Advances in legume research in the genomics era

Abstract

Next-generation sequencing (NGS) technologies and applications have enabled numerous critical advances in legume biology, from marker discovery to whole-genome sequencing, and will provide many new avenues for legume research in the future. The past 6 years in particular have seen revolutionary advances in legume science because of the use of high-throughput sequencing, including the development of numerous types of markers and data useful for evolutionary studies above and below the species level that have enabled resolution of relationships that were previously unattainable. Such resolution, in turn, affords opportunities for hypothesis testing and inference to improve our understanding of legume biodiversity and the patterns and processes that have created one of the most diverse plant families on earth. In addition, the genomics era has seen significant advances in our understanding of the ecology of legumes, including their role as nitrogen fixers in global ecosystems. The accumulation of genetic and genomic data in the form of sequenced genomes and gene-expression profiles made possible through NGS platforms has also vastly affected plant-breeding and conservation efforts. Here, we summarise the knowledge gains enabled by NGS methods in legume biology from the perspectives of evolution, ecology, and development of genetic and genomic resources.

Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae

“…Numerous WGD events across Fabaceae supported by clusters of GDs WGD or polyploidy has been supported by the analyses of chromosome numbers both in early Fabaceae history and in specific lineages (for a review, see Doyle, 2012). In the past decade, nearly 40 legume genomes have been sequenced (Egan and Vatanparast, 2019) (https://peanutbase.org/data/public/), facilitating the detection of molecular evidence for WGD in Fabaceae using genomic synteny analyses (Cannon et al, 2006;Schmutz et al, 2010;Hane et al, 2017;Wang et al, 2017;Stai et al, 2019;Zhuang et al, 2019) or intragenomic gene cluster analyses (e.g., Egan and Doyle, 2010). In addition, phylotranscriptomics or comparative genomics has been used for the phylogenetic detection of GD clusters in the ancestors of Fabaceae and several subfamilies (Cannon et al, 2015;Leebens-Mack et al, 2019;Stai et al, 2019;Koenen et al, 2020b), as performed previously for other plant groups (e.g., Jiao et al, 2011;Huang et al, 2016b;Ren et al, 2018;Zhang et al, 2020c).…”

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

“…Capture of additional, less conserved target regions across the legume family could be achieved by designing multiple probes for hybridization in the same target region in different legume groups, as applied for studies across angiosperms (Johnson et al, 2019 ). Such a probe design could profit from existing legume probe sets but should rely on a stringent selection of targets that accounts for paralogues (Vatanparast et al, 2018 ), which originated as a consequence of multiple whole‐genome duplication events in legumes (Egan & Vatanparast, 2019 ; Koenen et al, 2021 ).…”

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergiaspp.) and the legume family (Fabaceae)

“…Capture of additional, less conserved target regions across the legume family could be achieved by designing multiple probes for hybridization in the same target region in different legume groups, as applied for studies across angiosperms (Johnson et al, 2019). Such a probe design could profit from existing legume probe sets but should rely on a stringent selection of targets that accounts for paralogs (Vatanparast et al, 2018), which originated as a consequence of multiple whole-genome duplication events in legumes (Egan & Vatanparast, 2019;Koenen et al, 2021).…”