Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree.
Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree.
复制标题
DOI：
10.1186/1472-6785-13-8
复制
发表时间：
2013-03-14
期刊：
影响因子：
--
通讯作者：
Rossetto M
中科院分区：
文献类型：
--
作者：
McPherson H;van der Merwe M;Delaney SK;Edwards MA;Henry RJ;McIntosh E;Rymer PD;Milner ML;Siow J;Rossetto M
下一代测序技术具有数据量大、质量高、成本低的特点，有望为单物种和多物种的植物地理学研究提供新的机遇。在这里，我们提出了一种方法，在硅叶绿体DNA组装和单核苷酸多态性检测短读鸟枪测序。该方法简单有效，可以使用标准生物信息学工具实现。在Illumina平台上使用重叠群的从头组装从鸟枪测序组装了159，514个碱基对长的红椿（楝科）的叶绿体基因组。为了评估其实用性，价值和质量，我们比较了短读组装与使用叶绿体DNA分离后获得的454个数据完成的组装。桑格序列验证表明，Illumina数据集优于较长的读取454数据。在鸟枪文库的制备过程中汇集几个个体使得能够检测信息丰富的叶绿体SNP标记。验证后，我们使用所确定的SNP进行了T. ciliata在澳大利亚，并确认整个分布的多样性低。我们的方法提供了一种简单的方法，用于使用短读数据从全基因组DNA的鸟枪测序构建全叶绿体基因组，并且没有可用的密切相关的参考基因组（例如来自相同的物种或属）。Illumina序列数据的高覆盖率也使得该方法适合于多路复用和SNP发现，因此是用于进化生态学的景观水平研究的有用方法。
With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution. Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology.
登录
查看更多内容
影响因子：
5.3
作者：
Bausher MG;Singh ND;Lee SB;Jansen RK;Daniell H
通讯作者：
Daniell H
影响因子：
5.4
作者：
Parks M;Cronn R;Liston A
通讯作者：
Liston A
影响因子：
3
作者：
Cronn, Richard;Knaus, Brian J.;Udall, Joshua
通讯作者：
Udall, Joshua
影响因子：
4.9
作者：
Heuertz, M;Fineschi, S;Vendramin, GG
通讯作者：
Vendramin, GG
影响因子：
4.9
作者：
Morris GP;Grabowski PP;Borevitz JO
通讯作者：
Borevitz JO