Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.
Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.
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DOI：
10.1093/gbe/evv103
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发表时间：
2015-05-27
影响因子：
3.3
通讯作者：
Janke A
中科院分区：
文献类型：
--
作者：
Bidon T;Schreck N;Hailer F;Nilsson MA;Janke A
男性遗传的Y染色体是哺乳动物基因组的主要单倍体部分，使得Y连锁序列成为进化研究不可或缺的资源。然而，尽管最近的大规模基因组测序方法，只有少数的Y染色体序列已被确定，主要是在模式生物。使用北极熊（Ursus maritimus）基因组，我们比较了两种不同的计算机方法来识别Y连锁序列：1）与已知Y连锁基因的相似性和2）常染色体与性染色体支架的平均读取深度差异。具体来说，我们将来自雄性和雌性北极熊的可用基因组测序短片段与参考基因组进行了映射，并确定了112个Y染色体支架，总长度为1.9 Mb。我们通过雄性特异性体外扩增验证了较长北极熊支架的计算机结果，证明了平均读取深度方法的可靠性。所获得的Y染色体序列包含蛋白质编码序列、单核苷酸多态性、微卫星和可转座元件，这些对进化研究是有用的。北极熊父系的高分辨率同源性显示了两个高度不同的Y染色体谱系，从12个先前发表的雄性北极熊基因组中鉴定的Y支架分析中获得。此外，我们发现ZFX和ZFY序列之间的基因转换的证据在大熊猫谱系和熊和tremarctine熊的祖先。因此，从无序的基因组序列中鉴定Y-连接的支架序列产生了有价值的数据，以推断熊的染色体组和种群基因组模式。
The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears.