Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1
We report the sequence of the Halobacterium salinarum strain R1 chromosome and its four megaplasmids. Our set of protein-coding genes is supported by extensive proteomic and sequence homology data. The structures of the plasmids, which show three large-scale duplications (adding up to 100 kb), were...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2008-04, Vol.91 (4), p.335-346 |
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| creator | Pfeiffer, F. Schuster, S.C. Broicher, A. Falb, M. Palm, P. Rodewald, K. Ruepp, A. Soppa, J. Tittor, J. Oesterhelt, D. |
| description | We report the sequence of the
Halobacterium salinarum strain R1 chromosome and its four megaplasmids. Our set of protein-coding genes is supported by extensive proteomic and sequence homology data. The structures of the plasmids, which show three large-scale duplications (adding up to 100 kb), were unequivocally confirmed by cosmid analysis. The chromosome of strain R1 is completely colinear and virtually identical to that of strain NRC-1. Correlation of the plasmid sequences revealed 210 kb of sequence that occurs only in strain R1. The remaining 350 kb shows virtual sequence identity in the two strains. Nevertheless, the number and overall structure of the plasmids are largely incompatible. Also, 20% of the protein sequences differ despite the near identity at the DNA sequence level. Finally, we report genome-wide mobility data for insertion sequences from which we conclude that strains R1 and NRC-1 originate from the same natural isolate. This exemplifies evolution in the laboratory. |
| doi_str_mv | 10.1016/j.ygeno.2008.01.001 |
| format | Article |
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Halobacterium salinarum strain R1 chromosome and its four megaplasmids. Our set of protein-coding genes is supported by extensive proteomic and sequence homology data. The structures of the plasmids, which show three large-scale duplications (adding up to 100 kb), were unequivocally confirmed by cosmid analysis. The chromosome of strain R1 is completely colinear and virtually identical to that of strain NRC-1. Correlation of the plasmid sequences revealed 210 kb of sequence that occurs only in strain R1. The remaining 350 kb shows virtual sequence identity in the two strains. Nevertheless, the number and overall structure of the plasmids are largely incompatible. Also, 20% of the protein sequences differ despite the near identity at the DNA sequence level. Finally, we report genome-wide mobility data for insertion sequences from which we conclude that strains R1 and NRC-1 originate from the same natural isolate. This exemplifies evolution in the laboratory.</description><subject>Amino Acid Sequence</subject><subject>Archaea</subject><subject>Archaeal Proteins - chemistry</subject><subject>Archaeal Proteins - genetics</subject><subject>Biological and medical sciences</subject><subject>Biological Evolution</subject><subject>Chromosomes, Archaeal</subject><subject>Comparative genomics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome sequence</subject><subject>Genome, Archaeal</subject><subject>Halobacterium salinarum</subject><subject>Halobacterium salinarum - genetics</subject><subject>Halobacterium salinarum; Insertion sequence</subject><subject>Halophilicity</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Molecular Sequence Data</subject><subject>Plasmids</subject><subject>Sequence Homology, Amino Acid</subject><subject>Species Specificity</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkV-L1DAUxYMo7jj6CQTJi7613vxrUsEHGVZXWBSW9TmkaaoZ2mZM0oX59qZO0Td9SsL9nXPDOQi9JFATIM3bY33-7uZQUwBVA6kByCO0I6DaSjW8eYx2oJSqpODsCj1L6QgALVP0KboiihGmWrFD0_VDGJfsw4z9jPMPh0fThWhyiOd3-L681x2Tw2HAN2YMnbHZRb9MOJnRzyautxxNEd8RbMN0MtH1OIfiZfKq2qZf7g4VeY6eDGZM7sV27tG3j9f3h5vq9uunz4cPt5XlDcsVEcwJbokyknLFKOOCUiqUAilFQ6HlZdzRznJqGeWNbUFCz3vJWwZODWyP3lx8TzH8XFzKevLJunE0swtL0hI4J0zI_4IUpAJVEtwjdgFtDClFN-hT9JOJZ01Ar3Xoo_5dh17r0EB0qaOoXm32Sze5_q9my78ArzfAJGvGIZrZ-vSHo0BFy9W6_v2FcyW1B--iTta72breR2ez7oP_50d-AaBCp0E</recordid><startdate>20080401</startdate><enddate>20080401</enddate><creator>Pfeiffer, F.</creator><creator>Schuster, S.C.</creator><creator>Broicher, A.</creator><creator>Falb, M.</creator><creator>Palm, P.</creator><creator>Rodewald, K.</creator><creator>Ruepp, A.</creator><creator>Soppa, J.</creator><creator>Tittor, J.</creator><creator>Oesterhelt, D.</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>IQODW</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>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20080401</creationdate><title>Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1</title><author>Pfeiffer, F. ; Schuster, S.C. ; Broicher, A. ; Falb, M. ; Palm, P. ; Rodewald, K. ; Ruepp, A. ; Soppa, J. ; Tittor, J. ; Oesterhelt, D.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c463t-153e54c18a724832345222588077562094e54b2bc42c3246c9070d4d74930e8f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Amino Acid Sequence</topic><topic>Archaea</topic><topic>Archaeal Proteins - chemistry</topic><topic>Archaeal Proteins - genetics</topic><topic>Biological and medical sciences</topic><topic>Biological Evolution</topic><topic>Chromosomes, Archaeal</topic><topic>Comparative genomics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome sequence</topic><topic>Genome, Archaeal</topic><topic>Halobacterium salinarum</topic><topic>Halobacterium salinarum - genetics</topic><topic>Halobacterium salinarum; Insertion sequence</topic><topic>Halophilicity</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Molecular Sequence Data</topic><topic>Plasmids</topic><topic>Sequence Homology, Amino Acid</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pfeiffer, F.</creatorcontrib><creatorcontrib>Schuster, S.C.</creatorcontrib><creatorcontrib>Broicher, A.</creatorcontrib><creatorcontrib>Falb, M.</creatorcontrib><creatorcontrib>Palm, P.</creatorcontrib><creatorcontrib>Rodewald, K.</creatorcontrib><creatorcontrib>Ruepp, A.</creatorcontrib><creatorcontrib>Soppa, J.</creatorcontrib><creatorcontrib>Tittor, J.</creatorcontrib><creatorcontrib>Oesterhelt, D.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pfeiffer, F.</au><au>Schuster, S.C.</au><au>Broicher, A.</au><au>Falb, M.</au><au>Palm, P.</au><au>Rodewald, K.</au><au>Ruepp, A.</au><au>Soppa, J.</au><au>Tittor, J.</au><au>Oesterhelt, D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2008-04-01</date><risdate>2008</risdate><volume>91</volume><issue>4</issue><spage>335</spage><epage>346</epage><pages>335-346</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>We report the sequence of the
Halobacterium salinarum strain R1 chromosome and its four megaplasmids. Our set of protein-coding genes is supported by extensive proteomic and sequence homology data. The structures of the plasmids, which show three large-scale duplications (adding up to 100 kb), were unequivocally confirmed by cosmid analysis. The chromosome of strain R1 is completely colinear and virtually identical to that of strain NRC-1. Correlation of the plasmid sequences revealed 210 kb of sequence that occurs only in strain R1. The remaining 350 kb shows virtual sequence identity in the two strains. Nevertheless, the number and overall structure of the plasmids are largely incompatible. Also, 20% of the protein sequences differ despite the near identity at the DNA sequence level. Finally, we report genome-wide mobility data for insertion sequences from which we conclude that strains R1 and NRC-1 originate from the same natural isolate. This exemplifies evolution in the laboratory.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>18313895</pmid><doi>10.1016/j.ygeno.2008.01.001</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Amino Acid Sequence Archaea Archaeal Proteins - chemistry Archaeal Proteins - genetics Biological and medical sciences Biological Evolution Chromosomes, Archaeal Comparative genomics Fundamental and applied biological sciences. Psychology Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Genome sequence Genome, Archaeal Halobacterium salinarum Halobacterium salinarum - genetics Halobacterium salinarum Insertion sequence Halophilicity Molecular and cellular biology Molecular genetics Molecular Sequence Data Plasmids Sequence Homology, Amino Acid Species Specificity |
| title | Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1 |
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