Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.
Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.
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DOI：
10.1111/j.1755-0998.2009.02750.x
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发表时间：
2010-03
影响因子：
7.7
通讯作者：
Pollock DD
中科院分区：
文献类型：
--
作者：
Castoe TA;Poole AW;Gu W;Jason de Koning AP;Daza JM;Smith EN;Pollock DD
下一代测序与主流研究的最佳整合需要重新评估如何合理地克服问题以及可以提出什么问题。一个潜在的应用是快速获取基因组信息，以确定微卫星基因座的进化，群体遗传和染色体连锁图谱的非模型和以前没有测序的生物体的研究。在这里，我们报告的结果，使用高通量测序，以获得大量的微卫星位点的毒蛇捻转蝮蛇，铜斑蛇。我们使用454 Genome Sequencer FLX下一代测序平台随机抽取了约26.8 Mbp（128，773个读段）的铜头鱼基因组样本，从而抽取了该物种约2%的基因组样本。我们在获得的所有读段的11.3%中鉴定了微卫星位点，总共鉴定了14，612个微卫星位点，其中4，564个具有适合PCR引物设计的侧翼序列。基于随机测序的方法来识别微卫星是快速的，具有成本效益的，并在以前未研究的物种中识别出数千个有用的微卫星位点。
Optimal integration of next-generation sequencing into mainstream research requires reevaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic and chromosome linkage mapping research on non-model and not previously sequenced organisms. Here, we report on results using high-throughput sequencing to obtain a large number of microsatellite loci from the venomous snake Agkistrodon contortrix, the copperhead. We used the 454 Genome Sequencer FLX next-generation sequencing platform to randomly sample approximately 26.8 Mbp (128,773 reads) of the copperhead genome, thus sampling about 2% of the genome of this species. We identified microsatellite loci in 11.3% of all reads obtained, with 14,612 microsatellite loci identified in total, 4,564 of which had flanking sequences suitable for PCR primer design. The random sequencing-based approach to identify microsatellites was rapid, cost-effective, and identified thousands of useful microsatellite loci in a previously unstudied species.
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