Academic Journal
Long-read sequence assembly: A technical evaluation in barley.
| العنوان: | Long-read sequence assembly: A technical evaluation in barley. |
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| المؤلفون: | 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. |
| المصدر: | Plant Cell 33, 1888-1906 (2021) |
| بيانات النشر: | Oxford Univ Press Inc |
| سنة النشر: | 2021 |
| المجموعة: | PuSH - Publikationsserver des Helmholtz Zentrums München |
| الوصف: | 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. |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1040-4651 1532-298X |
| Relation: | info:eu-repo/semantics/altIdentifier/pmid/33710295; info:eu-repo/semantics/altIdentifier/wos/WOS:000685239200009; info:eu-repo/semantics/altIdentifier/isbn/1040-4651; info:eu-repo/semantics/alt; https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=61547; urn:isbn:1040-4651; urn:issn:1040-4651; urn:issn:1532-298X |
| DOI: | 10.1093/plcell/koab077 |
| الاتاحة: | https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=61547 https://doi.org/10.1093/plcell/koab077 |
| Rights: | info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.309236BA |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 10404651 1532298X |
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| DOI: | 10.1093/plcell/koab077 |