Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526 T and Zobellia laminariae KMM 3676 T
We obtained two novel draft genomes of type strains with estimated genome sizes of 5.14 Mb for KMM 3526 and 5.16 Mb for KMM 3676 . Comparative genomic analysis has been carried out between obtained and known genomes of representatives. The pan-genome of genus is composed of 4853 orthologous clusters...
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| Veröffentlicht in: | Marine drugs 2019-11, Vol.17 (12) |
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| container_title | Marine drugs |
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| creator | Chernysheva, Nadezhda Bystritskaya, Evgeniya Stenkova, Anna Golovkin, Ilya Nedashkovskaya, Olga Isaeva, Marina |
| description | We obtained two novel draft genomes of type
strains with estimated genome sizes of 5.14 Mb for
KMM 3526
and 5.16 Mb for
KMM 3676
. Comparative genomic analysis has been carried out between obtained and known genomes of
representatives. The pan-genome of
genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries. |
| doi_str_mv | 10.3390/md17120661 |
| format | Article |
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strains with estimated genome sizes of 5.14 Mb for
KMM 3526
and 5.16 Mb for
KMM 3676
. Comparative genomic analysis has been carried out between obtained and known genomes of
representatives. The pan-genome of
genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.</description><identifier>EISSN: 1660-3397</identifier><identifier>DOI: 10.3390/md17120661</identifier><identifier>PMID: 31771309</identifier><language>eng</language><publisher>Switzerland</publisher><subject>Aquatic Organisms - enzymology ; Aquatic Organisms - genetics ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Biotechnology - methods ; Carbohydrate Metabolism ; Flavobacteriaceae - enzymology ; Flavobacteriaceae - genetics ; Genome, Bacterial - genetics ; Genomics ; Phylogeny ; Polysaccharides - metabolism ; Seaweed - chemistry ; Seaweed - metabolism ; Sequence Analysis, DNA</subject><ispartof>Marine drugs, 2019-11, Vol.17 (12)</ispartof><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><orcidid>0000-0002-2395-0485</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,860,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31771309$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chernysheva, Nadezhda</creatorcontrib><creatorcontrib>Bystritskaya, Evgeniya</creatorcontrib><creatorcontrib>Stenkova, Anna</creatorcontrib><creatorcontrib>Golovkin, Ilya</creatorcontrib><creatorcontrib>Nedashkovskaya, Olga</creatorcontrib><creatorcontrib>Isaeva, Marina</creatorcontrib><title>Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526 T and Zobellia laminariae KMM 3676 T</title><title>Marine drugs</title><addtitle>Mar Drugs</addtitle><description>We obtained two novel draft genomes of type
strains with estimated genome sizes of 5.14 Mb for
KMM 3526
and 5.16 Mb for
KMM 3676
. Comparative genomic analysis has been carried out between obtained and known genomes of
representatives. The pan-genome of
genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.</description><subject>Aquatic Organisms - enzymology</subject><subject>Aquatic Organisms - genetics</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biotechnology - methods</subject><subject>Carbohydrate Metabolism</subject><subject>Flavobacteriaceae - enzymology</subject><subject>Flavobacteriaceae - genetics</subject><subject>Genome, Bacterial - genetics</subject><subject>Genomics</subject><subject>Phylogeny</subject><subject>Polysaccharides - metabolism</subject><subject>Seaweed - chemistry</subject><subject>Seaweed - metabolism</subject><subject>Sequence Analysis, DNA</subject><issn>1660-3397</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFjsFqAjEURUOhOFN14weU9wPWxDhJZ1mGWkFmI67cyNN5QnSSDMlYmF0_vYO13XZ14XDu5TI2EfxFypzPbCW0mHOlxANLhVJ82mOdsKcYz5zL7DVfDFgihdZC8jxlX4W3DQZszSfBBzlvzTECugqKt11n74xgQw2F1ptAEfwJSgzGEez8geraIKC9hnjpyEUTYV2WILO5gu1t6E-q0RrXF5F-FKV7ZcQeT1hHGt9zyJ6X79tiNW2uB0vVvgnGYuj2v5flv8I317hPIQ</recordid><startdate>20191124</startdate><enddate>20191124</enddate><creator>Chernysheva, Nadezhda</creator><creator>Bystritskaya, Evgeniya</creator><creator>Stenkova, Anna</creator><creator>Golovkin, Ilya</creator><creator>Nedashkovskaya, Olga</creator><creator>Isaeva, Marina</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><orcidid>https://orcid.org/0000-0002-2395-0485</orcidid></search><sort><creationdate>20191124</creationdate><title>Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526 T and Zobellia laminariae KMM 3676 T</title><author>Chernysheva, Nadezhda ; Bystritskaya, Evgeniya ; Stenkova, Anna ; Golovkin, Ilya ; Nedashkovskaya, Olga ; Isaeva, Marina</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-pubmed_primary_317713093</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Aquatic Organisms - enzymology</topic><topic>Aquatic Organisms - genetics</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>Biotechnology - methods</topic><topic>Carbohydrate Metabolism</topic><topic>Flavobacteriaceae - enzymology</topic><topic>Flavobacteriaceae - genetics</topic><topic>Genome, Bacterial - genetics</topic><topic>Genomics</topic><topic>Phylogeny</topic><topic>Polysaccharides - metabolism</topic><topic>Seaweed - chemistry</topic><topic>Seaweed - metabolism</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chernysheva, Nadezhda</creatorcontrib><creatorcontrib>Bystritskaya, Evgeniya</creatorcontrib><creatorcontrib>Stenkova, Anna</creatorcontrib><creatorcontrib>Golovkin, Ilya</creatorcontrib><creatorcontrib>Nedashkovskaya, Olga</creatorcontrib><creatorcontrib>Isaeva, Marina</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><jtitle>Marine drugs</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chernysheva, Nadezhda</au><au>Bystritskaya, Evgeniya</au><au>Stenkova, Anna</au><au>Golovkin, Ilya</au><au>Nedashkovskaya, Olga</au><au>Isaeva, Marina</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526 T and Zobellia laminariae KMM 3676 T</atitle><jtitle>Marine drugs</jtitle><addtitle>Mar Drugs</addtitle><date>2019-11-24</date><risdate>2019</risdate><volume>17</volume><issue>12</issue><eissn>1660-3397</eissn><abstract>We obtained two novel draft genomes of type
strains with estimated genome sizes of 5.14 Mb for
KMM 3526
and 5.16 Mb for
KMM 3676
. Comparative genomic analysis has been carried out between obtained and known genomes of
representatives. The pan-genome of
genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.</abstract><cop>Switzerland</cop><pmid>31771309</pmid><doi>10.3390/md17120661</doi><orcidid>https://orcid.org/0000-0002-2395-0485</orcidid></addata></record> |
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| identifier | EISSN: 1660-3397 |
| ispartof | Marine drugs, 2019-11, Vol.17 (12) |
| issn | 1660-3397 |
| language | eng |
| recordid | cdi_pubmed_primary_31771309 |
| source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; PubMed Central Open Access |
| subjects | Aquatic Organisms - enzymology Aquatic Organisms - genetics Bacterial Proteins - genetics Bacterial Proteins - metabolism Biotechnology - methods Carbohydrate Metabolism Flavobacteriaceae - enzymology Flavobacteriaceae - genetics Genome, Bacterial - genetics Genomics Phylogeny Polysaccharides - metabolism Seaweed - chemistry Seaweed - metabolism Sequence Analysis, DNA |
| title | Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526 T and Zobellia laminariae KMM 3676 T |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-28T16%3A25%3A18IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-pubmed&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparative%20Genomics%20and%20CAZyme%20Genome%20Repertoires%20of%20Marine%20Zobellia%20amurskyensis%20KMM%203526%20T%20and%20Zobellia%20laminariae%20KMM%203676%20T&rft.jtitle=Marine%20drugs&rft.au=Chernysheva,%20Nadezhda&rft.date=2019-11-24&rft.volume=17&rft.issue=12&rft.eissn=1660-3397&rft_id=info:doi/10.3390/md17120661&rft_dat=%3Cpubmed%3E31771309%3C/pubmed%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_id=info:pmid/31771309&rfr_iscdi=true |