A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology.
A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology.
复制标题
DOI：
10.1534/g3.114.015438
复制
发表时间：
2014-12-17
期刊：
影响因子：
--
通讯作者：
Gross JB
中科院分区：
文献类型：
--
作者：
Carlson BM;Onusko SW;Gross JB
墨西哥四足动物 Astyanax mexicanus 是一个独特的模式系统，由适应洞穴的形态类型和地表形态类型组成，在超过 100 万年前（My）发生了分化。这项非凡的自然实验使得对洞穴适应的强大遗传分析成为可能。在这里，我们描述了新一代测序技术在创建高密度连锁图谱中的应用。我们的图谱包含超过 2200 个标记，填充了 25 个连锁群，这些连锁群是根据单个基因分型测序项目生成的基因型数据构建的。我们利用新兴的基因组和转录组资源将数百个匿名 Astyanax 标记锚定到斑马鱼 (Danio rerio) 的基因组上，斑马鱼是与我们研究物种关系最密切的模式生物。这有助于识别我们的连锁图谱和斑马鱼基因组之间的 784 个不同的连接，突出显示两个物种之间保守基因组结构的几个区域，尽管存在约 150 My 的差异。使用孟德尔洞穴相关性状作为原理验证，我们成功恢复了 Oca2 基因附近白化病基因座的基因组位置。此外，我们的图谱成功地告知了特定连锁群内未放置的 Astyanax 基因组支架的位置。这种识别未对齐基因组支架的相对位置、方向和线性顺序的能力将有助于改进当前早期草案并组装 Astyanax 物理基因组的未来版本。此外，这种改进的连锁图谱将实现更高分辨率的遗传分析，并促进洞穴相关表型遗传基础的发现。
The Mexican tetra, Astyanax mexicanus, is a unique model system consisting of cave-adapted and surface-dwelling morphotypes that diverged >1 million years (My) ago. This remarkable natural experiment has enabled powerful genetic analyses of cave adaptation. Here, we describe the application of next-generation sequencing technology to the creation of a high-density linkage map. Our map comprises more than 2200 markers populating 25 linkage groups constructed from genotypic data generated from a single genotyping-by-sequencing project. We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species. This facilitated the identification of 784 distinct connections between our linkage map and the Danio rerio genome, highlighting several regions of conserved genomic architecture between the two species despite ∼150 My of divergence. Using a Mendelian cave-associated trait as a proof-of-principle, we successfully recovered the genomic position of the albinism locus near the gene Oca2. Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups. This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome. Moreover, this improved linkage map will enable higher-resolution genetic analyses and catalyze the discovery of the genetic basis for cave-associated phenotypes.
登录
查看更多内容
影响因子：
3.7
作者：
Gross JB;Furterer A;Carlson BM;Stahl BA
通讯作者：
Stahl BA
影响因子：
3.3
作者：
Gross, Joshua B.;Krutzler, Amanda J.;Carlson, Brian M.
通讯作者：
Carlson, Brian M.
影响因子：
4.4
作者：
Houston RD;Davey JW;Bishop SC;Lowe NR;Mota-Velasco JC;Hamilton A;Guy DR;Tinch AE;Thomson ML;Blaxter ML;Gharbi K;Bron JE;Taggart JB
通讯作者：
Taggart JB
影响因子：
3.1
作者：
Borowsky, R;Wilkens, H
通讯作者：
Wilkens, H
影响因子：
4.4
作者：
Everett MV;Miller MR;Seeb JE
通讯作者：
Seeb JE