Phylogenetic annotation and genomic architecture of opsin genes in Crustacea
Phylogenetic annotation and genomic architecture of opsin genes in Crustacea
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DOI：
10.1007/s10750-018-3678-9
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发表时间：
2018-12-01
期刊：
影响因子：
2.6
通讯作者：
Bracken-Grissom, Heather D.
中科院分区：
文献类型：
--
作者：
Perez-Moreno, Jorge L.;DeLeo, Danielle M.;Bracken-Grissom, Heather D.
进化生物学的一个主要目标是了解适应过程对感觉系统的作用。视觉能力受到环境和生态条件的强烈影响，视觉的进化优势体现在其复杂性和在后生动物中的普遍性。甲壳类动物占据了大量的栖息地和生态位，因此是研究视觉系统进化的理想类群。这里采用比较方法来有效识别和分类视蛋白基因，即参与色觉的光感受色素蛋白，重点关注两种甲壳类模式生物：阿兹特克斑纹藻和水蚤。这两个物种的转录组都是从头组装的，以阐明在强大的系统发育背景下表达的视蛋白的多样性和功能。为此，我们开发了系统发生知情注释工具管道的修改版本，以可扩展且高效的方式从转录组中过滤和识别视觉基因。此外，这些物种的参考基因组用于验证我们的管道，同时表征视蛋白基因的基因组结构。下一代测序和系统发育学为研究模型和非模型生物的感觉系统、适应和进化提供了未来的场所。
A major goal of evolutionary biology is to understand the role of adaptive processes on sensory systems. Visual capabilities are strongly influenced by environmental and ecological conditions, and the evolutionary advantages of vision are manifest by its complexity and ubiquity throughout Metazoa. Crustaceans occupy a vast array of habitats and ecological niches, and are thus ideal taxa to investigate the evolution of visual systems. A comparative approach is taken here for efficient identification and classification of opsin genes, photoreceptive pigment proteins involved in color vision, focusing on two crustacean model organisms:Hyalella azteca and Daphnia pulex. Transcriptomes of both species were assembled de novo to elucidate the diversity and function of expressed opsins within a robust phylogenetic context. For this purpose, we developed a modified version of the Phylogenetically Informed Annotation tool's pipeline to filter and identify visual genes from transcriptomes in a scalable and efficient manner. In addition, reference genomes of these species were used to validate our pipeline while characterizing the genomic architecture of the opsin genes. Next-generation sequencing and phylogenetics provide future venues for the study of sensory systems, adaptation, and evolution in model and nonmodel organisms.