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An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance
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SYSNO ASEP 0476520 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance Tvůrce(i) 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, ORCIDCelkový počet autorů 11 Zdroj.dok. Plant Biotechnology Journal. - : Wiley - ISSN 1467-7644
Roč. 15, č. 8 (2017), s. 1034-1046Poč.str. 13 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova advanced reference assembly ; BioNano ; forage legumes ; gene expression ; Legume comparative genomics ; transcriptome Vědní obor RIV EB - Genetika a molekulární biologie Obor OECD Environmental biotechnology CEP LO1204 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy GBP501/12/G090 GA ČR - Grantová agentura ČR Institucionální podpora UEB-Q - RVO:61389030 UT WOS 000405276200010 EID SCOPUS 85016428732 DOI 10.1111/pbi.12697 Anotace 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. Pracoviště Ústav experimentální botaniky Kontakt David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Rok sběru 2018
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