HKBU Institute of Research and Continuing Education, Shenzhen, China.
Department of Biology, Hong Kong Baptist University, Hong Kong, China.
BMC Genomics. 2018 Mar 5;19(1):179. doi: 10.1186/s12864-018-4553-9.
Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) are globally distributed in tropical and subtropical freshwater ecosystems and many species are ecologically and economically important. Ampullariids exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying adaptation, population divergence, speciation, and larger-scale patterns of diversity, including the biogeography of native and invasive populations. The limited availability of genomic data, however, hinders in-depth ecological and evolutionary studies of these non-model organisms.
Using Illumina Hiseq platforms, we sequenced 1220 million reads for seven species of apple snails. Together with the previously published RNA-Seq data of two apple snails, we conducted de novo transcriptome assembly of eight species that belong to five genera of Ampullariidae, two of which represent Old World lineages and the other three New World lineages. There were 20,730 to 35,828 unigenes with predicted open reading frames for the eight species, with N50 (shortest sequence length at 50% of the unigenes) ranging from 1320 to 1803 bp. 69.7% to 80.2% of these unigenes were functionally annotated by searching against NCBI's non-redundant, Gene Ontology database and the Kyoto Encyclopaedia of Genes and Genomes. With these data we developed AmpuBase, a relational database that features online BLAST functionality for DNA/protein sequences, keyword searching for unigenes/functional terms, and download functions for sequences and whole transcriptomes.
In summary, we have generated comprehensive transcriptome data for multiple ampullariid genera and species, and created a publicly accessible database with a user-friendly interface to facilitate future basic and applied studies on ampullariids, and comparative molecular studies with other invertebrates.
腹足纲动物约有 8 万种现存物种，是软体动物中最大的一纲。在腹足纲动物中，苹果螺（瓶螺科）分布于全球热带和亚热带淡水生态系统，许多种具有重要的生态和经济意义。瓶螺科表现出各种形态和生理适应，使它们成为研究适应、种群分歧、物种形成以及更大规模多样性模式的理想候选物种，包括本地和入侵种群的生物地理学。然而，基因组数据的有限可用性阻碍了这些非模式生物的深入生态和进化研究。
我们使用 Illumina Hiseq 平台为 7 种苹果螺测序了 1.22 亿条reads。结合之前发表的 2 种苹果螺的 RNA-Seq 数据，我们对属于瓶螺科 5 个属的 8 个种进行了 de novo 转录组组装，其中 2 个代表旧世界谱系，另外 3 个代表新世界谱系。这 8 个种有 20730 到 35828 个具有预测开放阅读框的 unigenes，N50（unigenes 长度的 50%最短序列长度）范围从 1320 到 1803 bp。这些 unigenes中有 69.7%到 80.2%通过对 NCBI 的非冗余、基因本体数据库和京都基因与基因组百科全书进行搜索，具有功能注释。利用这些数据，我们开发了 AmpuBase，这是一个关系型数据库，具有 DNA/蛋白质序列的在线 BLAST 功能、unigenes/功能术语的关键字搜索以及序列和整个转录组的下载功能。
总之，我们为多个瓶螺科属和种生成了综合的转录组数据，并创建了一个具有用户友好界面的公共可访问数据库，以促进未来对瓶螺科的基础和应用研究，以及与其他无脊椎动物的比较分子研究。
