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Mascher, M.* ; Wicker, T.* ; Jenkins, J.* ; Plott, C.* ; Lux, T. ; Koh, C.S.* ; Ens, J.* ; Gundlach, H. ; Boston, L.B.* ; Tulpová, Z.* ; Holden, S.* ; Hernández-Pinzón, I.* ; Scholz, U.* ; Mayer, K.F.X. ; Spannagl, M. ; Pozniak, C.J.* ; Sharpe, A.G.* ; Šimková, H.* ; Moscou, M.J.* ; Grimwood, J.* ; Schmutz, J.* ; Stein, N.*

Long-read sequence assembly: A technical evaluation in barley.

Plant Cell 33, 1888-1906 (2021)
Publ. Version/Full Text Research data DOI
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even 5-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Disease Resistance; Genome; Alignment; Gene; Length; Rna; Evolution; Reveals; Locus; Wheat
ISSN (print) / ISBN 1040-4651
e-ISSN 1532-298X
Journal The Plant cell
Quellenangaben Volume: 33, Issue: 6, Pages: 1888-1906 Article Number: , Supplement: ,
Publisher American Society of Plant Biologists (ASPB)
Publishing Place Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
Reviewing status Peer reviewed
Grants Canada First Research Excellence Fund through the Designing Crops for Global Food Security initiative at the University of Saskatchewan
Canadian Triticum Applied Genomics - Genome Canada
Czech Science Foundation
ERDF project
Gatsby Charitable Foundation
UKRI-BBSRC
Canadian Triticum Applied Genomics grant - Genome Canada
German Ministry of Education and Research (BMBF)