Survey and analysis of microsatellites in the silkworm, Bombyx mori:: Frequency, distribution, mutations, marker potential and their conservation in heterologous species
Survey and analysis of microsatellites in the silkworm, Bombyx mori:: Frequency, distribution, mutations, marker potential and their conservation in heterologous species
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DOI：
10.1534/genetics.104.031005
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发表时间：
2005-01-01
期刊：
影响因子：
3.3
通讯作者：
Nagaraju, J
中科院分区：
文献类型：
--
作者：
Prasad, MD;Muthulakshmi, M;Nagaraju, J
本文研究了家蚕21.76-Mb随机基因组序列、Z染色体0.67-Mb BAC序列和6.3-Mb EST序列中微卫星的频率和分布。我们挖掘了大于或等于15个碱基的单颗粒重复序列和大于或等于5个重复单元的其他类型的重复序列的微卫星。我们估计微卫星占B基因组的0.31%。桑。A，AT和ATT的微卫星束是最丰富的，而它们的数量急剧下降的重复基序的长度增加。一般而言，三核苷酸和六核苷酸重复在转录序列中过度表达，除了TAA、GTA和TGA，它们在基因组序列中过量。Z染色体序列除了富含AT重复序列的丰度更高之外，还含有比其余染色体更短的重复类型。我们的研究结果表明，侧翼序列的碱基组成对微卫星的起源和进化有影响。转换/颠换是高的微卫星的EST，而基因组序列有相同数量的取代和插入缺失。23个多态性微卫星位点在13个家蚕品种中的平均杂合度为0.54，等位基因数为2-14。在198个微卫星位点中，只有36个位点（18.2%）在两个不同的家蚕群体间表现出多态性，10个位点（5%）表现出无效等位基因。利用这些多态性标记构建的微卫星图谱可划分出8个连锁群。B。mori微卫星位点在其直系祖先B中最为保守。其次是野生天蚕，即天蚕。
We studied microsatellite frequency and distribution in 21.76-Mb random genomic sequences, 0.67-Mb BAC sequences from the Z chromosome, and 6.3-Mb EST sequences of Bombyx mori. We mined microsatellites of greater than or equal to 15 bases of mononucleoticle repeats and greater than or equal to5 repeat units of other classes of repeats. We estimated that microsatellites account for 0.31% of the genome of B. mori. Microsatellite tracts of A, AT, and ATT were the most abundant whereas their number drastically decreased as the length of the repeat motif increased. In general, tri- and hexanucleotide repeats were overrepresented in the transcribed sequences except TAA, GTA, and TGA, which were in excess in genomic sequences. The Z chromosome sequences contained shorter repeat types than the rest of the chromosomes in addition to a higher abundance of AT-rich repeats. Our results showed that base composition of the flanking sequence has an influence on the origin and evolution of microsatellites. Transitions/transversions were high in microsatellites of ESTs, whereas the genomic sequence had an equal number of substitutions and indels. The average heterozygosity value for 23 polymorphic microsatellite loci surveyed in 13 diverse silkmoth strains having 2-14 alleles was 0.54. Only 36 (18.2%) of 198 microsatellite loci were polymorphic between the two divergent silkworm populations and 10 (5%) loci revealed null alleles. The microsatellite map generated using these polymorphic markers resulted in 8 linkage groups. B. mori microsatellite loci were the most conserved in its immediate ancestor, B. mandarina, followed by the wild saturniid silkmoth, Antheraea assama.