Representing sex chromosomes in genome assemblies
Representing sex chromosomes in genome assemblies
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DOI：
10.1016/j.xgen.2022.100132
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发表时间：
2022-05-11
期刊：
影响因子：
--
通讯作者：
Harkess, Alex
中科院分区：
文献类型：
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作者：
Carey, Sarah B.;Lovell, John T.;Harkess, Alex
性染色体在真核生物中已经独立进化了数百次。随着基因组测序、组装和支架技术的迅速改进，现在构建完全定相的性染色体组装是可行的。尽管技术进步使得整个染色体的分阶段组装成为可能，但目前在公开发布基因组时还没有代表性染色体的标准。此外，大多数计算分析工具无法有效地研究其相对于常染色体的独特生物学。我们讨论了性染色体系统的多样性，并考虑了在基因组组装中代表性染色体对的挑战。随着染色体组装全定相技术的成熟，现在通过解决这些问题，我们可以共同确保未来的基因组分析工具包可以广泛应用于具有不同类型性染色体系统的所有真核生物。在这里，我们提供了展示包含性染色体的基因组组装的最佳实践指南。这些指南还可以应用于其他非重组基因组区域，例如植物中的 S 基因座以及真菌和藻类中的交配型基因座。
Sex chromosomes have evolved hundreds of independent times across eukaryotes. As genome sequencing, assembly, and scaffolding techniques rapidly improve, it is now feasible to build fully phased sex chromosome assemblies. Despite technological advances enabling phased assembly of whole chromosomes, there are currently no standards for representing sex chromosomes when publicly releasing a genome. Furthermore, most computational analysis tools are unable to efficiently investigate their unique biology relative to autosomes. We discuss a diversity of sex chromosome systems and consider the challenges of representing sex chromosome pairs in genome assemblies. By addressing these issues now as technologies for full phasing of chromosomal assemblies are maturing, we can collectively ensure that future genome analysis toolkits can be broadly applied to all eukaryotes with diverse types of sex chromosome systems. Here we provide best practice guidelines for presenting a genome assembly that contains sex chromosomes. These guidelines can also be applied to other non-recombining genomic regions, such as S-loci in plants and mating-type loci in fungi and algae.