Carlson David E, Hedin Marshal
Department of Biology, San Diego State University, San Diego, California, United States of America.
Department of Ecology & Evolution, Stony Brook University, Stony Brook, New York, United States of America.
PLoS One. 2017 Apr 5;12(4):e0174102. doi: 10.1371/journal.pone.0174102. eCollection 2017.
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.
新一代测序技术正在迅速改变进化生物学的格局，并已成为一种为非模式生物收集外显子组信息的经济高效手段。由于蜘蛛具有分类多样性、能产生有趣的毒液和丝蛋白，且现有基因组资源相对稀缺，蜘蛛尤其适合作为新一代测序（NGS）方法的研究对象。在本研究中，对来自三个属（特拉维斯卷叶蛛、维博拉卷叶蛛、纹背猛蛛、焦背猛蛛、毕氏褛网蛛和库珀褛网蛛）的六种新蛛亚目蜘蛛的转录组进行了测序和从头组装。对每个组装结果进行质量和完整性评估，并使用基因本体信息进行功能注释。发现了大约100个与毒液蛋白具有同源性证据的转录本。在确定了所有六个分类单元中3000多个假定的直系同源基因后，我们通过比较分析确定了24个正选择基因实例。此外，在每个属中发现了约550至1100个独特的孤儿基因。这些独特的、未表征的基因表现出较高的氨基酸替代率，这可能与谱系特异性适应性进化一致。本研究产生的数据是未来系统发育和分子进化研究的宝贵资源，我们的结果为驱动跨越新蛛亚目蜘蛛系统发育根源的分类单元基因组进化的力量提供了新的见解。
