{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T14:26:34Z","timestamp":1758810394808,"version":"3.37.3"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,11,27]],"date-time":"2017-11-27T00:00:00Z","timestamp":1511740800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"DOI":"10.1093\/gigascience\/gix114","type":"journal-article","created":{"date-parts":[[2017,11,26]],"date-time":"2017-11-26T22:16:15Z","timestamp":1511734575000},"source":"Crossref","is-referenced-by-count":21,"title":["Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1650-0064","authenticated-orcid":false,"given":"Mark F","family":"Richardson","sequence":"first","affiliation":[{"name":"Deakin University, Bioinformatics Core Research Group, 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia"},{"name":"Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0740-7981","authenticated-orcid":false,"given":"Fernando","family":"Sequeira","sequence":"additional","affiliation":[{"name":"CIBIO-InBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, Campus Agr\u00e1rio de Vair\u00e3o, Universidade do Porto, 4485-661, Vair\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4780-1564","authenticated-orcid":false,"given":"Daniel","family":"Selechnik","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9882-7775","authenticated-orcid":false,"given":"Miguel","family":"Carneiro","sequence":"additional","affiliation":[{"name":"CIBIO-InBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, Campus Agr\u00e1rio de Vair\u00e3o, Universidade do Porto, 4485-661, Vair\u00e3o, Portugal"},{"name":"Departamento de Biologia, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre s\/n., 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3465-3830","authenticated-orcid":false,"given":"Marcelo","family":"Vallinoto","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Evolu\u00e7\u00e3o (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Par\u00e1, Campus de Bragan\u00e7a, Par\u00e1, Brasil"}]},{"given":"Jack G","family":"Reid","sequence":"additional","affiliation":[{"name":"Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5692-0899","authenticated-orcid":false,"given":"Andrea J","family":"West","sequence":"additional","affiliation":[{"name":"Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia"}]},{"given":"Michael R","family":"Crossland","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7529-5657","authenticated-orcid":false,"given":"Richard","family":"Shine","sequence":"additional","affiliation":[{"name":"School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3279-7005","authenticated-orcid":false,"given":"Lee A","family":"Rollins","sequence":"additional","affiliation":[{"name":"Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia"}]}],"member":"286","published-online":{"date-parts":[[2017,11,27]]},"reference":[{"key":"key\n\t\t\t\t20180415221407_bib1","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1023\/A:1016072014259","article-title":"Transposable elements and the evolution of genome size in eukaryotes","volume":"115","author":"Kidwell","year":"2002","journal-title":"Genetica"},{"key":"key\n\t\t\t\t20180415221407_bib2","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nrg3117","article-title":"Repetitive DNA and next-generation sequencing: computational challenges and solutions","volume":"13","author":"Treangen","year":"2011","journal-title":"Nat Rev Genet"},{"article-title":"Animal Genome Size Database","year":"2015.","author":"Gregory","key":"key\n\t\t\t\t20180415221407_bib3"},{"key":"key\n\t\t\t\t20180415221407_bib4","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1126\/science.1183670","article-title":"The genome of the Western Clawed frog Xenopus tropicalis","volume":"328","author":"Hellsten","year":"2010","journal-title":"Science"},{"key":"key\n\t\t\t\t20180415221407_bib5","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/nature19840","article-title":"Genome evolution in the allotetraploid frog Xenopus laevis","volume":"538","author":"Session","year":"2016","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180415221407_bib6","doi-asserted-by":"crossref","first-page":"E1257","DOI":"10.1073\/pnas.1501764112","article-title":"Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes","volume":"112","author":"Sun","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"key\n\t\t\t\t20180415221407_bib7","doi-asserted-by":"crossref","first-page":"e0156419","DOI":"10.1371\/journal.pone.0156419","article-title":"A single transcriptome of a green toad (Bufo viridis) yields candidate genes for sex determination and -differentiation and non-anonymous population genetic markers","volume":"11","author":"Gerchen","year":"2016","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180415221407_bib8","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4020-8946-6","volume-title":"Alien Reptiles and Amphibians: A Scientific Compendium and Analysis","author":"Kraus","year":"2009"},{"key":"key\n\t\t\t\t20180415221407_bib9","doi-asserted-by":"crossref","first-page":"2264","DOI":"10.1111\/mec.13184","article-title":"A genetic perspective on rapid evolution in cane toads (Rhinella marina)","volume":"24","author":"Rollins","year":"2015","journal-title":"Mol Ecol"},{"key":"key\n\t\t\t\t20180415221407_bib10","first-page":"183","article-title":"A simplified table for staging anuran embryos and larvae with notes on identification","volume":"16","author":"Gosner","year":"1960","journal-title":"Herpetologica"},{"key":"key\n\t\t\t\t20180415221407_bib11","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1111\/1755-0998.12340","article-title":"Genomic resources notes accepted 1 August 2014-30 September 2014","volume":"15","author":"Arthofer","year":"2015","journal-title":"Mol Ecol Resour"},{"key":"key\n\t\t\t\t20180415221407_bib12","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180415221407_bib13","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20180415221407_bib14","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1093\/bioinformatics\/btu077","article-title":"SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads","volume":"30","author":"Xie","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180415221407_bib15","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20180415221407_bib16","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1093\/bioinformatics\/bts094","article-title":"Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels","volume":"28","author":"Schulz","year":"2012","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180415221407_bib17","article-title":"Accurate and complete gene construction with EvidentialGene","volume":"5","author":"Gilbert","year":"2016","journal-title":"F1000Res"},{"key":"key\n\t\t\t\t20180415221407_bib18","article-title":"Transvestigator early release, Version v0.1-alpha","author":"DeRego","year":"2014","journal-title":"Zenodo"},{"key":"key\n\t\t\t\t20180415221407_bib19","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180415221407_bib20","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database","volume":"42","author":"Finn","year":"2014","journal-title":"Nucl Acids Res"},{"key":"key\n\t\t\t\t20180415221407_bib21","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20180415221407_bib22","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/nmeth.1701","article-title":"SignalP 4.0: discriminating signal peptides from transmembrane regions","volume":"8","author":"Petersen","year":"2011","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20180415221407_bib23","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J Mol Biol"},{"key":"key\n\t\t\t\t20180415221407_bib24","doi-asserted-by":"crossref","first-page":"D284","DOI":"10.1093\/nar\/gkr1060","article-title":"eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges","volume":"40","author":"Powell","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180415221407_bib25","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"article-title":"Supporting data for \u201cImproving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.\u201d GigaScience Database","year":"2017","author":"Richardson","key":"key\n\t\t\t\t20180415221407_bib26"},{"key":"key\n\t\t\t\t20180415221407_bib27","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180415221407_bib28","doi-asserted-by":"crossref","first-page":"e0130720","DOI":"10.1371\/journal.pone.0130720","article-title":"De novo transcriptome assemblies of rana (Lithobates) catesbeiana and Xenopus laevis tadpole livers for comparative genomics without reference genomes","volume":"10","author":"Birol","year":"2015","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180415221407_bib29","doi-asserted-by":"crossref","first-page":"24069","DOI":"10.1038\/srep24069","article-title":"Comparative transcriptome analyses of seven anurans reveal functions and adaptations of amphibian skin","volume":"6","author":"Huang","year":"2016","journal-title":"Sci Rep"},{"key":"key\n\t\t\t\t20180415221407_bib30","doi-asserted-by":"crossref","first-page":"27310","DOI":"10.1038\/srep27310","article-title":"Transcriptome profiles of metamorphosis in the ornamented pygmy frog Microhyla fissipes clarify the functions of thyroid hormone receptors in metamorphosis","volume":"6","author":"Zhao","year":"2016","journal-title":"Sci Rep"},{"key":"key\n\t\t\t\t20180415221407_bib31","doi-asserted-by":"crossref","first-page":"e23010","DOI":"10.1002\/dvg.23010","article-title":"AmphiBase: a new genomic resource for non-model amphibian species","volume":"55","author":"Kwon","year":"2017","journal-title":"Genesis"},{"key":"key\n\t\t\t\t20180415221407_bib32","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"Emms","year":"2015","journal-title":"Genome Biol"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/gigascience\/article-pdf\/7\/1\/gix114\/24620436\/gix114.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,6]],"date-time":"2019-10-06T17:13:01Z","timestamp":1570381981000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/gix114\/4662864"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,27]]},"references-count":32,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,11,27]]},"published-print":{"date-parts":[[2018,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gigascience\/gix114","relation":{},"ISSN":["2047-217X"],"issn-type":[{"type":"electronic","value":"2047-217X"}],"subject":[],"published-other":{"date-parts":[[2018,1]]},"published":{"date-parts":[[2017,11,27]]}}}