Draft genome sequence of subterranean clover, a reference for genus Trifolium

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Abstract

Clovers (genus Trifolium) are widely cultivated across the world as forage legumes and make a large contribution to livestock feed production and soil improvement. Subterranean clover ( T. subterraneum L.) is well suited for genomic and genetic studies as a reference species in the Trifolium genus, because it is an annual with a simple genome structure (autogamous and diploid), unlike the other economically important perennial forage clovers, red clover ( T. pratense) and white clover ( T. repens). This report represents the first draft genome sequence of subterranean clover. The 471.8 Mb assembled sequence covers 85.4% of the subterranean clover genome and contains 42,706 genes. Eight pseudomolecules of 401.1 Mb in length were constructed, based on a linkage map consisting of 35,341 SNPs. The comparative genomic analysis revealed that different clover chromosomes showed different degrees of conservation with other Papilionoideae species. These results provide a reference for genetic and genomic analyses in the genus Trifolium and new insights into evolutionary divergence in Papilionoideae species.

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Most cited references 7

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Gene Ontology: tool for the unification of biology

Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

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The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

Nevin D Young, Frédéric Debellé, Giles E D Oldroyd … (2011)

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.

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Genome Structure of the Legume, Lotus japonicus

Shusei Sato, Yasukazu Nakamura, Takakazu Kaneko … (2008)

The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes.

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Author and article information

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group

ISSN (Electronic): 2045-2322

Publication date (Electronic): 22 August 2016

Publication date Collection: 2016

Volume: 6

Electronic Location Identifier: 30358

Affiliations

[1 ]Kazusa DNA Research Institute , Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan

[2 ]Centre for Plant Genetics and Breeding, The University of Western Australia , 35 Stirling Highway, Crawley, WA 6009, Australia

[3 ]Department of Agriculture and Food Western Australia , 3 Baron-Hay Court, South Perth, WA 6151, Australia

[4 ]School of Plant Biology, The University of Western Australia , 35 Stirling Highway, Crawley, WA 6009, Australia

[5 ]Murdoch University , 90 South Street, Murdoch, WA 6150, Australia

Author notes

[a ] sisobe@ 123456kazusa.or.jp

[*]

These authors contributed equally to this work.

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Publisher Item ID: srep30358

DOI: 10.1038/srep30358

PMC ID: 4992838

PubMed ID: 27545089

SO-VID: dbd91c28-dc57-4bdd-9b9c-abf28b15b2f0

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Draft genome sequence of subterranean clover, a reference for genus Trifolium

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Genome Integrity

Most cited references 7

Gene Ontology: tool for the unification of biology

The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

Genome Structure of the Legume, Lotus japonicus

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