Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov

A Gram-staining-negative, aerobic bacterium, designated strain PT3.sup.T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3.sup.T was closely related to Amphritea ceti...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:PloS one 2022-08, Vol.17 (8), p.e0271174-e0271174
Hauptverfasser: Yamano, Ryota, Yu, Juanwen, Jiang, Chunqi, Harjuno Condro Haditomo, Alfabetian, Mino, Sayaka, Sakai, Yuichi, Sawabe, Tomoo
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page e0271174
container_issue 8
container_start_page e0271174
container_title PloS one
container_volume 17
creator Yamano, Ryota
Yu, Juanwen
Jiang, Chunqi
Harjuno Condro Haditomo, Alfabetian
Mino, Sayaka
Sakai, Yuichi
Sawabe, Tomoo
description A Gram-staining-negative, aerobic bacterium, designated strain PT3.sup.T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3.sup.T was closely related to Amphritea ceti RA1.sup.T (= KCTC 42154.sup.T = NBRC 110551.sup.T) and Amphritea spongicola MEBiC05461.sup.T (= KCCM 42943.sup.T = JCM 16668.sup.T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3.sup.T . Furthermore, the average amino acid identity (AAI) values of PT3.sup.T against other Amphritea species were on the reported genus delineation boundary (64-67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3.sup.T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3.sup.T, A. cetiKCTC 42154.sup.T and A. spongicola JCM 16668.sup.T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1.sup.T = KCTC 42154.sup.T = NBRC 110551.sup.T ), Aliamphritea spongicola comb. nov. (type strain MEBiC05461.sup.T = KCCM 42943.sup.T = JCM 16668.sup.T ), and Aliamphritea hakodatensis sp. nov. (type strain PT3.sup.T = JCM 34607.sup.T = KCTC 82591.sup.T) were suggested.
doi_str_mv 10.1371/journal.pone.0271174
format Article
fullrecord <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_2700582189</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A713272019</galeid><doaj_id>oai_doaj_org_article_48af9922da034ffea8a5926fa7b4b0e9</doaj_id><sourcerecordid>A713272019</sourcerecordid><originalsourceid>FETCH-LOGICAL-c669t-6709d847062da380324407a3c2960828323d6fcce9521d5fdf7877b8a4b3ce03</originalsourceid><addsrcrecordid>eNqNk92K1DAUgIso7rr6BoIFQRScMU3aJL1ZGBZ_BhYWdPA2nKbpNEOb1KQddp7CVzadqcNW9kJ60ZJ85zsnpzlR9DpBy4Sw5NPODs5As-ysUUuEWZKw9El0meQELyhG5OmD74vohfc7hDLCKX0eXZAsT1mWssvo9wburbGtlrFTe-21NbGt4r5W8VaZwcertqud7hXEfug663pVxsVh3DwGgSljbWKvGy1tLGvV2v5shFDfwSv_8YiNzs7ZznpoxhyrRsNZHnzL2Nj9y-hZBY1Xr6b3VbT58nlz821xe_d1fbO6XUhK835BGcpLnjJEcQmEI4LTFDEgEucUccwJJiWtpFR5hpMyq8qKccYKDmlBpELkKnpz0naN9WJqpReYhR5xnPA8EOsTUVrYic7pFtxBWNDiuGDdVoDrtWyUSDlUeY5DJYikVaWAQ5ZjWgEr0gKp0XU9ZRuKVpVSmd5BM5POd4yuxdbuRU5oluAsCN5PAmd_Dcr3otVeqqYBo-xwqpsSzjIe0Lf_oI-fbqK2EA6gTWVDXjlKxYolBDOMkpFaPkKFp1Th94Z7V-mwPgv4MAsITK_u-y0M3ov1j-__z979nLPvHrC1gqavvW2GPlxXPwfTEyid9d6p6tzkBIlxbP52Q4xjI6axIX8A_9oJ8g</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2700582189</pqid></control><display><type>article</type><title>Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov</title><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Public Library of Science (PLoS)</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Yamano, Ryota ; Yu, Juanwen ; Jiang, Chunqi ; Harjuno Condro Haditomo, Alfabetian ; Mino, Sayaka ; Sakai, Yuichi ; Sawabe, Tomoo</creator><contributor>Yurchenko, Vyacheslav</contributor><creatorcontrib>Yamano, Ryota ; Yu, Juanwen ; Jiang, Chunqi ; Harjuno Condro Haditomo, Alfabetian ; Mino, Sayaka ; Sakai, Yuichi ; Sawabe, Tomoo ; Yurchenko, Vyacheslav</creatorcontrib><description>A Gram-staining-negative, aerobic bacterium, designated strain PT3.sup.T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3.sup.T was closely related to Amphritea ceti RA1.sup.T (= KCTC 42154.sup.T = NBRC 110551.sup.T) and Amphritea spongicola MEBiC05461.sup.T (= KCCM 42943.sup.T = JCM 16668.sup.T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3.sup.T . Furthermore, the average amino acid identity (AAI) values of PT3.sup.T against other Amphritea species were on the reported genus delineation boundary (64-67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3.sup.T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3.sup.T, A. cetiKCTC 42154.sup.T and A. spongicola JCM 16668.sup.T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1.sup.T = KCTC 42154.sup.T = NBRC 110551.sup.T ), Aliamphritea spongicola comb. nov. (type strain MEBiC05461.sup.T = KCCM 42943.sup.T = JCM 16668.sup.T ), and Aliamphritea hakodatensis sp. nov. (type strain PT3.sup.T = JCM 34607.sup.T = KCTC 82591.sup.T) were suggested.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0271174</identifier><identifier>PMID: 35947547</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Amino acid sequence ; Amino acids ; Analysis ; Bacteria ; Biology and Life Sciences ; Computer and Information Sciences ; Deoxyribonucleic acid ; DNA ; DNA-directed RNA polymerase ; Fatty acids ; Gene sequencing ; Genes ; Genetic aspects ; Genomes ; Genomics ; Hybridization ; Larvae ; New species ; Nucleotide sequence ; Nucleotides ; Phylogenetics ; Phylogeny ; RecA protein ; Reclassification ; Research and Analysis Methods ; rRNA 16S ; Sequence analysis ; Taxonomic revision ; Taxonomy</subject><ispartof>PloS one, 2022-08, Vol.17 (8), p.e0271174-e0271174</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Yamano et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Yamano et al 2022 Yamano et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c669t-6709d847062da380324407a3c2960828323d6fcce9521d5fdf7877b8a4b3ce03</citedby><cites>FETCH-LOGICAL-c669t-6709d847062da380324407a3c2960828323d6fcce9521d5fdf7877b8a4b3ce03</cites><orcidid>0000-0002-4015-9046 ; 0000-0002-6013-2369</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365125/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365125/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23864,27922,27923,53789,53791,79370,79371</link.rule.ids></links><search><contributor>Yurchenko, Vyacheslav</contributor><creatorcontrib>Yamano, Ryota</creatorcontrib><creatorcontrib>Yu, Juanwen</creatorcontrib><creatorcontrib>Jiang, Chunqi</creatorcontrib><creatorcontrib>Harjuno Condro Haditomo, Alfabetian</creatorcontrib><creatorcontrib>Mino, Sayaka</creatorcontrib><creatorcontrib>Sakai, Yuichi</creatorcontrib><creatorcontrib>Sawabe, Tomoo</creatorcontrib><title>Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov</title><title>PloS one</title><description>A Gram-staining-negative, aerobic bacterium, designated strain PT3.sup.T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3.sup.T was closely related to Amphritea ceti RA1.sup.T (= KCTC 42154.sup.T = NBRC 110551.sup.T) and Amphritea spongicola MEBiC05461.sup.T (= KCCM 42943.sup.T = JCM 16668.sup.T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3.sup.T . Furthermore, the average amino acid identity (AAI) values of PT3.sup.T against other Amphritea species were on the reported genus delineation boundary (64-67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3.sup.T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3.sup.T, A. cetiKCTC 42154.sup.T and A. spongicola JCM 16668.sup.T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1.sup.T = KCTC 42154.sup.T = NBRC 110551.sup.T ), Aliamphritea spongicola comb. nov. (type strain MEBiC05461.sup.T = KCCM 42943.sup.T = JCM 16668.sup.T ), and Aliamphritea hakodatensis sp. nov. (type strain PT3.sup.T = JCM 34607.sup.T = KCTC 82591.sup.T) were suggested.</description><subject>Amino acid sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Bacteria</subject><subject>Biology and Life Sciences</subject><subject>Computer and Information Sciences</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA-directed RNA polymerase</subject><subject>Fatty acids</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Hybridization</subject><subject>Larvae</subject><subject>New species</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>RecA protein</subject><subject>Reclassification</subject><subject>Research and Analysis Methods</subject><subject>rRNA 16S</subject><subject>Sequence analysis</subject><subject>Taxonomic revision</subject><subject>Taxonomy</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk92K1DAUgIso7rr6BoIFQRScMU3aJL1ZGBZ_BhYWdPA2nKbpNEOb1KQddp7CVzadqcNW9kJ60ZJ85zsnpzlR9DpBy4Sw5NPODs5As-ysUUuEWZKw9El0meQELyhG5OmD74vohfc7hDLCKX0eXZAsT1mWssvo9wburbGtlrFTe-21NbGt4r5W8VaZwcertqud7hXEfug663pVxsVh3DwGgSljbWKvGy1tLGvV2v5shFDfwSv_8YiNzs7ZznpoxhyrRsNZHnzL2Nj9y-hZBY1Xr6b3VbT58nlz821xe_d1fbO6XUhK835BGcpLnjJEcQmEI4LTFDEgEucUccwJJiWtpFR5hpMyq8qKccYKDmlBpELkKnpz0naN9WJqpReYhR5xnPA8EOsTUVrYic7pFtxBWNDiuGDdVoDrtWyUSDlUeY5DJYikVaWAQ5ZjWgEr0gKp0XU9ZRuKVpVSmd5BM5POd4yuxdbuRU5oluAsCN5PAmd_Dcr3otVeqqYBo-xwqpsSzjIe0Lf_oI-fbqK2EA6gTWVDXjlKxYolBDOMkpFaPkKFp1Th94Z7V-mwPgv4MAsITK_u-y0M3ov1j-__z979nLPvHrC1gqavvW2GPlxXPwfTEyid9d6p6tzkBIlxbP52Q4xjI6axIX8A_9oJ8g</recordid><startdate>20220810</startdate><enddate>20220810</enddate><creator>Yamano, Ryota</creator><creator>Yu, Juanwen</creator><creator>Jiang, Chunqi</creator><creator>Harjuno Condro Haditomo, Alfabetian</creator><creator>Mino, Sayaka</creator><creator>Sakai, Yuichi</creator><creator>Sawabe, Tomoo</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-4015-9046</orcidid><orcidid>https://orcid.org/0000-0002-6013-2369</orcidid></search><sort><creationdate>20220810</creationdate><title>Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov</title><author>Yamano, Ryota ; Yu, Juanwen ; Jiang, Chunqi ; Harjuno Condro Haditomo, Alfabetian ; Mino, Sayaka ; Sakai, Yuichi ; Sawabe, Tomoo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c669t-6709d847062da380324407a3c2960828323d6fcce9521d5fdf7877b8a4b3ce03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Amino acid sequence</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Bacteria</topic><topic>Biology and Life Sciences</topic><topic>Computer and Information Sciences</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA-directed RNA polymerase</topic><topic>Fatty acids</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Hybridization</topic><topic>Larvae</topic><topic>New species</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>RecA protein</topic><topic>Reclassification</topic><topic>Research and Analysis Methods</topic><topic>rRNA 16S</topic><topic>Sequence analysis</topic><topic>Taxonomic revision</topic><topic>Taxonomy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yamano, Ryota</creatorcontrib><creatorcontrib>Yu, Juanwen</creatorcontrib><creatorcontrib>Jiang, Chunqi</creatorcontrib><creatorcontrib>Harjuno Condro Haditomo, Alfabetian</creatorcontrib><creatorcontrib>Mino, Sayaka</creatorcontrib><creatorcontrib>Sakai, Yuichi</creatorcontrib><creatorcontrib>Sawabe, Tomoo</creatorcontrib><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing &amp; Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological &amp; Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health &amp; Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science &amp; Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies &amp; Aerospace Collection</collection><collection>Agricultural &amp; Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing &amp; Allied Health Database (Alumni Edition)</collection><collection>Meteorological &amp; Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing &amp; Allied Health Premium</collection><collection>Advanced Technologies &amp; Aerospace Database</collection><collection>ProQuest Advanced Technologies &amp; Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yamano, Ryota</au><au>Yu, Juanwen</au><au>Jiang, Chunqi</au><au>Harjuno Condro Haditomo, Alfabetian</au><au>Mino, Sayaka</au><au>Sakai, Yuichi</au><au>Sawabe, Tomoo</au><au>Yurchenko, Vyacheslav</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov</atitle><jtitle>PloS one</jtitle><date>2022-08-10</date><risdate>2022</risdate><volume>17</volume><issue>8</issue><spage>e0271174</spage><epage>e0271174</epage><pages>e0271174-e0271174</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>A Gram-staining-negative, aerobic bacterium, designated strain PT3.sup.T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3.sup.T was closely related to Amphritea ceti RA1.sup.T (= KCTC 42154.sup.T = NBRC 110551.sup.T) and Amphritea spongicola MEBiC05461.sup.T (= KCCM 42943.sup.T = JCM 16668.sup.T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3.sup.T . Furthermore, the average amino acid identity (AAI) values of PT3.sup.T against other Amphritea species were on the reported genus delineation boundary (64-67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3.sup.T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3.sup.T, A. cetiKCTC 42154.sup.T and A. spongicola JCM 16668.sup.T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1.sup.T = KCTC 42154.sup.T = NBRC 110551.sup.T ), Aliamphritea spongicola comb. nov. (type strain MEBiC05461.sup.T = KCCM 42943.sup.T = JCM 16668.sup.T ), and Aliamphritea hakodatensis sp. nov. (type strain PT3.sup.T = JCM 34607.sup.T = KCTC 82591.sup.T) were suggested.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>35947547</pmid><doi>10.1371/journal.pone.0271174</doi><tpages>e0271174</tpages><orcidid>https://orcid.org/0000-0002-4015-9046</orcidid><orcidid>https://orcid.org/0000-0002-6013-2369</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1932-6203
ispartof PloS one, 2022-08, Vol.17 (8), p.e0271174-e0271174
issn 1932-6203
1932-6203
language eng
recordid cdi_plos_journals_2700582189
source DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry
subjects Amino acid sequence
Amino acids
Analysis
Bacteria
Biology and Life Sciences
Computer and Information Sciences
Deoxyribonucleic acid
DNA
DNA-directed RNA polymerase
Fatty acids
Gene sequencing
Genes
Genetic aspects
Genomes
Genomics
Hybridization
Larvae
New species
Nucleotide sequence
Nucleotides
Phylogenetics
Phylogeny
RecA protein
Reclassification
Research and Analysis Methods
rRNA 16S
Sequence analysis
Taxonomic revision
Taxonomy
title Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-14T02%3A41%3A56IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Taxonomic%20revision%20of%20the%20genus%20Amphritea%20supported%20by%20genomic%20and%20in%20silico%20chemotaxonomic%20analyses,%20and%20the%20proposal%20of%20Aliamphritea%20gen.%20nov&rft.jtitle=PloS%20one&rft.au=Yamano,%20Ryota&rft.date=2022-08-10&rft.volume=17&rft.issue=8&rft.spage=e0271174&rft.epage=e0271174&rft.pages=e0271174-e0271174&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0271174&rft_dat=%3Cgale_plos_%3EA713272019%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2700582189&rft_id=info:pmid/35947547&rft_galeid=A713272019&rft_doaj_id=oai_doaj_org_article_48af9922da034ffea8a5926fa7b4b0e9&rfr_iscdi=true