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Team Sequences Legume Plant with Eye to Understanding Roots of Rhizobial Symbioses

NEW YORK (GenomeWeb News) – In Nature today, members of a large international consortium reported that they have sequenced a draft genome for the model legume Medicago truncatula, using it to explore the plant's evolutionary history and relationship with symbiotic soil bacteria, or "rhizobia," that reside in its specialized root nodules and help it fix nitrogen.

"Legume symbiosis with rhizobia is the largest source of natural, non-synthetic, nitrogen fertilizer in agriculture," University of Minnesota plant pathology and plant biology researcher Nevin Young, co-first author on the paper, said in a statement. "We sequenced the Medicago genome primarily to learn about its evolution."

The group used a combination of Sanger sequencing and Illumina short-read technology to sequence M. truncatula euchromatin. Based on their analyses of the genome and comparisons with other plants, including soybean and a wild legume, researchers believe that an ancient whole-genome duplication event in a legume ancestor provided the genetic fodder for the genes now involved in root nodulation and interactions with rhizobial bacterial.

And because it is closely related to alfalfa, a cultivated crop plant with a more complicated genome, the study author's explained, "the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox."

In the researchers work, they got Sanger sequences for more than 2,500 bacterial artificial chromosomes that were assembled into eight so-called "pseudomolecules" covering 375 million bases of the genome with nearly 250 million bases of non-redundant sequence.

To fill in gaps in the sequence and regions of the genome that weren't represented in the BAC assembly, the team incorporated Illumina reads, adding another 104 million bases of M. truncatula sequence.

Together, the assembled sequence appears to represent an estimated 94 percent of the plant's genes, including 44,124 gene loci in the pseudomolecules and unassembled BACs and 18,264 more genes in assemblies of Illumina sequence reads.

The researchers also detected tens of thousands of DNA transposons and hundreds of thousands of retroelement-related regions.

When they compared the M. truncatula sequences to those from soybean, Glycine max, or the wild legume Lotus japonicus, the team saw synteny between the genomes, though the M. truncatula sequence contained more extensive rearrangements than that of soybean.

M. truncatula and crop plants such as peas and soybeans belong to a clade known as the papilionoids. In addition to more ancient genome hexaploidization involving the ancestors of other plant lineages, researchers explained, past studies suggested that a whole-genome duplication had occurred in the papilionoid lineage around 58 million years ago.

"Apparently, there have been many more changes, large and small, in M. truncatula than in G. max since the legume [whole-genome duplication]," researchers wrote. "This is borne out by the fact that synteny block in M. truncatula are one-third the length of those remaining in the papilionoid [whole-genome duplication] in G. max."

The team also found evidence for local gene duplications within the M. truncatula genome, along with numerous base substitutions.

From their genome sequence data, combined with RNA sequence information from several plant tissues, meanwhile, the researchers tracked down several paralogous genes that seem to have taken on distinct roles in nodulation, signaling, and interactions with rhizobial bacteria since being duplicated in the papilionoid ancestor.

Among them: the transcription factor gene ERN1, the NFP gene, which codes for a receptor for bacterial signaling molecules known as Nod factors, and the paralogues of ERN1 and NFP.

"Our results indicate that the [whole-genome duplication] early in papilionoid evolution allowed the emergence of critical components in Nod factor signaling and contributed to the complexity of rhizobial nodulation observed in this clade," the team concluded. "As such, the [whole-genome duplication] seems to have had a crucial role in the success of papilionoid legumes, enhancing their utility to humans."

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