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...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Genome biology and evolution 2020-04, Vol.12 (4), p.282-292
Hauptverfasser: Brueckner, Julia, Martin, William F
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 292
container_issue 4
container_start_page 282
container_title Genome biology and evolution
container_volume 12
creator Brueckner, Julia
Martin, William F
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.
doi_str_mv 10.1093/gbe/evaa047
format Article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7151554</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/gbe/evaa047</oup_id><sourcerecordid>2374332248</sourcerecordid><originalsourceid>FETCH-LOGICAL-c412t-df546b36197ced73bc42e251dda30964671a7437ca01ed48d236c5742e1d226f3</originalsourceid><addsrcrecordid>eNp9kM1Lw0AQxRdRbK2evEtOIkhs9iO7zUWopVah0Iuel83upI0m2bqbFPzv3dJa6sXTDPN-vHk8hK5x8oCTjA6XOQxho1TCxAnqY5FmMecpPT3ae-jC-48k4Zxxeo56lGBGMOZ99PikdAuuVFU0gwZ8tOjapqtzcNHY6ZWCg1A20bT7VO7btqXe3mwN_hKdFarycLWfA_T-PH2bvMTzxex1Mp7HmmHSxqZIGc8px5nQYATNNSNAUmyMokkWQgmsBKNCqwSDYSNDKNepCBA2hPCCDtDjznfd5TUYDU3rVCXXrqxDImlVKf8qTbmSS7uRAqc4TVkwuNsbOPvVgW9lXXoNVaUasJ2XhIb_lBA2Cuj9DtXOeu-gOLzBidw2LkPjct94oG-Okx3Y34oDcLsDbLf-1-kHwXqKPA</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2374332248</pqid></control><display><type>article</type><title>Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes</title><source>Oxford Journals Open Access Collection</source><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Brueckner, Julia ; Martin, William F</creator><creatorcontrib>Brueckner, Julia ; Martin, William F</creatorcontrib><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><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>
fulltext fulltext
identifier ISSN: 1759-6653
ispartof Genome biology and evolution, 2020-04, Vol.12 (4), p.282-292
issn 1759-6653
1759-6653
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7151554
source Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central
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
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-09T11%3A49%3A06IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Bacterial%20Genes%20Outnumber%20Archaeal%20Genes%20in%20Eukaryotic%20Genomes&rft.jtitle=Genome%20biology%20and%20evolution&rft.au=Brueckner,%20Julia&rft.date=2020-04-01&rft.volume=12&rft.issue=4&rft.spage=282&rft.epage=292&rft.pages=282-292&rft.issn=1759-6653&rft.eissn=1759-6653&rft_id=info:doi/10.1093/gbe/evaa047&rft_dat=%3Cproquest_pubme%3E2374332248%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2374332248&rft_id=info:pmid/32142116&rft_oup_id=10.1093/gbe/evaa047&rfr_iscdi=true