Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis

Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis. Armstrong, E. J. & Stillman, J. H. Integrative and Comparative Biology, 56(6):1092–1102, December, 2016.

Paper

Paper doi abstract bibtex 3 downloads

Crustaceans have commonly been used as non-model systems in basic biological research, especially physiological regulation. With the recent and rapid adoption of functional genomic tools, crustaceans are increasingly becoming model systems for ecological investigations of development and evolution and for mechanistic examinations of genotype–phenotype interactions and molecular pathways of response to environmental stressors. Comparative transcriptomic approaches, however, remain constrained by a lack of sequence data in closely related crustacean taxa. We identify challenges in the use of functional genomics tools in comparative analysis among decapod crustacean in light of recent advances. We present RNA-seq data from two congeneric species of porcelain crabs (Petrolisthes cinctipes and P. manimaculis) used to construct two de novo transcriptome assemblies with ∼194K and ∼278K contigs, respectively. We characterize and contrast these assemblies and compare them to a previously generated EST sequence library for P. cinctipes. We also discuss the potential use of these data as a case-study system in the broader context of crustacean comparative transcriptomics.

@article{armstrong_construction_2016,
	title = {Construction and {Characterization} of {Two} {Novel} {Transcriptome} {Assemblies} in the {Congeneric} {Porcelain} {Crabs} \textit{{Petrolisthes} cinctipes} and \textit{{P}. manimaculis}},
	volume = {56},
	copyright = {All rights reserved},
	issn = {1540-7063, 1557-7023},
	url = {https://academic.oup.com/icb/article/56/6/1092/2647077},
	doi = {10.1093/icb/icw043},
	abstract = {Crustaceans have commonly been used as non-model systems in basic biological research, especially physiological regulation. With the recent and rapid adoption of functional genomic tools, crustaceans are increasingly becoming model systems for ecological investigations of development and evolution and for mechanistic examinations of genotype–phenotype interactions and molecular pathways of response to environmental stressors. Comparative transcriptomic approaches, however, remain constrained by a lack of sequence data in closely related crustacean taxa. We identify challenges in the use of functional genomics tools in comparative analysis among decapod crustacean in light of recent advances. We present RNA-seq data from two congeneric species of porcelain crabs (Petrolisthes cinctipes and P. manimaculis) used to construct two de novo transcriptome assemblies with ∼194K and ∼278K contigs, respectively. We characterize and contrast these assemblies and compare them to a previously generated EST sequence library for P. cinctipes. We also discuss the potential use of these data as a case-study system in the broader context of crustacean comparative transcriptomics.},
	language = {en},
	number = {6},
	urldate = {2024-01-09},
	journal = {Integrative and Comparative Biology},
	author = {Armstrong, Eric J. and Stillman, Jonathon H.},
	month = dec,
	year = {2016},
	pages = {1092--1102},
	url_paper={https://api.zotero.org/users/6071409/publications/items/YBAP7E7J/file/view}
}

Downloads: 3

{"_id":"kePqiD3jpf7MH6c2A","bibbaseid":"armstrong-stillman-constructionandcharacterizationoftwonoveltranscriptomeassembliesinthecongenericporcelaincrabsipetrolisthescinctipesiandipmanimaculisi-2016","author_short":["Armstrong, E. J.","Stillman, J. H."],"bibdata":{"bibtype":"article","type":"article","title":"Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis","volume":"56","copyright":"All rights reserved","issn":"1540-7063, 1557-7023","url":"https://academic.oup.com/icb/article/56/6/1092/2647077","doi":"10.1093/icb/icw043","abstract":"Crustaceans have commonly been used as non-model systems in basic biological research, especially physiological regulation. With the recent and rapid adoption of functional genomic tools, crustaceans are increasingly becoming model systems for ecological investigations of development and evolution and for mechanistic examinations of genotype–phenotype interactions and molecular pathways of response to environmental stressors. Comparative transcriptomic approaches, however, remain constrained by a lack of sequence data in closely related crustacean taxa. We identify challenges in the use of functional genomics tools in comparative analysis among decapod crustacean in light of recent advances. We present RNA-seq data from two congeneric species of porcelain crabs (Petrolisthes cinctipes and P. manimaculis) used to construct two de novo transcriptome assemblies with ∼194K and ∼278K contigs, respectively. We characterize and contrast these assemblies and compare them to a previously generated EST sequence library for P. cinctipes. We also discuss the potential use of these data as a case-study system in the broader context of crustacean comparative transcriptomics.","language":"en","number":"6","urldate":"2024-01-09","journal":"Integrative and Comparative Biology","author":[{"propositions":[],"lastnames":["Armstrong"],"firstnames":["Eric","J."],"suffixes":[]},{"propositions":[],"lastnames":["Stillman"],"firstnames":["Jonathon","H."],"suffixes":[]}],"month":"December","year":"2016","pages":"1092–1102","url_paper":"https://api.zotero.org/users/6071409/publications/items/YBAP7E7J/file/view","bibtex":"@article{armstrong_construction_2016,\n\ttitle = {Construction and {Characterization} of {Two} {Novel} {Transcriptome} {Assemblies} in the {Congeneric} {Porcelain} {Crabs} \\textit{{Petrolisthes} cinctipes} and \\textit{{P}. manimaculis}},\n\tvolume = {56},\n\tcopyright = {All rights reserved},\n\tissn = {1540-7063, 1557-7023},\n\turl = {https://academic.oup.com/icb/article/56/6/1092/2647077},\n\tdoi = {10.1093/icb/icw043},\n\tabstract = {Crustaceans have commonly been used as non-model systems in basic biological research, especially physiological regulation. With the recent and rapid adoption of functional genomic tools, crustaceans are increasingly becoming model systems for ecological investigations of development and evolution and for mechanistic examinations of genotype–phenotype interactions and molecular pathways of response to environmental stressors. Comparative transcriptomic approaches, however, remain constrained by a lack of sequence data in closely related crustacean taxa. We identify challenges in the use of functional genomics tools in comparative analysis among decapod crustacean in light of recent advances. We present RNA-seq data from two congeneric species of porcelain crabs (Petrolisthes cinctipes and P. manimaculis) used to construct two de novo transcriptome assemblies with ∼194K and ∼278K contigs, respectively. We characterize and contrast these assemblies and compare them to a previously generated EST sequence library for P. cinctipes. We also discuss the potential use of these data as a case-study system in the broader context of crustacean comparative transcriptomics.},\n\tlanguage = {en},\n\tnumber = {6},\n\turldate = {2024-01-09},\n\tjournal = {Integrative and Comparative Biology},\n\tauthor = {Armstrong, Eric J. and Stillman, Jonathon H.},\n\tmonth = dec,\n\tyear = {2016},\n\tpages = {1092--1102},\n\turl_paper={https://api.zotero.org/users/6071409/publications/items/YBAP7E7J/file/view}\n}\n\n\n\n","author_short":["Armstrong, E. J.","Stillman, J. H."],"key":"armstrong_construction_2016","id":"armstrong_construction_2016","bibbaseid":"armstrong-stillman-constructionandcharacterizationoftwonoveltranscriptomeassembliesinthecongenericporcelaincrabsipetrolisthescinctipesiandipmanimaculisi-2016","role":"author","urls":{"Paper":"https://academic.oup.com/icb/article/56/6/1092/2647077"," paper":"https://api.zotero.org/users/6071409/publications/items/YBAP7E7J/file/view"},"metadata":{"authorlinks":{}},"downloads":3},"bibtype":"article","biburl":"https://bibbase.org/zotero-mypublications/armst185","dataSources":["p48HAcWwdToiSZ2QJ","vzQnKyKjKrdynJxFW"],"keywords":[],"search_terms":["construction","characterization","two","novel","transcriptome","assemblies","congeneric","porcelain","crabs","petrolisthes","cinctipes","manimaculis","armstrong","stillman"],"title":"Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis","year":2016,"downloads":3}