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

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.

Adapting legume crops to climate change using genomic approaches

“…DNA sequencing technology has made major advances over the last decade, making many of the previous marker‐based systems redundant, and genome sequences are now available for many legume species, including cultivated soybean (Schmutz et al, ), Medicago truncatula (Young et al, ), Lotus japonicus (Sato et al, ), common bean (Schmutz et al, ; Vlasova et al, ), chickpea (Varshney et al, ), pigeonpea (Varshney et al, ), wild soybean (Kim et al, ), narrow‐leafed lupin (Hane et al, ), subterranean clover (Hirakawa et al, ; Kaur, Bayer, et al, ), and diploid ancestors ( Arachis duranensis and Arachis ipaensis ) of cultivated peanut (Bertioli et al, ). The availability of these resources provides an unprecedented opportunity for trait improvement through marker‐assisted evaluation of plant material (e.g., assessment of cultivars and genetic diversity), identification of QTL and gene discovery, marker‐assisted selection, and genomic selection.…”

Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum

“…Despite these limitations, comparative analysis with other legume species (see Fig. 2) suggests that TrSub3 is a considerable improvement over prior efforts to advance subterranean clover assembly using genetic and optical mapping (Hirakawa, Kaur et al 2016;Kaur et al 2017).…”

“…We compared these results with those obtained in a prior study, where we used optical and linkage maps to improve TSUd_r1.1, and to thereby generate large scaffolds for T. subterraneum (Hirakawa, Kaur et al 2016;Kaur et al 2017). (Note that these optical and linkage maps were not employed in the generation of TrSub3.)…”

“…Legumes are of great interest for such efforts: because they produce their own nitrogen via symbiotic nitrogen fixation, legumes can actually improve the soil (Chikowo et al 2004;Saha, and Mandal 2009). Among legumes, pasture legumes tend to be more resilient to stress and more capable of thriving in marginal land (Beuselinck et al 1994;Nichols et al 2013;Hirakawa, Kaur et al 2016).…”

“…Two years ago, we published a draft genome of subterranean clover, Trifolium subterraneum (Hirakawa, Kaur et al 2016). The draft, TSUd_r1.1, was created using a combination of Illumina and Roche 454 GS FLX+ sequencing.…”