The Medicago genome provides insight into the evolution of rhizobial symbioses

Abstract

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation 1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Mya). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species 2. Medicago truncatula (Mt) is a long-established model for the study of legume biology. Here we describe the draft sequence of the Mt euchromatin based on a recently completed BAC-assembly supplemented with Illumina-shotgun sequence, together capturing ~94% of all Mt genes. A whole-genome duplication (WGD) approximately 58 Mya played a major role in shaping the Mt genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the Mt genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max (Gm) and Lotus japonicus (Lj). Mt is a close relative of alfalfa (M. sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the Mt genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

“…(Fig. 1), which is comparable to other sequenced legumes: M. truncatula (30.5%) 13 , pigeonpea (C. cajan, 51.6%) 14 and soybean (59%) 15 . Long-terminal repeat (LTR) retrotransposons are the most abundant transposable element class, and cover >45% of the total nuclear genome ( Fig.…”

“…Reciprocal pair-wise comparisons 20 of the 28,269 chickpea gene models with 230,161 gene models from four sequenced legumes (M. truncatula 13 , L. japonicus 21 , pigeonpea 14 , soybean 15 ) and two nonlegume species (A. thaliana 22 and grape 23 ) identified 15,441 orthologous groups (Supplementary Table 14). On the one hand, 5,940 of these orthologous groups contain only a single chickpea gene, suggestive of simple orthology (Supplementary Table 15 and Supplementary Fig.…”

“…Furthermore, a functional flowering time quantitative trait locus is roughly mapped to the same location on Ca3 as this 54-gene set and breeding-based manipulation of flowering time has been a crucial factor in adapting elite chickpea germplasm to different agro-climatic zones. 13 and L. japonicus 21 ) and three crop legume species (chickpea, soybean 15 and pigeonpea 14 ). The availability of these genome sequences should facilitate de novo assembly of the genomes of other important but less-studied galegoid legume crops such as pea (Pisum sativum), lentil (Lens culinaris) and faba bean (Vicia faba).…”

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

“…We extracted each SNP and its 150 bp flanking sequences in soybean genome, then blasted to the M. truncatula genome sequence 56 with an e value <1e −6 and only kept the best hit with a conservative cut-off value of ≥70% identity and 60 bp coverage (including the SNP). SNPs within orthologous regions were extracted, and genotypes of M. truncatula were used to provide outgroup information at corresponding positions.…”

On plant defense signaling networks and early land plant evolution

“…Additionally, numbers of NBS-LRRs reported in Zhang et al [88] seem to not necessarily be related to genome size. For example Medicago truncatula has “only” a 370 Mbp genome [91], but a similar number of NBS-LRRs as P. abies [88]. Likewise, the monocot Triticum aestivum has a 17 Gbp genome, similar in size to some gymnosperms [92], but has roughly double the number of NBS-LRRs than P. abies [88].…”