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dc.contributor.author
Ip, Jack C.H.
dc.contributor.author
Mu, Huawei
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Chen, Qian
dc.contributor.author
Jin Sun
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Ituarte, Santiago
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Heras, Horacio
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Van Bocxlaer, Bert
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Ganmanee, Monthon
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Huang, Xin
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Qiu, Jian Wen
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dc.date.available
2020-03-20T20:38:08Z
dc.date.issued
2018-03
dc.identifier.citation
Ip, Jack C.H.; Mu, Huawei; Chen, Qian; Jin Sun; Ituarte, Santiago; et al.; AmpuBase: A transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae); BioMed Central; BMC Genomics; 19; 1; 3-2018; 1-9
dc.identifier.issn
1471-2164
dc.identifier.uri
http://hdl.handle.net/11336/100520
dc.description.abstract
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.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
BioMed Central
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by/2.5/ar/
dc.subject
(3 TO 10) BIOLOGICAL INVASION
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ASOLENE
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CAENOGASTROPODA
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GENOMIC DATABASE
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LANISTES
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MARISA
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PILA
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POMACEA
dc.subject
RNA-SEQ
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Bioquímica y Biología Molecular
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dc.subject.classification
Ciencias Biológicas
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CIENCIAS NATURALES Y EXACTAS
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dc.title
AmpuBase: A transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae)
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2019-10-18T18:58:12Z
dc.journal.volume
19
dc.journal.number
1
dc.journal.pagination
1-9
dc.journal.pais
Reino Unido
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dc.journal.ciudad
Londres
dc.description.fil
Fil: Ip, Jack C.H.. Hong Kong Baptist University; China. Institute of Research and Continuing Education; China
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Fil: Mu, Huawei. Institute of Research and Continuing Education; China
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Fil: Chen, Qian. Hong Kong Baptist University; China
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Fil: Jin Sun. The Hong Kong University of Science and Technology; China
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Fil: Ituarte, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner". Universidad Nacional de la Plata. Facultad de Ciencias Médicas. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner"; Argentina
dc.description.fil
Fil: Heras, Horacio. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner". Universidad Nacional de la Plata. Facultad de Ciencias Médicas. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner"; Argentina
dc.description.fil
Fil: Van Bocxlaer, Bert. Université de Lille; Francia. Ghent University; Bélgica
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Fil: Ganmanee, Monthon. King Mongkut’s Institute of Technology Ladkrabang; Tailandia
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Fil: Huang, Xin. Hong Kong Baptist University; China
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Fil: Qiu, Jian Wen. Institute of Research and Continuing Education; China. Hong Kong Baptist University; China
dc.journal.title
BMC Genomics
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4553-9
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1186/s12864-018-4553-9
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