variation in compositional heterogeneity highlights the need to investigate signal of biological processes
stc1 gene is evolving particularly fast evolutionary rate Zea mays; Zea teosintes mays ssp. mexicana; Zea luxurians; Zea diploperennis; Tripsacum dactyloides; Coix lacryma-jobi; Sorghum propinquum
sub-functionalization of SHP genes occurred after divergence of the asterids and the rosids
plants and fungi have evolved different transcription factors and cis-regulatory elements for proteasome control
nucleotide sequence of MADS domain of CiFL1 is most similar to Asteraceae ESTs Cichorium intybus var. sativum
older genes have been under stronger purifying selection
average levels of sequence divergence between the two species among different categories of (ATNACK2, NACK2, TES, AT3G43210) were analyzed using shared TE set Brassica rapa; Brassica oleracea
group II RNAs are evolutionary precursors to spliceosomal introns
CAM-specific PEPC isoforms evolved from ancestral non-photosynthetic PEPC isoforms
most abundantly transcribed isoform for C3 species clustered with most abundantly transcribed isoforms for weak- and strong-CAM species
Peace protein clustered with anthocyanin regulators of monocotyledonous plants ZmC1, ZmPl, and OsC1 Prunus persica
numbers of substitutions in Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) are large Arabidopsis lyrata; Arabidopsis thaliana
shift between 1,2 and 1,6 specificities may have occurred more than once during plant evolution
group II intron splicing in plant mitochondria is expected to shed light into functions and mechanisms of spliceosomal descendants within the nucleus Arabidopsis thaliana
equal rates of dN and dS substitutions (ω=1) suggest neutral evolution
bacterial genes encoded by symbiosis or pathogenicity islands have deviating evolutionary rates
SlTPL6 homologue was found in all Asterids Solanum tuberosum; Nicotiana benthamiana; Mimulus guttatus
(AtcathB2, AT1G02305) has orthologous genes in Brassicaceae species Arabidopsis thaliana; Arabidopsis lyrata; Capsella rubella; Arabis alpina; Eutrema salsugineum; Brassica rapa
residue 733 (maize numbering) has posterior probability >0.99 of positive selection positive selection Suaedoideae
branch lengths of six additional IPTs indicating changes in the rate of evolution Physcomitrella patens
(TPL, WSIP1, AT1G15750) from Physcomitrella patens and Selaginella moellendorffii clustered in same branch Physcomitrella patens; Selaginella moellendorffii
evolution of amino acid biosynthesis pathways seems to have expanded by horizontal gene transfer from various cyanobacterial, eukaryotic, and prokaryotic sources
low synonymous divergence in first 500 bp of Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) largely causes Ka > Ks in first 500 bp Arabidopsis thaliana; Arabidopsis lyrata
ARGONAUTE 1 (AGO1, AtAGO1, ICU9, AT1G48410) belongs to same clade as ARGONAUTE 5 (AGO5, AtAGO5, AT2G27880) and ARGONAUTE 10 (AGO10, PNH, ZLL, AT5G43810) Arabidopsis thaliana
PEPC genes have approximately 10% (or approximately 100 residues) invariant across all PEPC genes
Phylogenetic analysis of Pgl (ATPGIP1, PGIP1, AT5G06860) and other monocot and dicot PGIP sequences showed monocot and dicot PGIPs forming separate clusters
ω (omega) for Arabidopsis thaliana Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) lineage is 0.568 ± 0.181 Arabidopsis thaliana
well-defined branches in dendrogram lack plum sequences Prunus spp.
available data, especially the topology and branch lengths of the PpIPT subtree based on alternative (ii) seems to be the most probable evolutionary scenario Physcomitrella patens
low dN values in motif regions compared with flanking regions suggest motifs are ancient sequences conserved over long periods
TEF gene phylogenetic tree includes species from monocots, eudicots, and Saccharomyces cerevisiae Saccharomyces cerevisiae
monocot Orchidaceae ppc sequences are embedded within eudicots ppc1-E1 lineage
AMP-IPT clade is formed entirely by proteins from slime moulds; cyanobacterial and proteobacterial plant symbionts or pathogens
no significant difference between lineages in ratio of replacement to synonymous substitutions is observed Arabidopsis lyrata and Arabidopsis thaliana Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) Arabidopsis lyrata; Arabidopsis thaliana
UDP-glucose 4-epimerase 4 (REB1, RHD1, UGE4, AT1G64440) shares high sequence similarity with UDP-glucose 4-epimerase 2 (ATUGE2, UGE2, AT4G23920) Arabidopsis thaliana
clade D displays highest level of sequence conservation Solanum habrochaites
ppc-1 consensus tree reveals two main lineages in flowering plants
three characterized PEPC genes in Alternthera (Amaranthaceae) were phylogenetically sister to Flaveria PEPC genes Alternthera
Peace protein clustered with (ATMYB123, ATTT2, MYB123, TT2, AT5G35550) Prunus persica
averaging of the degrees of synonymous divergence over a number of genes should reduce inaccuracies in estimating the evolutionary molecular clock
phylogenetic analysis clearly shows that CrDL7H and SLS genes grouped separately from other CYP72 family members Catharanthus roseus; Vinca minor; Rauwolfia serpentina; Tabernaemontana elegans; Amsonia hubrichtii; Cinchona ledgeriana; Lonicera japonica
maturases have ancient relationships to host introns
direct repeats in Vat can mediate evolution
tandem repeats in C-terminal region of (PLDrp1, AT5G39570) points to recent evolutionary events plant kingdom
clade D consists of accessions from group I Solanum habrochaites
sequence divergence within the Solanum habrochaites TPS-e/f family raises questions about evolutionary origins of this diversity Solanum habrochaites
NF5 genes have significantly higher Ka/Ks ratio than NF1 genes Chlamydomonas reinhardtii; Volvox carteri; Physcomitrella patens; Selaginella moellendorffii; Brachypodium distachyon; Oryza sativa; Sorghum bicolor; Zea mays; Arabidopsis thaliana; Carica papaya; Glycine max; Populus trichocarpa; Solanum tuberosum; Vitis vinifera
(NTRC, AT2G41680) gene shows evolutionary success among photosynthetic eukaryotes
gene duplication arises from unequal crossing-over events Arabidopsis thaliana
sequence identities and percentage of Prunus persica sequence length aligned with homologues suggest high degree of conservation of gene products in plants Prunus persica; Arabidopsis thaliana; Oryza sativa
Ms10 35, StbHLH, AtDYT1, and OsUDT1 are within the same clade phylogenetic tree Solanum lycopersicum; Solanum tuberosum; Arabidopsis thaliana; Oryza sativa
ppc lineage composed of Pyrrosia and Isoetes is basal to angiosperm and gymnosperm ppc lineages Pyrrosia; Isoetes
cumulative distinctive features support idea that SlTPL6 has partially lost its ancestral function and may have gained new functionality Solanum lycopersicum
most abundantly transcribed isoform of all Oncidiinae species grouped within ppc1-M1 lineage
seven Physcomitrella IPTs cluster within clade of class I tRNA-IPTs Physcomitrella patens
SlTPL6 has already diverged from other family members by low expression level, high amino acid substitution rate and different subcellular localization Solanum lycopersicum
group of MATE transporters related to proanthocyanidin accumulation is clearly distinct from known anthocyanin MATE transporters, anthoMATE1 (AM1), AM3 from V. vinifera, and MTP77 from Zea mays, as well as a nicotine MATE from tobacco Vitis vinifera; Zea mays; Nicotiana
cystatins in plants cluster in phylogenetic branch distinct from other cystatin families
PPCKA isoform branching reflects photosynthetic type of the species Flaveria pringlei; Flaveria robusta; Flaveria ramosissima; Flaveria trinervia; Flaveria bidentis; Flaveria chloraefolia; Flaveria pubescens; Flaveria anomala; Flaveria brownii
(REM11, VAL, AT5G60140) has been introduced in the further evolved C3-C4 intermediates and the C4 species in two independent evolutionary paths Flaveria trinervia; Flaveria bidentis; Flaveria brownii; Flaveria pubescens; Flaveria anomala
691 genes in Brassica rapa showed significantly lower level of Ka than in Brassica oleracea Brassica rapa; Brassica oleracea
rates of nucleotide substitution of genic sequences shows asymmetry based on different chromatin environments Oryza sativa; Arabidopsis thaliana; Glycine max
tandem repeats in (AT3G29075) and (PLDrp1, AT5G39570) might have originated through gene duplication Arabidopsis thaliana
incongruence among Triticeae gene-trees may reflect introgressive hybridization or incomplete lineage sorting, or the mixing of paralogues with orthologues Triticeae
ω (omega) for Arabidopsis lyrata Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) lineage is slightly higher than ω for Arabidopsis thaliana Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) lineage Arabidopsis lyrata; Arabidopsis thaliana
high divergence in Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) 5′ region found across multiple populations is more consistent with balancing selection Arabidopsis lyrata
two clades of (PGAP1, AT3G27325) homologs divergence can be traced back to ancient whole genome duplication event
molecular clock suggested by Gaut (1998) is based on mean of nine nuclear genes
late role of PLE-like genes in controlling dehiscence may pre-date divergence of rosids and asterids
cluster S is subdivided into clades D and E Solanum habrochaites
ppc1-M1 was composed of ppc sequences from closely related Oncidiinae species
two paralogous eudicot PEPC genes are identified by recent phylogenetic analysis
equal rates of dN and dS substitutions (ω=1) suggest low selective pressure for a specific amino acid at that residue
SlTPL6 is contained in the last clade Solanum lycopersicum
correlation between gene expression level and amino acid substitution rate has already been observed in genome-wide comparisons of expression patterns and protein evolution in Arabidopsis-related plants and in the Poaceae family Arabidopsis thaliana; Poaceae
genes in land, vascular, and seed plant clades tend to shift in the same direction across gene regions
rate shifts are distributed throughout Ericales
(AtUVR8, UVR8, AT5G63860) protein sequence is strongly conserved in plant lineage
amino acid sequences of CTPSs are highly conserved among divergent organisms
Intron 2 in (CLPP1, PCLPP, ATCG00670) was identified in M. endlicherianum Mesotaenium endlicherianum
some slow species (Cucumis sativus, Solanum lycopersicum and Vitis vinifera) have dN/dS ratios more characteristic of accelerated species Cucumis sativus; Solanum lycopersicum; Vitis vinifera
Vacuolar Protein Sorting 26C (VPS26C, AT1G48550) is absent from grasses
beginning of the handle domain of (CLPP1, PCLPP, ATCG00670) appeared to be hot spot for structural variants
(CLPP1, PCLPP, ATCG00670) and the other core plastid Clp subunits had a significant rate correlation plastid- and nuclear-encoded Clp subunits are subject to shared variation in selection pressures
expression patterns of CTEGs are more affected by speciation
estimated date of maize–Tripsacum divergence does not differ much whether using molecular clock based on Ks values for bz, tac7077 and uce2 from Brachypodium and rice Zea mays; Tripsacum; Brachypodium; Oryza
24 of the 38 (RLK, AT5G67280) subfamilies (63%) show association between sequence evolution and expression divergence Arabidopsis thaliana
Trx h class shows monocot species clustering separately in phylogenetic analysis
second main group of MSRBs includes all 1-Cys MSRBs photosynthetic organisms
ages depicted in Figure 5 are relative Arabidopsis thaliana
(AtsesterTPS1, AtTPS18, TPS18, AT3G14520) forms the out group for all sequences Solanum lycopersicum; Solanum habrochaites
631 predicted (PGAP1, AT3G27325) protein homologs from >300 eukaryotic species identified two major phylogenetic clades for plants
FeSUT1 shows high sequence similarities to AmSUT1 and AbSUT1 from Alonsoa meridionalis and Asarina barclaiana Fraxinus excelsior; Alonsoa meridionalis; Asarina barclaiana
low number of dN substitutions relative to dS substitutions (ω<1) indicates purifying selection pressure against changes to the amino acid present
DOF family rapidly expanded in ferns
(AtcathB1, AT1G02300) and (AtcathB2, AT1G02305) are paralogous to AlCathB1 and AlCathB2 Arabidopsis thaliana; Arabidopsis lyrata
lncRNAs may represent conserved genes in eukaryotes undergoing rapid sequence evolution
documented occurrence of gene conversion at SRK gene suggests that nonselective process might similarly drive accumulation of polymorphisms in eSRK Arabidopsis thaliana; Arabidopsis lyrata; Brassica species; Capsella grandiflora
clade E predominantly from group II Solanum habrochaites
non-synonymous substitution (Ka) in triplicates retained in Brassica rapa genome was significantly lower than in Brassica oleracea Brassica rapa; Brassica oleracea
NTRCs from different sources produced phylogenetic tree with major groups of photosynthetic organisms
balancing selection in Medea (EMB173, FIS1, MEA, SDG5, AT1G02580) 5′ promoter region is suggested by high diversity in 5′ promoter region Arabidopsis lyrata
Brassica rapa has significantly higher Ks than Brassica oleracea Brassica rapa; Brassica oleracea
sequence conservation of CysPc–C2L domains in land plant (ATDEK1, DEK1, EMB1275, EMB80, AT1G55350) sub-clade reflects functional conservation
fourth clade includes rose RAG04722 Rosa chinensis; Prunus persica
diverse and previously unexplored lineages of flowering plants facilitate exploration of emergence of EG16s vis-à-vis XTH gene products
Bathycoccus prasinos has lost (CLPP1, PCLPP, ATCG00670) Bathycoccus prasinos
widespread (CLPP1, PCLPP, ATCG00670) pseudogenization and/or gene replacement was not found evidence for accelerated lineages
analysis of (CLPP1, PCLPP, ATCG00670) acceleration has characterized remarkable extent and repeatability of (CLPP1, PCLPP, ATCG00670) acceleration
TALE homeobox heterodimers are found in animals and unicellular relatives such as choanoflagellates
average sequence divergence between common outcrossing species is less than half of divergence between these species and A. thaliana Arabidopsis thaliana; Arabidopsis halleri; Arabidopsis lyrata; Arabidopsis arenosa
Brassica rapa has lower ω than Brassica oleracea Brassica rapa; Brassica oleracea
additional taxa would considerably enhance sensitivity of method to identify positively selected genes
tandem repeats in (PLDrp1, AT5G39570) occur exclusively in members of the Brassicaceae family Brassicaceae
class-1 and class-2 non-symbiotic hemoglobins (Hbs) arose through gene duplication event
AtMRI and MpMRI genes evolved independently for approximately 450–470 million years Arabidopsis thaliana; Marchantia polymorpha
AtPGAP1 (PGAP1, AT3G27325) is classified into different clade from (AT5G17670) Arabidopsis thaliana
GALS homologous proteins were divided into four clades: dicot-I and -II, monocot, and a loose subgroup of other land plants
dN substitution analysis results indicated motif regions less frequently subject to substitution than flanking regions
reduced contribution of the euAG ortholog to the C-function may be restricted to FARINELLI (AmFAR) in the Antirrhinum lineage Antirrhinum majus
long generation time is accompanied by slow molecular clock rate
Vacuolar Protein Sorting 26C (VPS26C, AT1G48550) large retromer subunit shows deep conservation of cellular function across plant and animal kingdoms
Intron 1 in (CLPP1, PCLPP, ATCG00670) is present in Chara vulgaris Chara vulgaris
(CLPP1, PCLPP, ATCG00670) in some lineages contains internal stop codon