An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome.
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome.
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DOI：
10.1093/gigascience/giab096
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发表时间：
2022-02-04
期刊：
影响因子：
9.2
通讯作者：
Rosen BD
中科院分区：
文献类型：
--
作者：
Davenport KM;Bickhart DM;Worley K;Murali SC;Salavati M;Clark EL;Cockett NE;Heaton MP;Smith TPL;Murdoch BM;Rosen BD
家养绵羊（Ovis aries）是一种重要的农业物种，在世界各地饲养的肉，毛和奶。一个高质量的参考基因组，这一物种提高了发现影响生物性状的遗传机制的能力。此外，高质量的参考基因组允许基因调控元件的精确功能注释。基因组组装算法的快速发展和具有越来越长的读段的测序技术的出现为绵羊参考基因组的改进的从头组装提供了机会。短读Illumina（55×覆盖率），长读Pacific Biosciences（75×覆盖率）和从公共数据库中检索的来自该母羊的Hi-C数据与另外50×覆盖率的Oxford Nanopore数据相结合，并与canu v1.9组装。使用Salsa v2.2的Hi-C数据，用PBsuitev15.8.24填充缺口，并用Nanopolish v0.12.5抛光组装的重叠群。用PurgeDups v1.0.1去除重复重叠群后，用2轮流水线对染色体进行定向和抛光，该流水线由freebayes v1.3.1（用于调用变体）、Merfin（用于验证变体）和BCF工具（用于生成共识fasta）组成。ARS-UI_Ramb_v2.0组装体的长度为2.63 Gb，并且具有改进的连续性（重叠群NG 50为43.18 Mb），与Oar_rambouillet_v1.0和Oar_v4.0相比，支架的数量减少了19倍和38倍。ARS-UI_Ramb_v2.0具有更高的每碱基准确性，并且从映射的RNA序列中鉴定的插入和缺失比以前的组装更少。ARS-UI_Ramb_v2.0组装是邻接性的实质性改进，其将优化绵羊基因组的功能注释，并促进绵羊中遗传变体和性状表达数据的改进的作图准确性。
The domestic sheep (Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Furthermore, a high-quality reference genome allows for precise functional annotation of gene regulatory elements. The rapid advances in genome assembly algorithms and emergence of sequencing technologies with increasingly long reads provide the opportunity for an improved de novo assembly of the sheep reference genome. Short-read Illumina (55× coverage), long-read Pacific Biosciences (75× coverage), and Hi-C data from this ewe retrieved from public databases were combined with an additional 50× coverage of Oxford Nanopore data and assembled with canu v1.9. The assembled contigs were scaffolded using Hi-C data with Salsa v2.2, gaps filled with PBsuitev15.8.24, and polished with Nanopolish v0.12.5. After duplicate contig removal with PurgeDups v1.0.1, chromosomes were oriented and polished with 2 rounds of a pipeline that consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly is 2.63 Gb in length and has improved continuity (contig NG50 of 43.18 Mb), with a 19- and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. The ARS-UI_Ramb_v2.0 assembly is a substantial improvement in contiguity that will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits in sheep.