Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes
Abstract Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,42...
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Veröffentlicht in: | Genome biology and evolution 2020-04, Vol.12 (4), p.282-292 |
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Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups. |
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Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.</description><identifier>ISSN: 1759-6653</identifier><identifier>EISSN: 1759-6653</identifier><identifier>DOI: 10.1093/gbe/evaa047</identifier><identifier>PMID: 32142116</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Archaea - genetics ; Bacteria - genetics ; Biological Evolution ; Eukaryota - genetics ; Genes, Archaeal ; Genes, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Phylogeny</subject><ispartof>Genome biology and evolution, 2020-04, Vol.12 (4), p.282-292</ispartof><rights>The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c412t-df546b36197ced73bc42e251dda30964671a7437ca01ed48d236c5742e1d226f3</citedby><cites>FETCH-LOGICAL-c412t-df546b36197ced73bc42e251dda30964671a7437ca01ed48d236c5742e1d226f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151554/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151554/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32142116$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Brueckner, Julia</creatorcontrib><creatorcontrib>Martin, William F</creatorcontrib><title>Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes</title><title>Genome biology and evolution</title><addtitle>Genome Biol Evol</addtitle><description>Abstract
Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.</description><subject>Archaea - genetics</subject><subject>Bacteria - genetics</subject><subject>Biological Evolution</subject><subject>Eukaryota - genetics</subject><subject>Genes, Archaeal</subject><subject>Genes, Bacterial</subject><subject>Genome, Archaeal</subject><subject>Genome, Bacterial</subject><subject>Phylogeny</subject><issn>1759-6653</issn><issn>1759-6653</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kM1Lw0AQxRdRbK2evEtOIkhs9iO7zUWopVah0Iuel83upI0m2bqbFPzv3dJa6sXTDPN-vHk8hK5x8oCTjA6XOQxho1TCxAnqY5FmMecpPT3ae-jC-48k4Zxxeo56lGBGMOZ99PikdAuuVFU0gwZ8tOjapqtzcNHY6ZWCg1A20bT7VO7btqXe3mwN_hKdFarycLWfA_T-PH2bvMTzxex1Mp7HmmHSxqZIGc8px5nQYATNNSNAUmyMokkWQgmsBKNCqwSDYSNDKNepCBA2hPCCDtDjznfd5TUYDU3rVCXXrqxDImlVKf8qTbmSS7uRAqc4TVkwuNsbOPvVgW9lXXoNVaUasJ2XhIb_lBA2Cuj9DtXOeu-gOLzBidw2LkPjct94oG-Okx3Y34oDcLsDbLf-1-kHwXqKPA</recordid><startdate>20200401</startdate><enddate>20200401</enddate><creator>Brueckner, Julia</creator><creator>Martin, William F</creator><general>Oxford University Press</general><scope>TOX</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>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200401</creationdate><title>Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes</title><author>Brueckner, Julia ; Martin, William F</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-df546b36197ced73bc42e251dda30964671a7437ca01ed48d236c5742e1d226f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Archaea - genetics</topic><topic>Bacteria - genetics</topic><topic>Biological Evolution</topic><topic>Eukaryota - genetics</topic><topic>Genes, Archaeal</topic><topic>Genes, Bacterial</topic><topic>Genome, Archaeal</topic><topic>Genome, Bacterial</topic><topic>Phylogeny</topic><toplevel>online_resources</toplevel><creatorcontrib>Brueckner, Julia</creatorcontrib><creatorcontrib>Martin, William F</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Brueckner, Julia</au><au>Martin, William F</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes</atitle><jtitle>Genome biology and evolution</jtitle><addtitle>Genome Biol Evol</addtitle><date>2020-04-01</date><risdate>2020</risdate><volume>12</volume><issue>4</issue><spage>282</spage><epage>292</epage><pages>282-292</pages><issn>1759-6653</issn><eissn>1759-6653</eissn><abstract>Abstract
Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>32142116</pmid><doi>10.1093/gbe/evaa047</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Archaea - genetics Bacteria - genetics Biological Evolution Eukaryota - genetics Genes, Archaeal Genes, Bacterial Genome, Archaeal Genome, Bacterial Phylogeny |
title | Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes |
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