Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
BMC Genomics. 2022 Apr 27;23(1):328. doi: 10.1186/s12864-022-08432-9.
Sex chromosomes have evolved numerous times, as revealed by recent genomic studies. However, large gaps in our knowledge of sex chromosome diversity across the tree of life remain. Filling these gaps, through the study of novel species, is crucial for improved understanding of why and how sex chromosomes evolve. Characterization of sex chromosomes in already well-studied organisms is also important to avoid misinterpretations of population genomic patterns caused by undetected sex chromosome variation.
Here we present findZX, an automated Snakemake-based computational pipeline for detecting and visualizing sex chromosomes through differences in genome coverage and heterozygosity between any number of males and females. A main feature of the pipeline is the option to perform a genome coordinate liftover to a reference genome of another species. This allows users to inspect sex-linked regions over larger contiguous chromosome regions, while also providing important between-species synteny information. To demonstrate its effectiveness, we applied findZX to publicly available genomic data from species belonging to widely different taxonomic groups (mammals, birds, reptiles, and fish), with sex chromosome systems of different ages, sizes, and levels of differentiation. We also demonstrate that the liftover method is robust over large phylogenetic distances (> 80 million years of evolution).
With findZX we provide an easy-to-use and highly effective tool for identification of sex chromosomes. The pipeline is compatible with both Linux and MacOS systems, and scalable to suit different computational platforms.
最近的基因组研究揭示，性染色体已经进化了很多次。然而，我们对生命之树中性染色体多样性的了解仍然存在很大的差距。通过研究新物种来填补这些空白，对于提高我们对性染色体为什么以及如何进化的理解至关重要。对已经研究得很好的生物体的性染色体进行特征描述，对于避免由于未检测到的性染色体变异而导致的群体基因组模式的误解也是很重要的。
在这里，我们提出了 findZX，这是一个自动化的基于 Snakemake 的计算管道，用于通过任何数量的雄性和雌性之间的基因组覆盖和杂合性差异来检测和可视化性染色体。该管道的一个主要特点是可以选择对另一个物种的参考基因组进行基因组坐标定位。这允许用户在更大的连续染色体区域上检查性连锁区域，同时还提供了重要的种间同线性信息。为了证明其有效性，我们将 findZX 应用于来自属于广泛不同分类群（哺乳动物、鸟类、爬行动物和鱼类）的公开可用的基因组数据，这些物种的性染色体系统具有不同的年龄、大小和分化程度。我们还证明了定位方法在很大的系统发育距离（超过 8000 万年的进化）上是稳健的。
我们使用 findZX 提供了一个易于使用且非常有效的识别性染色体的工具。该管道与 Linux 和 MacOS 系统兼容，并可扩展以适应不同的计算平台。
