Long-read sequence assembly: a technical evaluation in barley

Mascher, M., Wicker, T., Jenkins, J., Plott, Ch., Lux, T., Koh, Ch.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.
PLANT CELL 33: 1888-1906, 2021

Abstract: 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 pangenome 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.
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IEB authors: Hana Šimková, Zuzana Tulpová