Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Abstract

BackgroundLegumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes.ResultsWe report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools.ConclusionsThe genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0883-6) contains supplementary material, which is available to authorized users.

The Class II Trehalose 6-phosphate Synthase Gene PvTPS9 Modulates Trehalose Metabolism in Phaseolus vulgaris Nodules

“…These paralogs have been proposed to be the result of a recent whole-genome duplication event (Figure 1A). By contrast, other genes, like PvTPS9 or PvTPS7 , are grouped in clades formed by monocot or dicot species (Figure 1A), suggesting their presence in a common ancestor (Avonce et al, 2010; Vandesteene et al, 2012; Schmutz et al, 2014; Vlasova et al, 2016). …”

Alternative markers linked to the Phg-2 angular leaf spot resistance locus in common bean using the Phaseolus genes marker database

“…A crucial element in the identification of such marker is information on the genetic relationships between parents, which help determine the frequency of polymorphic markers that can be utilized for MAS. In common bean, the well-established divergence between the Andean and Mesoamerican gene pools predicates a preference for Andean x Mesoamerican crosses to maximize polymorphisms at the molecular level (Kwak and Gepts, 2009;Vlasova et al, 2016). However, most crosses in bean breeding often involve parents from the same gene pool or even closely related parents to increase progress from selection and avoid hybrid weakness (Beaver and Osorno, 2009), thereby limiting the potential for polymorphism.…”

“…P. vulgaris reference genomes, based on the Andean landrace G19833 (Chaucha Chuga, Peru), the Mesoamerican breeding line BAT93, and the Mesoamerican variety OAC Rex, introgressed with P. acutifolius, have been released recently (Schmutz et al, 2014;Vlasova et al 2016; http://www.beangenomics.ca/). These resources offer a means (in conjunction with the PhaseolusGenes database and linkage mapping of phenotypic traits by genetic and QTL analyses) to develop new markers for use in MAS and map-based gene isolation.…”

“…It originated from two geographically separate domestications, from an already diverged wild ancestor (Gepts et al, 1986). Numerous molecular investigations have confirmed the existence of two geographically diverged gene pools: Andean and Mesoamerican, most recently based on SSR data (Kwak and Gepts, 2009;Okii et al, 2014), SNP data (Cortés et al, 2011;Ariani et al, 2016), and DNA sequences (Schmutz et al, 2014;Vlasova et al, 2016;Rendón-Anaya et al, 2017). A consequence of this diversity organization is that genetic distances within each of the two gene pools are considerably smaller than between gene pools.…”

“…(Morrell et al, 2012). In common bean, two whole genome sequences are available, corresponding to the Andean (accession G19833; Schmutz et al 2014) and Mesoamerican (accession BAT93; Vlasova et al, 2016) gene pools. The Andean whole-genome sequence has been used as the current backbone for a "bean breeder" toolbox", that is, a marker database -Phaseolus Genes (http://phaseolusgenes.bioinformatics.ucdavis.edu), which combines information from both legacy molecular markers and more recent markers resulting from genomic analysis of the common bean genome.…”