Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.
Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.
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DOI：
10.1186/1471-2156-7-45
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发表时间：
2006-10-06
期刊：
影响因子：
2.9
通讯作者：
Savolainen P
中科院分区：
文献类型：
--
作者：
Natanaelsson C;Oskarsson MC;Angleby H;Lundeberg J;Kirkness E;Savolainen P
到目前为止，狗的种群遗传学研究主要基于线粒体DNA的分析，只描述了雌性狗的历史。为了了解男性病史，以及第二个独立的标记，需要对双等位基因Y染色体多态性进行研究。然而，没有双等位基因多态性的报道，并且只有3200 bp的非重复的狗Y染色体序列保存在GenBank中，需要鉴定狗Y染色体序列并寻找其中的多态性。一只雄性狗的基因组仅进行了部分测序，因此不允许将序列映射到特定染色体中。然而，通过将雄性基因组序列与完整的雌性狗基因组序列进行比较，可以通过排除来鉴定候选Y染色体序列。通过针对人类基因组的Blast搜索来分析雄性狗基因组序列，以鉴定与人类Y染色体最佳匹配的序列，并鉴定与雌性狗基因组最佳匹配的序列，以鉴定雌性基因组中不存在的序列。然后通过PCR对5只雄性和5只雌性犬测试候选序列的雄性特异性。基于与人Y染色体的匹配、雌性犬基因组中的缺失和雄性特异性PCR结果，来自雄性基因组的32个序列（总长度为24 kbp）被鉴定为雄性特异性。然后对来自欧洲、西南亚、西伯利亚、东亚、非洲和美洲的10只雄性狗的14437 bp进行测序。共发现9个单倍型，由14个替换定义。单倍型之间的遗传距离表明它们至少来自五种狼单倍型。单倍型的地理分布没有明显的趋势。我们已经确定了24159 bp的狗Y染色体序列用于人口遗传学研究。我们在全球范围内收集的狗测序14437 bp，确定14个SNP为未来的SNP分析，并给出了第一个描述的狗Y染色体同源性。
Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and giving a first description of the dog Y-chromosome phylogeny.
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影响因子：
56.9
作者：
Kirkness, EF;Bafna, V;Venter, JC
通讯作者：
Venter, JC
影响因子：
10.7
作者：
Hellborg, L;Ellegren, H
通讯作者：
Ellegren, H
影响因子：
56.9
作者：
Savolainen, P;Zhang, YP;Leitner, T
通讯作者：
Leitner, T
影响因子：
2.4
作者：
Olivier, M;Lust, G
通讯作者：
Lust, G
DOI：
10.1073/pnas.022629899
发表时间：
2002-01-22
影响因子：
11.1
作者：
Kumar, S;Subramanian, S
通讯作者：
Subramanian, S