Genome-wide identification and in silico gene expression analysis of the related to ABI3/VP1(RAV)transcription factor family in barley(Hordeum vulgare L.)

RAV(Related to ABI3/VP1)transcription factors are unique members of the AP2-ERF superfamily with AP2 and B3 domains and play important roles in the regulation of seed germination,plant growth,and stress response.In the study,7 RAV genes,named HvRAVs,were identified in barley based on the available genome sequences.While five of the seven HvRAVs were located on chromosome 3,HvRAV5 and HvRAV7 were located on chromosome 1 and 4,respectively.Six of the predicted HvRAVs were intron-less,except HvRAV2,which had one intron.HvRAV proteins have shown basic,instable,and hydrophilic properties.The AP2 domain specific RAYD and WLG motifs were detected in all HvRAV proteins.Besides,B3 repression domain,R/KLFGV,is also found in the C-terminal of HvRAVs.HvRAVs were found to have stress-related cis-acting elements,including MYB,MYC,and W-BOX.HvRAV2 was predicted to have no GARE motifs,TATCCCA or TAACAA(G/A),and LTREs.Under drought conditions,the expression level of HvRAVs did not significantly change in a drought-sensitive barley genotype,whereas HvRAV5 and HvRAV7 were dramatically down-regulated in a drought-tolerant genotype.Expression of HvRAV5 was also inhibited by salinity.HvRAV7 was strongly induced by plant pathogen attack.Only HvRAV6 was induced by exogenous gibberellin application and during the germination process.Interestingly,HvRAV6 transcript was detected higher than other HvRAVs in all stress and control conditions as well as during germination.In silico analyses have shown that HvRAVs play a role in response to different abiotic and biotic stresses as well as in plant development.However,the extensive biological roles of HvRAV genes in plant development and in response to abiotic and biotic stresses need further investigation.

Convergent evolution of AP2/ERF Ⅲ and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes

Whole-genome duplication(WGD or polyploidization)has been suggested as a genetic contributor to angiosperm adaptation to environmental changes.However,many eudicot lineages did not undergo recent WGD(R-WGD)around and/or after the Cretaceous-Paleogene(K-Pg)boundary,times of severe environmental changes;how those plants survived has been largely ignored.Here,we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD:12 R-WGD-containing plants(R-WGD-Y)and 10 R-WGD-lacking plants(R-WGD-N).Subsequently,we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold stimulation.The evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF Ⅲ and IX subfamilies through recurrent independent WGDs and tandem duplications(TDs)after the radiation of the plants.The expansions showed coincident enrichments in-times around and/or after the K-Pg boundary,when global cooling was a major environmental stressor.Consequently,convergent expansions and co-retentions of AP2/ERF Ⅲ C-repeat binding factor(CBF)duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory networks.Moreover,promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code(G-box:CACGTG).We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF Ⅲ and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes,and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD.