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Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus

2022-09Journal article Open access
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dc.contributor.authorCunha, Regina L.
dc.contributor.authorNicastro, Katy
dc.contributor.authorZardi, Gerardo I.
dc.contributor.authorMadeira, Celine
dc.contributor.authorMcQuaid, Christopher D.
dc.contributor.authorJ. Cox, Cymon
dc.contributor.authorCastilho, Rita
dc.date.accessioned2023-02-08T13:49:30Z
dc.date.available2023-02-08T13:49:30Z
dc.date.issued2022-09
dc.description.abstractBackground: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods: To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the "primer-walking" method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results: The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.pt_PT
dc.description.sponsorshipEMBRC.PT ALG-01-0145FEDER-022121
dc.description.sponsorshipBIODATA.PT ALG-01-0145-FEDER-022231
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.7717/peerj.13953pt_PT
dc.identifier.issn2167-8359
dc.identifier.urihttp://hdl.handle.net/10400.1/19022
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherPEERJpt_PT
dc.relationAlgarve Centre for Marine Sciences
dc.relationmicroCOOL: microbial endosymbiotic thermal buffer against heatwaves
dc.relationInterfacing spin waves with superconducting quantum circuits for single magnon creation and detection
dc.relationNot Available
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectMitogenomicspt_PT
dc.subjectPerna pernapt_PT
dc.subjectGene rearrangementspt_PT
dc.subjectPolyphylypt_PT
dc.subjectPrimer-walkingpt_PT
dc.titleComparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genuspt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleAlgarve Centre for Marine Sciences
oaire.awardTitlemicroCOOL: microbial endosymbiotic thermal buffer against heatwaves
oaire.awardTitleInterfacing spin waves with superconducting quantum circuits for single magnon creation and detection
oaire.awardTitleNot Available
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04326%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/EXPL%2FBIA-BMA%2F0682%2F2021/PT
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/648011/EU
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/DL 57%2F2016/DL 57%2F2016%2FCP1361%2FCT0013/PT
oaire.citation.startPagee13953pt_PT
oaire.citation.titlePeerJpt_PT
oaire.citation.volume10pt_PT
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream3599-PPCDT
oaire.fundingStreamH2020
oaire.fundingStreamDL 57/2016
person.familyNameLopes da Cunha
person.familyNameNicastro
person.familyNameCox
person.familyNameCastilho
person.givenNameRegina
person.givenNameKaty
person.givenNameCymon
person.givenNameRita
person.identifier452212
person.identifier.ciencia-id3E12-714B-AFE5
person.identifier.ciencia-id6B15-9771-1D04
person.identifier.ciencia-id0513-0407-A6C1
person.identifier.orcid0000-0002-4275-9723
person.identifier.orcid0000-0002-7071-141X
person.identifier.orcid0000-0002-4927-979X
person.identifier.orcid0000-0003-0727-3688
person.identifier.ridM-3463-2013
person.identifier.ridD-2259-2012
person.identifier.ridD-1303-2012
person.identifier.ridB-6185-2008
person.identifier.scopus-author-id8855869800
person.identifier.scopus-author-id12646675100
person.identifier.scopus-author-id7402112716
person.identifier.scopus-author-id56271196600
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameEuropean Commission
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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