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Article: De novo transcriptome assembly for Pachygrapsus marmoratus, an intertidal brachyuran crab

TitleDe novo transcriptome assembly for Pachygrapsus marmoratus, an intertidal brachyuran crab
Authors
KeywordsCrab
Crustacean
de novo transcriptome assembly
Decapoda
Marine pollution
Issue Date2021
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/issn/18747787
Citation
Marine Genomics, 2021, v. 55, p. article no. 100792 How to Cite?
AbstractThe marble crab Pachygrapsus marmoratus inhabits the rocky shores of the Mediterranean Sea, Black Sea and East Atlantic Ocean. As other intertidal species, it is considered a model species to study the effects of environmental stressors on natural populations. In this study, we performed Illumina next-generation sequencing on eleven P. marmoratus specimens with the aims to (i) reconstruct their whole transcriptome, (ii) perform a functional annotation of the assembled transcriptome and (iii) develop gene-based markers for future genetic and genomic studies on this as well as other brachyuran species. We obtained a transcriptome assembly constituted by 56,308 unigenes and covering about 60.3 Mbp. We detected 43,915 Simple Sequence Repeats (SSRs) and 192,631 high-quality Single Nucleotide Polymorphisms (SNPs). Due to the scarcity of genomic resources in decapods, and crabs in particular, our results constitute a valuable resource for future studies on brachyuran crabs. The present data also represent a sound resource to investigate biological responses to pollution in intertidal and marine populations.
Persistent Identifierhttp://hdl.handle.net/10722/288314
ISSN
2023 Impact Factor: 1.3
2023 SCImago Journal Rankings: 0.584
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorPinosio, S-
dc.contributor.authorFratini, S-
dc.contributor.authorCannicci, S-
dc.contributor.authorOliva, M-
dc.contributor.authorPretti, C-
dc.contributor.authorBaratti, M-
dc.date.accessioned2020-10-05T12:11:02Z-
dc.date.available2020-10-05T12:11:02Z-
dc.date.issued2021-
dc.identifier.citationMarine Genomics, 2021, v. 55, p. article no. 100792-
dc.identifier.issn1874-7787-
dc.identifier.urihttp://hdl.handle.net/10722/288314-
dc.description.abstractThe marble crab Pachygrapsus marmoratus inhabits the rocky shores of the Mediterranean Sea, Black Sea and East Atlantic Ocean. As other intertidal species, it is considered a model species to study the effects of environmental stressors on natural populations. In this study, we performed Illumina next-generation sequencing on eleven P. marmoratus specimens with the aims to (i) reconstruct their whole transcriptome, (ii) perform a functional annotation of the assembled transcriptome and (iii) develop gene-based markers for future genetic and genomic studies on this as well as other brachyuran species. We obtained a transcriptome assembly constituted by 56,308 unigenes and covering about 60.3 Mbp. We detected 43,915 Simple Sequence Repeats (SSRs) and 192,631 high-quality Single Nucleotide Polymorphisms (SNPs). Due to the scarcity of genomic resources in decapods, and crabs in particular, our results constitute a valuable resource for future studies on brachyuran crabs. The present data also represent a sound resource to investigate biological responses to pollution in intertidal and marine populations.-
dc.languageeng-
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/issn/18747787-
dc.relation.ispartofMarine Genomics-
dc.subjectCrab-
dc.subjectCrustacean-
dc.subjectde novo transcriptome assembly-
dc.subjectDecapoda-
dc.subjectMarine pollution-
dc.titleDe novo transcriptome assembly for Pachygrapsus marmoratus, an intertidal brachyuran crab-
dc.typeArticle-
dc.identifier.emailCannicci, S: cannicci@hku.hk-
dc.identifier.authorityCannicci, S=rp02079-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.margen.2020.100792-
dc.identifier.pmid32586711-
dc.identifier.scopuseid_2-s2.0-85086709564-
dc.identifier.hkuros315274-
dc.identifier.volume55-
dc.identifier.spagearticle no. 100792-
dc.identifier.epagearticle no. 100792-
dc.identifier.isiWOS:000618706500008-
dc.publisher.placeNetherlands-
dc.identifier.issnl1874-7787-

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