Comprehensive primer design for analysis of population genetics in non-sequenced organisms.
Comprehensive primer design for analysis of population genetics in non-sequenced organisms.
复制标题
DOI：
10.1371/journal.pone.0032314
复制
发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Makino T
中科院分区：
文献类型：
--
作者：
Tezuka A;Matsushima N;Nemoto Y;Akashi HD;Kawata M;Makino T
核序列标记是研究种群历史和适应的有用工具。然而，对于基因组序列信息很少或没有的生物体来说，获得多个核引物并不容易。在这里，我们使用已完全测序的生物体基因组来设计综合引物组，以扩增未测序生物体中多个核基因的多态性基因组片段。首先，我们鉴定了大量候选多态性区域，这些区域的两侧是参考基因组中的保守区域。然后，我们根据这些保守序列设计了引物，并检查该引物是否可用于扩增目标物种山地褐蛙（Rana ornativentris）、变色龙（Anolis sagrei）、孔雀鱼（Poecilia reticulata）和果蝇（Drosophila melanogaster）的序列，以进行群体遗传分析。我们成功获得了所有研究目标物种的多态性标记。此外，我们发现参考基因组中引物位点之间区域的序列同一性影响DNA扩增和目标基因组中多态位点鉴定的实验成功率，并且外显子引物在扩增可读序列方面比内含子引物具有更高的成功率。我们的结论是，这种比较基因组方法是一种获得非测序生物多态性标记的时间和成本有效的方法，它将有助于非测序生物进化生态学和群体遗传学的进一步发展，有助于理解适应的遗传基础。
Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time- and cost-effective way to obtain polymorphic markers for non-sequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation.
登录
查看更多内容
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
2.3
作者：
Hohenlohe PA;Phillips PC;Cresko WA
通讯作者：
Cresko WA
影响因子：
56.9
作者：
Balanya, Joan;Oller, Josep M.;Serra, Luis
通讯作者：
Serra, Luis
影响因子：
10.1
作者：
Storfer, Andrew;Eastman, Jonathan M.;Spear, Stephen F.
通讯作者：
Spear, Stephen F.
影响因子：
7
作者：
Primmer, CR;Raudsepp, T;Ellegren, H
通讯作者：
Ellegren, H