Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have be...Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have been Smited to gene screening h a single reference genome,faiing to account for the gene presence/absence variations(gPAVs)in a species.Here,we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups(OGGs).Usng the basic heix-bop-helix(bH_H)transcription factor family in barley as an example,we identified 161-176 bHLHs in 20 barley genomes,which can be classified into 201 OGGs.These 201 OGGs were further dassif jed into 140 core,12 softcore,29 shell,and 20 Ihe-spedfic/cloud bHLHs,reveaing the complete profile of bHLH genes in barley.Using a genome-scanning approach,we overcame the genome annotation bias and identified an average of 15 un-amotated core bHLHs per barley genome We found that whole-genome/segmental duplicates are predominant mechanisms contrixiting to the expansion of most core/softcore bHLHs,whereas dispensable bHLHs are more Ikely to result from small-scale dupication events.Interestingly,we noticed that the dispensable bHLHs tend to be enriched in the specific subfamiSes SF13,SF27,and SF28,rn plying the potentially based expansion of specific bHLHs h barley.We found that 50%of the bHLHs con tan at least 1 intact transposon element(TE)within the 2-kb upstream-to-downstream region.bHLHs with copy-number variations(CWs)have 1.48 TEs on average,sigrif icantiy more than core bhLHs without CNVs(1.36),supporting a potential role ofTEs in bHLH expansion.Analyses of selection pressure showed that dispensablebHLHs have experienced dearrelaxation of selection compared with core bHLHs,consistent with their conservation patterns.We also integrated the pangenome data with recently avaiable barley pantranscrip-tome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH sifofamiies.We conclude that pangenome-based gene-family analyses can better describe the previously untapped,genu'ne evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley.We expect that this study wil inspire similar analyses in many other gene famiies and species.展开更多
基金supported by the Australia Grain Research and Development Corporation(9176507).
文摘Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have been Smited to gene screening h a single reference genome,faiing to account for the gene presence/absence variations(gPAVs)in a species.Here,we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups(OGGs).Usng the basic heix-bop-helix(bH_H)transcription factor family in barley as an example,we identified 161-176 bHLHs in 20 barley genomes,which can be classified into 201 OGGs.These 201 OGGs were further dassif jed into 140 core,12 softcore,29 shell,and 20 Ihe-spedfic/cloud bHLHs,reveaing the complete profile of bHLH genes in barley.Using a genome-scanning approach,we overcame the genome annotation bias and identified an average of 15 un-amotated core bHLHs per barley genome We found that whole-genome/segmental duplicates are predominant mechanisms contrixiting to the expansion of most core/softcore bHLHs,whereas dispensable bHLHs are more Ikely to result from small-scale dupication events.Interestingly,we noticed that the dispensable bHLHs tend to be enriched in the specific subfamiSes SF13,SF27,and SF28,rn plying the potentially based expansion of specific bHLHs h barley.We found that 50%of the bHLHs con tan at least 1 intact transposon element(TE)within the 2-kb upstream-to-downstream region.bHLHs with copy-number variations(CWs)have 1.48 TEs on average,sigrif icantiy more than core bhLHs without CNVs(1.36),supporting a potential role ofTEs in bHLH expansion.Analyses of selection pressure showed that dispensablebHLHs have experienced dearrelaxation of selection compared with core bHLHs,consistent with their conservation patterns.We also integrated the pangenome data with recently avaiable barley pantranscrip-tome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH sifofamiies.We conclude that pangenome-based gene-family analyses can better describe the previously untapped,genu'ne evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley.We expect that this study wil inspire similar analyses in many other gene famiies and species.
