SLRfinder:利用连锁不平衡聚类检测候选性连锁区域的方法。

IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Ecology Resources Pub Date : 2024-06-08 DOI:10.1111/1755-0998.13985
Xueling Yi, Petri Kemppainen, Juha Merilä
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引用次数: 0

摘要

尽管性染色体在遗传性别决定中起着至关重要的作用,但在许多非模式生物中,尤其是那些最近才进化出性连锁区(SLR)的生物中,性染色体仍然是未知的。这些进化上年轻且易变的性染色体对了解早期性染色体的进化非常重要,但由于缺乏Y/W退化和SLR仅限于小基因组区域,因此很难识别。在此,我们介绍一种利用连锁不平衡(LD)聚类、杂合度和遗传差异来识别候选 SLR 的方法--SLRfinder。SLRfinder 不依赖于特定的测序方法或特定类型的参考基因组(如来自同源性别)。此外,SLRfinder 的输入不需要表型性别,而表型性别在种群采样中可能是未知的,但性别信息可以被纳入,并且是验证候选 SLR 所必需的。我们使用各种已发布的数据集对 SLRfinder 进行了测试,并将其与本地主成分分析(PCA)方法和基于深度的 "通过覆盖进行性别分配"(SATC)方法进行了比较。不出所料,本地 PCA 方法无法用于识别未知的 SLR。SATC 对保守性染色体的效果更好,而 SLRfinder 在分析易变性染色体时的效果优于 SATC,尤其是当 SLR 存在倒位时。功率分析表明,SLRfinder 在对具有相同 SLR 的更多群体进行取样时效果更好。如果只分析一个群体,则需要相对较大的样本量(约 50 个),才能有足够的统计能力检测出重要的 SLR 候选者,尽管真正的 SLR 可能总是排名靠前的。SLRfinder 为识别 SLR 和揭示自然界中更多的性染色体多样性提供了一种新颖的补充方法。
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SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering

Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.

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来源期刊
Molecular Ecology Resources
Molecular Ecology Resources 生物-进化生物学
CiteScore
15.60
自引率
5.20%
发文量
170
审稿时长
3 months
期刊介绍: Molecular Ecology Resources promotes the creation of comprehensive resources for the scientific community, encompassing computer programs, statistical and molecular advancements, and a diverse array of molecular tools. Serving as a conduit for disseminating these resources, the journal targets a broad audience of researchers in the fields of evolution, ecology, and conservation. Articles in Molecular Ecology Resources are crafted to support investigations tackling significant questions within these disciplines. In addition to original resource articles, Molecular Ecology Resources features Reviews, Opinions, and Comments relevant to the field. The journal also periodically releases Special Issues focusing on resource development within specific areas.
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