Abundance and Characterization of Perfect Microsatellites on the Cattle Y Chromosome.
Abundance and Characterization of Perfect Microsatellites on the Cattle Y Chromosome.
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牛 Y 染色体上完美微卫星的丰度和表征。
DOI：
10.1080/10495398.2016.1243551
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
Ma Zhi-Jie
中科院分区：
文献类型：
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作者：
Ma Zhi-Jie
微卫星或简单重复序列（SSR）存在于大多数生物中，在基因组的组织和功能中起着重要作用。为了表征牛Y染色体上SSR（1-6个碱基对[bp]）的丰度，基于已发表的Y染色体序列检查了完整或不间断SSR的相对频率和密度。共发现17，273个完整的SSR，总长度为324.78 kb，表明约0.75%的牛Y染色体序列（43.30 Mb）包含完整的SSR，平均长度为18.80 bp。相对频率和相对密度分别为398.92位点/Mb和7500.62 bp/Mb。牛Y染色体上六类完全SSR的比例变化很大。单核苷酸重复序列的总重复数为8073个（46.74%），平均长度为15.45 bp，是最丰富的SSR类型，而二、四、三、五和六核苷酸重复序列的百分比分别为22.86%、11.98%、11.58%、6.65%和0.19%。不同类别的SSR重复数不同，最高的是42个二核苷酸。结果表明，重复类别A，AC，AT，AAC，AGC，GTTT，CTTT，ATTT和AACTG占主导地位的Y染色体上。这项研究提供了深入了解牛Y染色体重复DNA的组织，以及开发更多的多态性牛Y染色体特异性SSR的有用信息。
Microsatellites or simple sequence repeats (SSRs) are found in most organisms and play an important role in genomic organization and function. To characterize the abundance of SSRs (1-6 base-pairs [bp]) on the cattle Y chromsome, the relative frequency and density of perfect or uninterrupted SSRs based on the published Y chromosome sequence were examined. A total of 17,273 perfect SSRs were found, with total length of 324.78 kb, indicating that approximately 0.75% of the cattle Y chromosome sequence (43.30 Mb) comprises perfect SSRs, with an average length of 18.80 bp. The relative frequency and density were 398.92 loci/Mb and 7500.62 bp/Mb, respectively. The proportions of the six classes of perfect SSRs were highly variable on the cattle Y chromosome. Mononucleotide repeats had a total number of 8073 (46.74%) and an average length of 15.45 bp, and were the most abundant SSRs class, while the percentages of di-, tetra-, tri-, penta-, and hexa-nucleotide repeats were 22.86%, 11.98%, 11.58%, 6.65%, and 0.19%, respectively. Different classes of SSRs varied in their repeat number, with the highest being 42 for dinucleotides. Results reveal that repeat categories A, AC, AT, AAC, AGC, GTTT, CTTT, ATTT, and AACTG predominate on the Y chromosome. This study provides insight into the organization of cattle Y chromosome repetitive DNA, as well as information useful for developing more polymorphic cattle Y-chromosome-specific SSRs.