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An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance

SYSNO ASEP	0476520
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance
Author(s)	Kaur, P. (AU) Bayer, P.E. (AU) Milec, Zbyněk (UEB-Q)_{RID, ORCID} Vrána, Jan (UEB-Q)_{RID, ORCID} Yuan, Y. (AU) Appels, R. (AU) Edwards, D. (AU) Batley, J. (AU) Nichols, P. (AU) Erskine, W. (AU) Doležel, Jaroslav (UEB-Q)_{RID, ORCID}
Number of authors	11
Source Title	Plant Biotechnology Journal. - : Wiley - ISSN 1467-7644 Roč. 15, č. 8 (2017), s. 1034-1046
Number of pages	13 s.
Language	eng - English
Country	US - United States
Keywords	advanced reference assembly ; BioNano ; forage legumes ; gene expression ; Legume comparative genomics ; transcriptome
Subject RIV	EB - Genetics ; Molecular Biology
OECD category	Environmental biotechnology
R&D Projects	LO1204 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	GBP501/12/G090 GA ČR - Czech Science Foundation (CSF)
Institutional support	UEB-Q - RVO:61389030
UT WOS	000405276200010
EID SCOPUS	85016428732
DOI	10.1111/pbi.12697
Annotation	Subterranean clover is an important annual forage legume, whose diploidy and inbreeding nature make it an ideal model for genomic analysis in Trifolium. We reported a draft genome assembly of the subterranean clover TSUd_r1.1. Here we evaluate genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano-based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. Multiple contigs (264) from the draft assembly coalesced into 97 super-scaffolds (43% of genome). Sequences longer than > 1 Mb increased from 40 to 189 Mb giving 1.4-fold increase in N50 with total genome in pseudomolecules improved from 73 to 80%. The advanced assembly was re-annotated using transcriptome atlas data to contain 31 272 protein-coding genes capturing > 96% of the gene content. Functional characterization and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24 893 Trifolium-specific and 6325 subterranean-clover-specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro-morphological traits, were fine-mapped on the high-density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker-assisted breeding, comparative mapping and identification of tissue-specific gene promoters for biotechnological improvement of forage legumes.
Workplace	Institute of Experimental Botany
Contact	David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469
Year of Publishing	2018

Number of the records: 1