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. 2018 Mar 5;19(1):179.
doi: 10.1186/s12864-018-4553-9.

AmpuBase: A Transcriptome Database for Eight Species of Apple Snails (Gastropoda: Ampullariidae)

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Free PMC article

AmpuBase: A Transcriptome Database for Eight Species of Apple Snails (Gastropoda: Ampullariidae)

Jack C H Ip et al. BMC Genomics. .
Free PMC article

Abstract

Background: 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.

Results: 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.

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.

Keywords: (3 to 10) biological invasion; Asolene; Caenogastropoda; Genomic database; Lanistes; Marisa; Pila; Pomacea; RNA-Seq.

Conflict of interest statement

Ethics approval

Our research adheres to the legislation of the Wild Animals Protection Ordinance of Hong Kong (Cap. 170), the Argentinean provincial Wildlife Hunting Law (Ley 5786, Art. 2) and the Wildlife Preservation and Protection Act (BE 2535) of Thailand. The sampling in Malawi was undertaken under the framework of research cooperation KM/1/1.64 between Ghent University, Belgium and the Karonga Museum, Ministry of Tourism, Wildlife and Culture, Malawi.

Consent for publication

All authors have endorsed the manuscript for publication.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Geographical distribution and phylogeny of apple snails used in the present study. a Rough native distribution ranges of the Old World (Lanistes and Pila) and New World (Asolene, Marisa and Pomacea) genera/species [7, 56]. b A maximum likelihood tree showing the phylogenetic relationship among the eight species of ampullariids based on sequences of three genes used in previous phylogenetic studies of ampullariids [6, 52]. Methodological details for the phylogenetic analysis can be found in Additional file 1. Bootstrap support values are shown, as is a scale bar of 0.05 substitution per site. Photo credit: L. nyassanus, Pila ampullacea and M. cornuarietis (JCHI); A. platae and P. scalaris (SI); P. canaliculata, P. maculata and P. diffusa (HM)
Fig. 2
Fig. 2
The web interface of AmpuBase. a Illustration of the Basic and Advanced BLAST search options. b An example of the search result of a BLAST search, showing matched sequences, each with their BLAST statistics. c Illustration of the search functions in AmpuBase based on annotation

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