Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication.
Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication.
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DOI：
10.1534/genetics.111.127324
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发表时间：
2011-08
期刊：
影响因子：
3.3
通讯作者：
Postlethwait JH
中科院分区：
文献类型：
--
作者：
Amores A;Catchen J;Ferrara A;Fontenot Q;Postlethwait JH
由于组装良好的基因组序列的费用和多代研究的困难，数百种具有进化、农业、经济和医学重要性的物种的基因组资源无法获得。硬骨鱼为人类疾病提供了许多模型，但拥有古老的重复基因组，有时会混淆连接。在硬骨鱼基因组复制（TGD）之前，代表一个鱼类谱系的基因组信息将为探索全基因组复制后的进化机制提供一个外群。我们利用大规模并行DNA测序开发减数分裂图节俭和速度的基因型F1后代的一个单一的女性和一个单一的男性斑点雀鳝（Lepisosteus oculatus）直接从自然界中收集，利用仅存在于这两个野生个体的多态性。使用Stacks软件，该软件可以自动从Illumina测序测定的多态性中识别基因型，我们构建了包含8406个标记的图谱。两个图交叉幼虫的RNA-seq提供了一个参考转录组，确定了近1000个映射的蛋白质编码标记，并允许全基因组分析保守的同线性。结果表明，雀鳝谱系在TGD之前从硬骨鱼类分化出来，其基因组的组织比硬骨鱼类更类似于人类。因此，斑点雀鳝提供了一个重要的联系之间的医学模型在硬骨鱼，雀鳝是生物学上相似，人类，雀鳝是基因组相似。将我们的F1密集作图策略应用于没有先前基因组信息的物种有望促进比较基因组学，并为下一代基因组测序产生的众多重叠群排序提供支架。
Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F1 offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F1 dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing.
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影响因子：
3.4
作者：
Albertson RC;Yan YL;Titus TA;Pisano E;Vacchi M;Yelick PC;Detrich HW 3rd;Postlethwait JH
通讯作者：
Postlethwait JH
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：
4.8
作者：
Katsu, Yoshinao;Kohno, Satomi;Iguchi, Taisen
通讯作者：
Iguchi, Taisen
影响因子：
64.8
作者：
Kasahara, Masahiro;Naruse, Kiyoshi;Kohara, Yuji
通讯作者：
Kohara, Yuji
影响因子：
1.9
作者：
EDWARDS, JH
通讯作者：
EDWARDS, JH