Institute of Neuroscience. University of Oregon, Eugene, Oregon 97403, USA.
Genetics. 2011 Aug;188(4):799-808. doi: 10.1534/genetics.111.127324.
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 F(1) 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 F(1) 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.
由于完整基因组序列的费用高昂以及多世代研究的困难，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仍然无法获得。硬骨鱼为人类疾病提供了许多模型，但它们拥有古老的重复基因组，这有时会混淆连通性。代表在硬骨鱼基因组加倍（TGD）之前分化的鱼类谱系的基因组信息将为探索全基因组加倍后进化机制提供一个外群。我们利用大规模平行 DNA 测序技术，通过对直接从自然界中收集的一雌一雄斑点叉尾鮰（Lepisosteus oculatus）的 F1 后代进行基因分型，以节俭和快速的方式开发了减数分裂图谱，仅利用这两个野生个体中存在的多态性。我们使用 Stacks 软件（一种自动从 Illumina 测序检测到的多态性中调用基因型的软件）构建了一个包含 8406 个标记的图谱。对两个图谱交叉幼虫进行 RNA-seq 提供了一个参考转录组，鉴定了近 1000 个映射的蛋白质编码标记，并允许对保守同线性进行全基因组分析。结果表明，鮰鱼谱系在 TGD 之前与硬骨鱼分离，其基因组组织与人类更相似，而与硬骨鱼不同。因此，斑点叉尾鮰为硬骨鱼中的医学模型（与鮰鱼在生物学上相似）和人类（与鮰鱼在基因组上相似）之间提供了一个关键联系。将我们的 F1 密集图谱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连续体提供排序支架。
