Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.
Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.
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DOI：
10.1093/gbe/evac042
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发表时间：
2022-04-10
影响因子：
3.3
通讯作者：
Andersen, Erik C.
中科院分区：
文献类型：
--
作者：
Stevens, Lewis;Moya, Nicolas D.;Tanny, Robyn E.;Gibson, Sophia B.;Tracey, Alan;Na, Huimin;Chitrakar, Rojin;Dekker, Job;Walhout, Albertha J. M.;Baugh, L. Ryan;Andersen, Erik C.
关键词：
2003 年，Caenorhabditis briggsae 参考基因组的出版首次实现了秀丽隐杆线虫和 C. briggsae 之间的比较基因组学研究，揭示了秀丽隐杆线虫属基因组内容和结构的进化。然而，尽管被广泛使用，目前可用的 C. briggsae 参考基因组在完整性和结构上都远不如秀丽隐杆线虫参考基因组。在这里，我们使用高覆盖率的 Oxford Nanopore 长读长和染色体构象捕获数据来生成两个 C. briggsae 菌株的染色体水平参考基因组：QX1410（一种与实验室 AF16 菌株密切相关的新参考菌株）和 VX34（一种在中国分离的高度分化菌株）。我们还对 QX1410 和 VX34 相互杂交产生的 99 个重组自交系进行了测序，以创建重组图谱并鉴定染色体结构域。此外，我们使用短读长和长读长 RNA 测序数据来生成高质量的基因注释。通过将这些新的参考基因组与当前的参考基因组进行比较，我们发现高度分化的单倍型覆盖了布里格斯假丝酵母基因组的大部分，类似于最近在秀丽隐杆线虫和热带假丝酵母中的报道。我们还表明，自交秀丽隐杆线虫物种的基因组比其异交亲属经历了更多的重排，这使得之前对秀丽隐杆线虫重排率的估计产生了偏差。这些新基因组为秀丽隐杆线虫的比较基因组学提供了一个显着改进的平台，并缩小了秀丽隐杆线虫和布里格斯可用基因组资源质量之间的差距。
The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome-conformation capture data to generate chromosome-level reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.
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DOI：
10.1093/g3journal/jkaa020
发表时间：
2021-01-18
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Gonzalez de la Rosa PM;Thomson M;Trivedi U;Tracey A;Tandonnet S;Blaxter M
通讯作者：
Blaxter M
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
3.3
作者：
Cutter, Asher D.;Wasmuth, James D.;Washington, Nicole L.
通讯作者：
Washington, Nicole L.
影响因子：
7
作者：
Coghlan, A;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
5.8
作者：
Broman, KW;Wu, H;Churchill, GA
通讯作者：
Churchill, GA