First assembly of the gene-space of Lolium multiflorum and comparison to other Poaceae genomes

TY - JOUR

T1 - First assembly of the gene-space of Lolium multiflorum and comparison to other Poaceae genomes

AU - Knorst, Verena

AU - Yates, Steven

AU - Byrne, Stephen

AU - Asp, Torben

AU - Widmer, Franco

AU - Studer, Bruno

AU - Kölliker, Roland

N1 - Publisher Copyright: © 2018 Japanese Society of Grassland Science

PY - 2019/4

Y1 - 2019/4

N2 - Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grasses of temperate regions. It is characterized by a high level of within cultivar diversity, making the fixation of traits in breeding programs difficult. The aim of this study was to develop a functional resource for L. multiflorum that will greatly assist the development of genomics-assisted breeding strategies. The genome of a diploid, heterozygous genotype was sequenced and assembled into 130k scaffolds with a total assembly size of 586 Mb. 61k gene models were annotated and 80.5% of BUSCOs were complete, indicating a good representation of the gene content. Simple sequence repeat (SSR) mining identified 29,840 SSR loci for L. multiflorum, with 4,601 being shared with Lolium perenne L. Proteome comparison with other Poaceae revealed several protein clusters including the SAUR-like auxin-responsive protein family, glutathione S-transferases, BTB-POZ and the photosystem II light harvesting complex gene B1B2 to be enriched in Lolium spp., while 86 clusters were more and 293 less abundant in L. multiflorum than in L. perenne. Here we present the first sequence, assembly and annotation of the gene-space of L. multiflorum, providing a valuable resource for marker identification for breeding programs, genome-wide association studies or evolutionary studies.

AB - Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grasses of temperate regions. It is characterized by a high level of within cultivar diversity, making the fixation of traits in breeding programs difficult. The aim of this study was to develop a functional resource for L. multiflorum that will greatly assist the development of genomics-assisted breeding strategies. The genome of a diploid, heterozygous genotype was sequenced and assembled into 130k scaffolds with a total assembly size of 586 Mb. 61k gene models were annotated and 80.5% of BUSCOs were complete, indicating a good representation of the gene content. Simple sequence repeat (SSR) mining identified 29,840 SSR loci for L. multiflorum, with 4,601 being shared with Lolium perenne L. Proteome comparison with other Poaceae revealed several protein clusters including the SAUR-like auxin-responsive protein family, glutathione S-transferases, BTB-POZ and the photosystem II light harvesting complex gene B1B2 to be enriched in Lolium spp., while 86 clusters were more and 293 less abundant in L. multiflorum than in L. perenne. Here we present the first sequence, assembly and annotation of the gene-space of L. multiflorum, providing a valuable resource for marker identification for breeding programs, genome-wide association studies or evolutionary studies.

KW - gene space

KW - Lolium multiflorum

KW - ryegrasses

UR - http://www.scopus.com/inward/record.url?scp=85057594806&partnerID=8YFLogxK

U2 - 10.1111/grs.12225

DO - 10.1111/grs.12225

M3 - Journal article

AN - SCOPUS:85057594806

SN - 1744-6961

VL - 65

SP - 125

EP - 134

JO - Grassland Science

JF - Grassland Science

IS - 2

ER -