Long-read sequence assembly: A technical evaluation in barley

0549408 - ÚEB 2022 RIV US eng J - Journal Article
Mascher, M. - Wicker, T. - Jenkins, J. - Plott, C. - Lux, T. - Koh, C. S. - Ens, J. - Gundlach, H. - Boston, L. B. - Tulpová, Zuzana - Holden, S. - Hernández-Pinzón, I. - Scholz, U. - Mayer, K. F. X. - Spannagl, M. - Pozniak, C. - Sharpe, A. J. - Šimková, Hana - Moscou, M. J. - Grimwood, J. - Schmutz, J. - Stein, N.
Long-read sequence assembly: A technical evaluation in barley.
Plant Cell. Roč. 33, č. 6 (2021), s. 1888-1906. ISSN 1040-4651. E-ISSN 1532-298X
R&D Projects: GA ČR(CZ) GA17-17564S; GA MŠMT(CZ) EF16_019/0000827; GA MŠMT(CZ) LM2015047
Institutional support: RVO:61389030
Keywords : DISEASE RESISTANCE * GENOME * ALIGNMENT
OECD category: Biochemistry and molecular biology
Impact factor: 12.085, year: 2021
Method of publishing: Open access
http://doi.org/10.1093/plcell/koab077

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 five-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.
Permanent Link: http://hdl.handle.net/11104/0325425