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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, DOI: 10.1093/plcell/koab077 (2021)
Verlagsversion Forschungsdaten 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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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
ISSN (print) / ISBN 1040-4651
e-ISSN 1532-298X
Zeitschrift The Plant cell
Verlag American Society of Plant Biologists (ASPB)
Begutachtungsstatus Peer reviewed