Centre for Crop Disease and Management, School of Molecular Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
BMC Res Notes. 2021 Aug 28;14(1):334. doi: 10.1186/s13104-021-05751-0.
The assembly of fungal genomes using short-reads is challenged by long repetitive and low GC regions. However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented genome assemblies derived from short reads only. Here, a necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) isolate 134 (Ptr134), which causes tan spot disease on wheat, was sequenced on a MinION using Oxford Nanopore Technologies (ONT), to improve on a previous Illumina short-read genome assembly and provide a more complete genome resource for pan-genomic analyses of Ptr.
The genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%. The long-read assembly provided 6.79 Mb of new sequence and 2846 extra annotated protein coding genes as compared to the previous short-read assembly. This improved genome sequence represents near complete chromosomes, an important resource for large scale and pan genomic comparative analyses.
使用短读长组装真菌基因组时会受到长重复序列和低 GC 区域的挑战。然而，长读长测序技术，如 PacBio 和 Oxford Nanopore，能够克服许多有问题的区域，从而为仅使用短读长组装的不完整基因组提供了改进的机会。在这里，一种坏死型真菌病原体禾谷镰刀菌（Ptr）分离株 134（Ptr134），它会引起小麦上的叶枯病，使用 Oxford Nanopore Technologies（ONT）的 MinION 进行测序，以改进之前的 Illumina 短读长基因组组装，并为 Ptr 的泛基因组分析提供更完整的基因组资源。
使用 ONT 的 MinION 对 Ptr134 进行测序的基因组组装成 28 个连续序列，总长度为 40.79 Mb，GC 含量为 50.81%。与之前的短读长组装相比，长读长组装提供了 6.79 Mb 的新序列和 2846 个额外注释的蛋白质编码基因。这个改进的基因组序列代表了近乎完整的染色体，这是大规模和泛基因组比较分析的重要资源。
