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Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae
The halotolerant yeast Scheffersomyces spartinae , commonly found in marine environments, holds significant potential for various industrial applications. Despite this, its genetic characteristics have been relatively underexplored. In this study, we isolated a strain of S. spartinae named YMxiao fr...
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| Published in: | Applied microbiology and biotechnology 2024-12, Vol.108 (1), p.539-539, Article 539 |
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| creator | Sharma, Awkash Liu, Xing Yin, Jun Yu, Pei-Jing Qi, Lei He, Min Li, Ke-Jing Zheng, Dao-Qiong |
| description | The halotolerant yeast
Scheffersomyces spartinae
, commonly found in marine environments, holds significant potential for various industrial applications. Despite this, its genetic characteristics have been relatively underexplored. In this study, we isolated a strain of
S. spartinae
named YMxiao from seawater in Zhoushan City, China. Through scanning electron microscopy and flow cytometry, we characterized
S. spartinae
YMxiao cells as urn-shaped, demonstrating asymmetric division via budding, and possessing a diploid genome. Compared to the model yeast
Saccharomyces cerevisiae
,
S. spartinae
YMxiao exhibited greater tolerance to various stressful conditions. Furthermore,
S. spartinae
YMxiao was capable of utilizing xylose, mannitol, sorbitol, and arabinose as sole carbon sources for growth. We conducted whole-genome sequencing of
S. spartinae
YMxiao using a combination of Nanopore and Illumina technologies, resulting in a telomere-to-telomere complete genome assembly of 12 Mb. Genome annotation identified 5311 protein-coding genes, 214 tRNA genes, and 236 transposable elements distributed across 8 chromosomes. Comparative genomics between
S. spartinae
strains YMxiao and ARV011 revealed genomic variations and evolutionary patterns within this species. Notably, certain genes in
S. spartinae
strains were found to be under strong positive selection. Additionally, we developed a genetic manipulation protocol that successfully enabled gene knockouts in
S. spartinae
. Our findings not only enhance our understanding of the
S. spartinae
genome but also provide a foundation for future research into its potential biotechnological applications.
Key points
•
The unique phenotypes and genetic characteristics of S. spartinae were disclosed.
•
Comparative genomics showed vast genetic variations between S. spartinae strains.
•
Genetic manipulation protocol was established for S. spartinae strain. |
| doi_str_mv | 10.1007/s00253-024-13382-1 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_11659333</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3147484687</sourcerecordid><originalsourceid>FETCH-LOGICAL-c389t-d9e6f950379a1feef2be69c23bbe50a5d1bffa0e70cbff6a529132d983c31f923</originalsourceid><addsrcrecordid>eNqNkctu1DAUhi0EotOBF2CBIrHpJuBLbMcrhCraIlVi0bLFcpzjGVeJPdgO0rw9nk4plwXCC9_Od_5z7B-hVwS_JRjLdxljylmLadcSxnrakidoRTpGWyxI9xStMJG8lVz1J-g05zuMCe2FeI5OmJKY9gyv0NdLCHH2trFbk4wtkHwu3ubGhLHZQIB6aGYT_G6ZTPExNNE1ZQv1LvkAzR5MLs2N3YJzkHKc9xZyk3cmFR8MvEDPnJkyvHxY1-jLxcfb86v2-vPlp_MP161lvSrtqEA4xTGTyhAH4OgAQlnKhgE4Nnwkg3MGg8S2boThVBFGR9Uzy4hTlK3R-6PubhlmGC2Eksykd8nXPvc6Gq__jAS_1Zv4XRMiuGJ1rNHZg0KK3xbIRc8-W5gmEyAuWTPCO8p70cn_QDvZ9Z3oD-ibv9C7uKRQv-KeopJIcahNj5RNMecE7rFxgvXBan20Wler9b3VdV6j178_-THlp7cVYEcg11DYQPpV-x-yPwBMIrZq</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3147271763</pqid></control><display><type>article</type><title>Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae</title><source>Springer Nature</source><source>Springer Nature - SpringerLink Journals - Fully Open Access </source><creator>Sharma, Awkash ; Liu, Xing ; Yin, Jun ; Yu, Pei-Jing ; Qi, Lei ; He, Min ; Li, Ke-Jing ; Zheng, Dao-Qiong</creator><creatorcontrib>Sharma, Awkash ; Liu, Xing ; Yin, Jun ; Yu, Pei-Jing ; Qi, Lei ; He, Min ; Li, Ke-Jing ; Zheng, Dao-Qiong</creatorcontrib><description>The halotolerant yeast
Scheffersomyces spartinae
, commonly found in marine environments, holds significant potential for various industrial applications. Despite this, its genetic characteristics have been relatively underexplored. In this study, we isolated a strain of
S. spartinae
named YMxiao from seawater in Zhoushan City, China. Through scanning electron microscopy and flow cytometry, we characterized
S. spartinae
YMxiao cells as urn-shaped, demonstrating asymmetric division via budding, and possessing a diploid genome. Compared to the model yeast
Saccharomyces cerevisiae
,
S. spartinae
YMxiao exhibited greater tolerance to various stressful conditions. Furthermore,
S. spartinae
YMxiao was capable of utilizing xylose, mannitol, sorbitol, and arabinose as sole carbon sources for growth. We conducted whole-genome sequencing of
S. spartinae
YMxiao using a combination of Nanopore and Illumina technologies, resulting in a telomere-to-telomere complete genome assembly of 12 Mb. Genome annotation identified 5311 protein-coding genes, 214 tRNA genes, and 236 transposable elements distributed across 8 chromosomes. Comparative genomics between
S. spartinae
strains YMxiao and ARV011 revealed genomic variations and evolutionary patterns within this species. Notably, certain genes in
S. spartinae
strains were found to be under strong positive selection. Additionally, we developed a genetic manipulation protocol that successfully enabled gene knockouts in
S. spartinae
. Our findings not only enhance our understanding of the
S. spartinae
genome but also provide a foundation for future research into its potential biotechnological applications.
Key points
•
The unique phenotypes and genetic characteristics of S. spartinae were disclosed.
•
Comparative genomics showed vast genetic variations between S. spartinae strains.
•
Genetic manipulation protocol was established for S. spartinae strain.</description><identifier>ISSN: 0175-7598</identifier><identifier>ISSN: 1432-0614</identifier><identifier>EISSN: 1432-0614</identifier><identifier>DOI: 10.1007/s00253-024-13382-1</identifier><identifier>PMID: 39702830</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Annotations ; Applied Genetics and Molecular Biotechnology ; Aquatic Organisms - genetics ; Arabinose ; Biomedical and Life Sciences ; Biotechnology ; carbon ; Carbon sources ; Chemical analysis ; China ; Chromosomes ; Diploids ; diploidy ; electron microscopy ; Flow cytometry ; Gene sequencing ; Genes ; Genetic diversity ; Genetic engineering ; genome assembly ; Genome, Fungal - genetics ; Genomes ; Genomics ; Industrial applications ; Life Sciences ; Mannitol ; Marine environment ; Microbial Genetics and Genomics ; Microbiology ; nanopores ; Phenotypes ; Phenotypic variations ; Positive selection ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae - metabolism ; Saccharomycetales - classification ; Saccharomycetales - genetics ; Saccharomycetales - metabolism ; Salinity tolerance ; salt tolerance ; Scanning electron microscopy ; Scheffersomyces ; Seawater ; Seawater - microbiology ; Sorbitol ; Spartina spartinae ; species ; Telomeres ; tRNA ; Water analysis ; Whole Genome Sequencing ; xylose ; Yeast ; Yeasts</subject><ispartof>Applied microbiology and biotechnology, 2024-12, Vol.108 (1), p.539-539, Article 539</ispartof><rights>The Author(s) 2024</rights><rights>2024. The Author(s).</rights><rights>Copyright Springer Nature B.V. Dec 2024</rights><rights>The Author(s) 2024 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c389t-d9e6f950379a1feef2be69c23bbe50a5d1bffa0e70cbff6a529132d983c31f923</cites><orcidid>0000-0001-9365-2339</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,777,781,882,27905,27906</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39702830$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sharma, Awkash</creatorcontrib><creatorcontrib>Liu, Xing</creatorcontrib><creatorcontrib>Yin, Jun</creatorcontrib><creatorcontrib>Yu, Pei-Jing</creatorcontrib><creatorcontrib>Qi, Lei</creatorcontrib><creatorcontrib>He, Min</creatorcontrib><creatorcontrib>Li, Ke-Jing</creatorcontrib><creatorcontrib>Zheng, Dao-Qiong</creatorcontrib><title>Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae</title><title>Applied microbiology and biotechnology</title><addtitle>Appl Microbiol Biotechnol</addtitle><addtitle>Appl Microbiol Biotechnol</addtitle><description>The halotolerant yeast
Scheffersomyces spartinae
, commonly found in marine environments, holds significant potential for various industrial applications. Despite this, its genetic characteristics have been relatively underexplored. In this study, we isolated a strain of
S. spartinae
named YMxiao from seawater in Zhoushan City, China. Through scanning electron microscopy and flow cytometry, we characterized
S. spartinae
YMxiao cells as urn-shaped, demonstrating asymmetric division via budding, and possessing a diploid genome. Compared to the model yeast
Saccharomyces cerevisiae
,
S. spartinae
YMxiao exhibited greater tolerance to various stressful conditions. Furthermore,
S. spartinae
YMxiao was capable of utilizing xylose, mannitol, sorbitol, and arabinose as sole carbon sources for growth. We conducted whole-genome sequencing of
S. spartinae
YMxiao using a combination of Nanopore and Illumina technologies, resulting in a telomere-to-telomere complete genome assembly of 12 Mb. Genome annotation identified 5311 protein-coding genes, 214 tRNA genes, and 236 transposable elements distributed across 8 chromosomes. Comparative genomics between
S. spartinae
strains YMxiao and ARV011 revealed genomic variations and evolutionary patterns within this species. Notably, certain genes in
S. spartinae
strains were found to be under strong positive selection. Additionally, we developed a genetic manipulation protocol that successfully enabled gene knockouts in
S. spartinae
. Our findings not only enhance our understanding of the
S. spartinae
genome but also provide a foundation for future research into its potential biotechnological applications.
Key points
•
The unique phenotypes and genetic characteristics of S. spartinae were disclosed.
•
Comparative genomics showed vast genetic variations between S. spartinae strains.
•
Genetic manipulation protocol was established for S. spartinae strain.</description><subject>Annotations</subject><subject>Applied Genetics and Molecular Biotechnology</subject><subject>Aquatic Organisms - genetics</subject><subject>Arabinose</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>carbon</subject><subject>Carbon sources</subject><subject>Chemical analysis</subject><subject>China</subject><subject>Chromosomes</subject><subject>Diploids</subject><subject>diploidy</subject><subject>electron microscopy</subject><subject>Flow cytometry</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic diversity</subject><subject>Genetic engineering</subject><subject>genome assembly</subject><subject>Genome, Fungal - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Industrial applications</subject><subject>Life Sciences</subject><subject>Mannitol</subject><subject>Marine environment</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiology</subject><subject>nanopores</subject><subject>Phenotypes</subject><subject>Phenotypic variations</subject><subject>Positive selection</subject><subject>Saccharomyces cerevisiae</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>Saccharomyces cerevisiae - metabolism</subject><subject>Saccharomycetales - classification</subject><subject>Saccharomycetales - genetics</subject><subject>Saccharomycetales - metabolism</subject><subject>Salinity tolerance</subject><subject>salt tolerance</subject><subject>Scanning electron microscopy</subject><subject>Scheffersomyces</subject><subject>Seawater</subject><subject>Seawater - microbiology</subject><subject>Sorbitol</subject><subject>Spartina spartinae</subject><subject>species</subject><subject>Telomeres</subject><subject>tRNA</subject><subject>Water analysis</subject><subject>Whole Genome Sequencing</subject><subject>xylose</subject><subject>Yeast</subject><subject>Yeasts</subject><issn>0175-7598</issn><issn>1432-0614</issn><issn>1432-0614</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNqNkctu1DAUhi0EotOBF2CBIrHpJuBLbMcrhCraIlVi0bLFcpzjGVeJPdgO0rw9nk4plwXCC9_Od_5z7B-hVwS_JRjLdxljylmLadcSxnrakidoRTpGWyxI9xStMJG8lVz1J-g05zuMCe2FeI5OmJKY9gyv0NdLCHH2trFbk4wtkHwu3ubGhLHZQIB6aGYT_G6ZTPExNNE1ZQv1LvkAzR5MLs2N3YJzkHKc9xZyk3cmFR8MvEDPnJkyvHxY1-jLxcfb86v2-vPlp_MP161lvSrtqEA4xTGTyhAH4OgAQlnKhgE4Nnwkg3MGg8S2boThVBFGR9Uzy4hTlK3R-6PubhlmGC2Eksykd8nXPvc6Gq__jAS_1Zv4XRMiuGJ1rNHZg0KK3xbIRc8-W5gmEyAuWTPCO8p70cn_QDvZ9Z3oD-ibv9C7uKRQv-KeopJIcahNj5RNMecE7rFxgvXBan20Wler9b3VdV6j178_-THlp7cVYEcg11DYQPpV-x-yPwBMIrZq</recordid><startdate>20241201</startdate><enddate>20241201</enddate><creator>Sharma, Awkash</creator><creator>Liu, Xing</creator><creator>Yin, Jun</creator><creator>Yu, Pei-Jing</creator><creator>Qi, Lei</creator><creator>He, Min</creator><creator>Li, Ke-Jing</creator><creator>Zheng, Dao-Qiong</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-9365-2339</orcidid></search><sort><creationdate>20241201</creationdate><title>Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae</title><author>Sharma, Awkash ; Liu, Xing ; Yin, Jun ; Yu, Pei-Jing ; Qi, Lei ; He, Min ; Li, Ke-Jing ; Zheng, Dao-Qiong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c389t-d9e6f950379a1feef2be69c23bbe50a5d1bffa0e70cbff6a529132d983c31f923</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Annotations</topic><topic>Applied Genetics and Molecular Biotechnology</topic><topic>Aquatic Organisms - genetics</topic><topic>Arabinose</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>carbon</topic><topic>Carbon sources</topic><topic>Chemical analysis</topic><topic>China</topic><topic>Chromosomes</topic><topic>Diploids</topic><topic>diploidy</topic><topic>electron microscopy</topic><topic>Flow cytometry</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic diversity</topic><topic>Genetic engineering</topic><topic>genome assembly</topic><topic>Genome, Fungal - genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Industrial applications</topic><topic>Life Sciences</topic><topic>Mannitol</topic><topic>Marine environment</topic><topic>Microbial Genetics and Genomics</topic><topic>Microbiology</topic><topic>nanopores</topic><topic>Phenotypes</topic><topic>Phenotypic variations</topic><topic>Positive selection</topic><topic>Saccharomyces cerevisiae</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>Saccharomyces cerevisiae - metabolism</topic><topic>Saccharomycetales - classification</topic><topic>Saccharomycetales - genetics</topic><topic>Saccharomycetales - metabolism</topic><topic>Salinity tolerance</topic><topic>salt tolerance</topic><topic>Scanning electron microscopy</topic><topic>Scheffersomyces</topic><topic>Seawater</topic><topic>Seawater - microbiology</topic><topic>Sorbitol</topic><topic>Spartina spartinae</topic><topic>species</topic><topic>Telomeres</topic><topic>tRNA</topic><topic>Water analysis</topic><topic>Whole Genome Sequencing</topic><topic>xylose</topic><topic>Yeast</topic><topic>Yeasts</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sharma, Awkash</creatorcontrib><creatorcontrib>Liu, Xing</creatorcontrib><creatorcontrib>Yin, Jun</creatorcontrib><creatorcontrib>Yu, Pei-Jing</creatorcontrib><creatorcontrib>Qi, Lei</creatorcontrib><creatorcontrib>He, Min</creatorcontrib><creatorcontrib>Li, Ke-Jing</creatorcontrib><creatorcontrib>Zheng, Dao-Qiong</creatorcontrib><collection>SpringerOpen</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Applied microbiology and biotechnology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sharma, Awkash</au><au>Liu, Xing</au><au>Yin, Jun</au><au>Yu, Pei-Jing</au><au>Qi, Lei</au><au>He, Min</au><au>Li, Ke-Jing</au><au>Zheng, Dao-Qiong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae</atitle><jtitle>Applied microbiology and biotechnology</jtitle><stitle>Appl Microbiol Biotechnol</stitle><addtitle>Appl Microbiol Biotechnol</addtitle><date>2024-12-01</date><risdate>2024</risdate><volume>108</volume><issue>1</issue><spage>539</spage><epage>539</epage><pages>539-539</pages><artnum>539</artnum><issn>0175-7598</issn><issn>1432-0614</issn><eissn>1432-0614</eissn><abstract>The halotolerant yeast
Scheffersomyces spartinae
, commonly found in marine environments, holds significant potential for various industrial applications. Despite this, its genetic characteristics have been relatively underexplored. In this study, we isolated a strain of
S. spartinae
named YMxiao from seawater in Zhoushan City, China. Through scanning electron microscopy and flow cytometry, we characterized
S. spartinae
YMxiao cells as urn-shaped, demonstrating asymmetric division via budding, and possessing a diploid genome. Compared to the model yeast
Saccharomyces cerevisiae
,
S. spartinae
YMxiao exhibited greater tolerance to various stressful conditions. Furthermore,
S. spartinae
YMxiao was capable of utilizing xylose, mannitol, sorbitol, and arabinose as sole carbon sources for growth. We conducted whole-genome sequencing of
S. spartinae
YMxiao using a combination of Nanopore and Illumina technologies, resulting in a telomere-to-telomere complete genome assembly of 12 Mb. Genome annotation identified 5311 protein-coding genes, 214 tRNA genes, and 236 transposable elements distributed across 8 chromosomes. Comparative genomics between
S. spartinae
strains YMxiao and ARV011 revealed genomic variations and evolutionary patterns within this species. Notably, certain genes in
S. spartinae
strains were found to be under strong positive selection. Additionally, we developed a genetic manipulation protocol that successfully enabled gene knockouts in
S. spartinae
. Our findings not only enhance our understanding of the
S. spartinae
genome but also provide a foundation for future research into its potential biotechnological applications.
Key points
•
The unique phenotypes and genetic characteristics of S. spartinae were disclosed.
•
Comparative genomics showed vast genetic variations between S. spartinae strains.
•
Genetic manipulation protocol was established for S. spartinae strain.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>39702830</pmid><doi>10.1007/s00253-024-13382-1</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0001-9365-2339</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0175-7598 |
| ispartof | Applied microbiology and biotechnology, 2024-12, Vol.108 (1), p.539-539, Article 539 |
| issn | 0175-7598 1432-0614 1432-0614 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_11659333 |
| source | Springer Nature; Springer Nature - SpringerLink Journals - Fully Open Access |
| subjects | Annotations Applied Genetics and Molecular Biotechnology Aquatic Organisms - genetics Arabinose Biomedical and Life Sciences Biotechnology carbon Carbon sources Chemical analysis China Chromosomes Diploids diploidy electron microscopy Flow cytometry Gene sequencing Genes Genetic diversity Genetic engineering genome assembly Genome, Fungal - genetics Genomes Genomics Industrial applications Life Sciences Mannitol Marine environment Microbial Genetics and Genomics Microbiology nanopores Phenotypes Phenotypic variations Positive selection Saccharomyces cerevisiae Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism Saccharomycetales - classification Saccharomycetales - genetics Saccharomycetales - metabolism Salinity tolerance salt tolerance Scanning electron microscopy Scheffersomyces Seawater Seawater - microbiology Sorbitol Spartina spartinae species Telomeres tRNA Water analysis Whole Genome Sequencing xylose Yeast Yeasts |
| title | Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae |
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