Data from: AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae)

Background: Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) have members that are widely distributed in tropical and subtropical freshwater ecosystems and are ecologically and economically important. They 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 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.

Results: Using Illumina Hiseq platforms, we sequenced 1,220 million reads for seven species of apple snails. Together with the RNA-Seq data of two apple snails, we conducted de novo transcriptome assembly of eight species covering five genera of Ampullariidae, including representatives of the Old World and New World lineages. There were 20,730 to 35,828 unigenes with predicted open read frames for the eight species, with N50 (shortest sequence length at 50% of the unigenes) ranging from 1,320 to 1,803 bp. 69.7 % to 80.2 % of these unigenes were functionally annotated by searching against databases of NCBI’s non-redundant, Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes. With these data we developed AmpuBase, a relational database that features online BLAST for DNA/protein sequences, keyword search for unigenes/functional terms, and download functions for sequences and whole transcriptomes.

Conclusions: 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.

背景：腹足纲（Gastropoda）现存约8万种，是软体动物门（Mollusca）中物种最为丰富的纲。在腹足类生物中，瓶螺科（Ampullariidae）的苹果螺类群广泛分布于热带与亚热带淡水生态系统，兼具重要的生态学与经济学价值。它们针对各自栖息环境演化出多样的形态与生理适应特征，使其成为研究适应性演化、种群分化、物种形成以及更大尺度生物多样性模式（包括本土与入侵种群的生物地理学）的理想研究对象。然而，基因组数据的匮乏阻碍了这类非模式生物的深度生态学与进化生物学研究。
结果：本研究依托Illumina Hiseq测序平台，对7种苹果螺进行测序，共获得12.20亿条读段。结合另外2种苹果螺的RNA-Seq数据，我们对覆盖瓶螺科5个属的8个物种开展了从头转录组组装，研究类群涵盖旧世界与新世界的演化支代表类群。8个物种的单基因簇（unigenes）数量介于20730至35828之间，均包含预测的开放阅读框；转录组的N50（即覆盖50%单基因簇的最短序列长度）范围为1320 bp至1803 bp。通过比对NCBI非冗余数据库、基因本体（Gene Ontology）数据库以及京都基因与基因组百科全书（Kyoto Encyclopaedia of Genes and Genomes）数据库，69.7%至80.2%的单基因簇获得了功能注释。基于上述数据，我们构建了AmpuBase关系型数据库，该数据库具备在线BLAST（DNA/蛋白序列比对）、单基因簇/功能术语关键词检索以及序列与全转录组下载功能。
结论：综上，本研究生成了覆盖多个瓶螺科属与物种的高质量转录组数据，并搭建了具备友好交互界面的公开可访问数据库，旨在为未来瓶螺科相关的基础与应用研究，以及与其他无脊椎动物的比较分子生物学研究提供支撑。