Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.
Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.
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DOI：
10.1371/journal.pone.0030953
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Pollock DD
中科院分区：
文献类型：
--
作者：
Castoe TA;Poole AW;de Koning AP;Jones KL;Tomback DF;Oyler-McCance SJ;Fike JA;Lance SL;Streicher JW;Smith EN;Pollock DD
微卫星或简单重复序列（SSR）的鉴定可能是一项耗时且昂贵的投资，需要对候选基因座进行富集、克隆和测序。然而，最近，高通量测序（有或没有特定的SSR基因座的事先富集）已被用于鉴定SSR基因座。直接“Seq-to-SSR”方法与基于富集的策略相比具有优势，因为它不需要特定基序的先验选择，或基因组SSR内容的先验知识。然而，每个SSR位点的回收成本更高，特别是对于SSR位点很少的基因组，如鸟类基因组。与较便宜的Illumina读数相比，更长但相对更昂贵的454读数更受青睐。在这里，我们使用Illumina配对末端序列数据来识别来自蛇（缅甸蟒蛇，蟒蛇molurus bivittatus）的潜在可重复SSR位点（帕尔斯），并将这些结果与来自454个数据的结果直接进行比较。我们还比较了蟒蛇的结果从Illumina测序的两种鸟类基因组（甘尼森圣松鸡，Centrocercus minimus，克拉克的胡桃夹子，Nucifraga科隆比亚纳），其中有相当少的SSR比蟒蛇的结果。我们表明，直接Illumina Seq-to-SSR可以识别和表征数千个潜在的可重复的SSR位点，每个样品只需10美元-这是454测序成本的一小部分。鉴于Illumina Seq-to-SSR是有效的，廉价的，可靠的，即使是对物种，如鸟类，有很少的SSR位点，似乎现在有几个情况下，优先杂交是合理的。
Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct “Seq-to-SSR” approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
7.7
作者：
Castoe TA;Poole AW;Gu W;Jason de Koning AP;Daza JM;Smith EN;Pollock DD
通讯作者：
Pollock DD
影响因子：
7
作者：
Kelkar, Yogeshwar D.;Tyekucheva, Svitlana;Makova, Kateryna D.
通讯作者：
Makova, Kateryna D.
影响因子：
2.7
作者：
Abdelkrim, Jawad;Robertson, Bruce C.;Gemmell, Neil J.
通讯作者：
Gemmell, Neil J.
DOI：
10.1073/pnas.0606204104
发表时间：
2007-02-20
影响因子：
11.1
作者：
Shedlock, Andrew M.;Botka, Christopher W.;Edward, Scott V.
通讯作者：
Edward, Scott V.