Efficient identification of Y chromosome sequences in the human and Drosophila genomes.
Efficient identification of Y chromosome sequences in the human and Drosophila genomes.
复制标题
有效鉴定人和果蝇基因组中的Y染色体序列。
DOI：
10.1101/gr.156034.113
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发表时间：
2013-11
期刊：
影响因子：
7
通讯作者：
Clark AG
中科院分区：
文献类型：
--
作者：
Carvalho AB;Clark AG
尽管Y染色体在生物学上很重要，但在大多数物种中仍然知之甚少。他们研究的一个主要障碍是Y染色体序列的鉴定；由于Y染色体序列中含有大量的重复DNA，在大多数基因组计划中，Y染色体序列被分割成大量小的、未映射的支架。在这些片段中识别Y连锁基因对Y染色体的起源和进化产生了重要的见解，但这一过程是劳动密集型的，限制了对少数物种的研究。除了这些零碎的组装，在少数哺乳动物物种中，由于艰苦的BAC作图和测序，Y的常染色质序列基本上是完整的。在这里，我们使用雌性短读测序和k-mer比对来鉴定两个非常不同的基因组中的Y-连锁序列，果蝇和人类。使用这种方法，基本上所有的马尾藻支架都被明确地归类为Y连接的或不Y连接的。我们发现了800个新的支架(总长度为8.5Mbp)，并在D.virilis的Y染色体上发现了4个新基因，其中包括与杂交雄性不育有关的JYpha基因。我们的结果也有力地支持了在果蝇Y的进化中基因获得的优势超过基因丢失的优势。在深入研究的人类基因组中，我们恢复了所有先前已知的基因或基因家族，外加少量(283kb)的新的未完成序列。因此，这种方法适用于大型而复杂的基因组，并可应用于任何有性染色体的物种。
Notwithstanding their biological importance, Y chromosomes remain poorly known in most species. A major obstacle to their study is the identification of Y chromosome sequences; due to its high content of repetitive DNA, in most genome projects, the Y chromosome sequence is fragmented into a large number of small, unmapped scaffolds. Identification of Y-linked genes among these fragments has yielded important insights about the origin and evolution of Y chromosomes, but the process is labor intensive, restricting studies to a small number of species. Apart from these fragmentary assemblies, in a few mammalian species, the euchromatic sequence of the Y is essentially complete, owing to painstaking BAC mapping and sequencing. Here we use female short-read sequencing and k-mer comparison to identify Y-linked sequences in two very different genomes, Drosophila virilis and human. Using this method, essentially all D. virilis scaffolds were unambiguously classified as Y-linked or not Y-linked. We found 800 new scaffolds (totaling 8.5 Mbp), and four new genes in the Y chromosome of D. virilis, including JYalpha, a gene involved in hybrid male sterility. Our results also strongly support the preponderance of gene gains over gene losses in the evolution of the Drosophila Y. In the intensively studied human genome, used here as a positive control, we recovered all previously known genes or gene families, plus a small amount (283 kb) of new, unfinished sequence. Hence, this method works in large and complex genomes and can be applied to any species with sex chromosomes.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
影响因子：
5.8
作者：
Barnett, Derek W.;Garrison, Erik K.;Marth, Gabor T.
通讯作者：
Marth, Gabor T.
影响因子：
4.5
作者：
Baker RH;Wilkinson GS
通讯作者：
Wilkinson GS
影响因子：
56.9
作者：
Hoskins, Roger A.;Carlson, Joseph W.;Celniker, Susan E.
通讯作者：
Celniker, Susan E.
DOI：
10.1098/rstb.2000.0717
发表时间：
2000-11-29
影响因子：
6.3
作者：
Charlesworth, B;Charlesworth, D
通讯作者：
Charlesworth, D