A census of nuclear cyanobacterial recruits in the plant kingdom
The plastids and mitochondria of the eukaryotic cell are of endosymbiotic origin. These events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. Previous studies demonstrated that the invasion of land affected plastids and mitochondria di...
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creator | Makai, Szabolcs Li, Xiao Hussain, Javeed Cui, Cuiju Wang, Yuesheng Chen, Mingjie Yang, Zhaowan Ma, Chuang Guo, An-Yuan Zhou, Yanhong Chang, Junli Yang, Guangxiao He, Guangyuan |
description | The plastids and mitochondria of the eukaryotic cell are of endosymbiotic origin. These events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. Previous studies demonstrated that the invasion of land affected plastids and mitochondria differently and that the paths of mitochondrial integration differed between animals and plants. Other studies examined the reasons why a set of proteins remained encoded in the organelles and were not transferred to the nuclear genome. However, our understanding of the functional relations of the transferred genes is insufficient. In this paper, we report a high-throughput phylogenetic analysis to identify genes of cyanobacterial origin for plants of different levels of complexity: Arabidopsis thaliana, Chlamydomonas reinhardtii, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorffii, Sorghum bicolor, Oryza sativa, and Ostreococcus tauri. Thus, a census of cyanobacterial gene recruits and a study of their function are presented to better understand the functional aspects of plastid symbiogenesis. From algae to angiosperms, the GO terms demonstrated a gradual expansion over functionally related genes in the nuclear genome, beginning with genes related to thylakoids and photosynthesis, followed by genes involved in metabolism, and finally with regulation-related genes, primarily in angiosperms. The results demonstrate that DNA is supplied to the nuclear genome on a permanent basis with no regard to function, and only what is needed is kept, which thereby expands on the GO space along the related genes. |
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These events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. Previous studies demonstrated that the invasion of land affected plastids and mitochondria differently and that the paths of mitochondrial integration differed between animals and plants. Other studies examined the reasons why a set of proteins remained encoded in the organelles and were not transferred to the nuclear genome. However, our understanding of the functional relations of the transferred genes is insufficient. In this paper, we report a high-throughput phylogenetic analysis to identify genes of cyanobacterial origin for plants of different levels of complexity: Arabidopsis thaliana, Chlamydomonas reinhardtii, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorffii, Sorghum bicolor, Oryza sativa, and Ostreococcus tauri. Thus, a census of cyanobacterial gene recruits and a study of their function are presented to better understand the functional aspects of plastid symbiogenesis. From algae to angiosperms, the GO terms demonstrated a gradual expansion over functionally related genes in the nuclear genome, beginning with genes related to thylakoids and photosynthesis, followed by genes involved in metabolism, and finally with regulation-related genes, primarily in angiosperms. The results demonstrate that DNA is supplied to the nuclear genome on a permanent basis with no regard to function, and only what is needed is kept, which thereby expands on the GO space along the related genes.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0120527</identifier><identifier>PMID: 25794152</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algae ; Analysis ; Angiosperms ; Arabidopsis thaliana ; Bioinformatics ; Biophysics ; Census ; Chlamydomonas reinhardtii ; Chloroplasts ; Cyanobacteria ; Cyanobacteria - classification ; Cyanobacteria - genetics ; Deoxyribonucleic acid ; DNA ; Education ; Evolution ; Gene expression ; Gene regulation ; Gene Transfer, Horizontal ; Genes ; Genetic engineering ; Genetic Variation ; Genome ; Genome, Mitochondrial ; Genome, Plastid ; Genomes ; Genomics ; Hypotheses ; International cooperation ; Laboratories ; Life sciences ; Metabolism ; Mitochondria ; Mitochondrial DNA ; Organelles ; Oryza sativa ; Ostreococcus tauri ; Photosynthesis ; Phylogeny ; Physcomitrella patens ; Physiological aspects ; Plants - genetics ; Plastids ; Plastids - genetics ; Populus balsamifera trichocarpa ; Proteins ; Selaginella moellendorffii ; Sorghum ; Sorghum bicolor ; Symbiosis ; Thylakoids</subject><ispartof>PloS one, 2015-03, Vol.10 (3), p.e0120527-e0120527</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Makai et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Makai et al 2015 Makai et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c641t-861a5119114e92f27b0dbe6262ffb8e9653ddee23e35b21b752b2fdc8c8d8c723</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/PMC4368824/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368824/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25794152$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Tian, Zhixi</contributor><creatorcontrib>Makai, Szabolcs</creatorcontrib><creatorcontrib>Li, Xiao</creatorcontrib><creatorcontrib>Hussain, Javeed</creatorcontrib><creatorcontrib>Cui, Cuiju</creatorcontrib><creatorcontrib>Wang, Yuesheng</creatorcontrib><creatorcontrib>Chen, Mingjie</creatorcontrib><creatorcontrib>Yang, Zhaowan</creatorcontrib><creatorcontrib>Ma, Chuang</creatorcontrib><creatorcontrib>Guo, An-Yuan</creatorcontrib><creatorcontrib>Zhou, Yanhong</creatorcontrib><creatorcontrib>Chang, Junli</creatorcontrib><creatorcontrib>Yang, Guangxiao</creatorcontrib><creatorcontrib>He, Guangyuan</creatorcontrib><title>A census of nuclear cyanobacterial recruits in the plant kingdom</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The plastids and mitochondria of the eukaryotic cell are of endosymbiotic origin. These events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. Previous studies demonstrated that the invasion of land affected plastids and mitochondria differently and that the paths of mitochondrial integration differed between animals and plants. Other studies examined the reasons why a set of proteins remained encoded in the organelles and were not transferred to the nuclear genome. However, our understanding of the functional relations of the transferred genes is insufficient. In this paper, we report a high-throughput phylogenetic analysis to identify genes of cyanobacterial origin for plants of different levels of complexity: Arabidopsis thaliana, Chlamydomonas reinhardtii, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorffii, Sorghum bicolor, Oryza sativa, and Ostreococcus tauri. Thus, a census of cyanobacterial gene recruits and a study of their function are presented to better understand the functional aspects of plastid symbiogenesis. From algae to angiosperms, the GO terms demonstrated a gradual expansion over functionally related genes in the nuclear genome, beginning with genes related to thylakoids and photosynthesis, followed by genes involved in metabolism, and finally with regulation-related genes, primarily in angiosperms. The results demonstrate that DNA is supplied to the nuclear genome on a permanent basis with no regard to function, and only what is needed is kept, which thereby expands on the GO space along the related genes.</description><subject>Algae</subject><subject>Analysis</subject><subject>Angiosperms</subject><subject>Arabidopsis thaliana</subject><subject>Bioinformatics</subject><subject>Biophysics</subject><subject>Census</subject><subject>Chlamydomonas reinhardtii</subject><subject>Chloroplasts</subject><subject>Cyanobacteria</subject><subject>Cyanobacteria - classification</subject><subject>Cyanobacteria - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Education</subject><subject>Evolution</subject><subject>Gene expression</subject><subject>Gene regulation</subject><subject>Gene Transfer, Horizontal</subject><subject>Genes</subject><subject>Genetic engineering</subject><subject>Genetic Variation</subject><subject>Genome</subject><subject>Genome, Mitochondrial</subject><subject>Genome, Plastid</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Hypotheses</subject><subject>International cooperation</subject><subject>Laboratories</subject><subject>Life sciences</subject><subject>Metabolism</subject><subject>Mitochondria</subject><subject>Mitochondrial DNA</subject><subject>Organelles</subject><subject>Oryza sativa</subject><subject>Ostreococcus tauri</subject><subject>Photosynthesis</subject><subject>Phylogeny</subject><subject>Physcomitrella patens</subject><subject>Physiological aspects</subject><subject>Plants - genetics</subject><subject>Plastids</subject><subject>Plastids - genetics</subject><subject>Populus balsamifera trichocarpa</subject><subject>Proteins</subject><subject>Selaginella moellendorffii</subject><subject>Sorghum</subject><subject>Sorghum bicolor</subject><subject>Symbiosis</subject><subject>Thylakoids</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl1v0zAYhSMEYmPwDxBEQkJw0RJ_xr5BVBMflSZN4uvWsp03rUsad7aD2L_HXbOpQbtAuUhkP-fY580piueomiNSo3cbP4Red_Od72FeIVwxXD8oTpEkeMZxRR4efZ8UT2LcVBUjgvPHxQlmtaSI4dPiw6K00Mchlr4t-8F2oENpr3XvjbYJgtNdGcCGwaVYur5Mayh3ne5T-cv1q8ZvnxaPWt1FeDa-z4ofnz5-P_8yu7j8vDxfXMwspyjNBEeaISQRoiBxi2tTNQY45rhtjQDJGWkaAEyAMIORqRk2uG2ssKIRtsbkrHh58N11PqoxfFSIcyoJwohlYnkgGq83ahfcVodr5bVTNws-rJQOyeWIivDKIEEkSF1TzZGRYBnTktSUcGZI9no_njaYLTR5RCnobmI63endWq38b5X1QmCaDd6MBsFfDRCT2rpoocujAz_c3JtjSaXYJ3v1D3p_upFa6RzA9a3P59q9qVpQTASTlKFMze-h8tPA1tnclNbl9Yng7USQmQR_0koPMarlt6__z17-nLKvj9g16C6to--G5HwfpyA9gDb4GAO0d0NGldoX_XYaal90NRY9y14c_6A70W2zyV9IS_aN</recordid><startdate>20150320</startdate><enddate>20150320</enddate><creator>Makai, Szabolcs</creator><creator>Li, Xiao</creator><creator>Hussain, Javeed</creator><creator>Cui, Cuiju</creator><creator>Wang, Yuesheng</creator><creator>Chen, Mingjie</creator><creator>Yang, Zhaowan</creator><creator>Ma, Chuang</creator><creator>Guo, An-Yuan</creator><creator>Zhou, Yanhong</creator><creator>Chang, Junli</creator><creator>Yang, Guangxiao</creator><creator>He, Guangyuan</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150320</creationdate><title>A census of nuclear cyanobacterial recruits in the plant kingdom</title><author>Makai, Szabolcs ; Li, Xiao ; Hussain, Javeed ; Cui, Cuiju ; Wang, Yuesheng ; Chen, Mingjie ; Yang, Zhaowan ; Ma, Chuang ; Guo, An-Yuan ; Zhou, Yanhong ; Chang, Junli ; Yang, Guangxiao ; He, Guangyuan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c641t-861a5119114e92f27b0dbe6262ffb8e9653ddee23e35b21b752b2fdc8c8d8c723</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Algae</topic><topic>Analysis</topic><topic>Angiosperms</topic><topic>Arabidopsis thaliana</topic><topic>Bioinformatics</topic><topic>Biophysics</topic><topic>Census</topic><topic>Chlamydomonas reinhardtii</topic><topic>Chloroplasts</topic><topic>Cyanobacteria</topic><topic>Cyanobacteria - classification</topic><topic>Cyanobacteria - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Education</topic><topic>Evolution</topic><topic>Gene expression</topic><topic>Gene regulation</topic><topic>Gene Transfer, Horizontal</topic><topic>Genes</topic><topic>Genetic engineering</topic><topic>Genetic Variation</topic><topic>Genome</topic><topic>Genome, Mitochondrial</topic><topic>Genome, Plastid</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Hypotheses</topic><topic>International cooperation</topic><topic>Laboratories</topic><topic>Life sciences</topic><topic>Metabolism</topic><topic>Mitochondria</topic><topic>Mitochondrial DNA</topic><topic>Organelles</topic><topic>Oryza sativa</topic><topic>Ostreococcus tauri</topic><topic>Photosynthesis</topic><topic>Phylogeny</topic><topic>Physcomitrella patens</topic><topic>Physiological aspects</topic><topic>Plants - genetics</topic><topic>Plastids</topic><topic>Plastids - genetics</topic><topic>Populus balsamifera trichocarpa</topic><topic>Proteins</topic><topic>Selaginella moellendorffii</topic><topic>Sorghum</topic><topic>Sorghum bicolor</topic><topic>Symbiosis</topic><topic>Thylakoids</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Makai, Szabolcs</creatorcontrib><creatorcontrib>Li, Xiao</creatorcontrib><creatorcontrib>Hussain, Javeed</creatorcontrib><creatorcontrib>Cui, Cuiju</creatorcontrib><creatorcontrib>Wang, Yuesheng</creatorcontrib><creatorcontrib>Chen, Mingjie</creatorcontrib><creatorcontrib>Yang, Zhaowan</creatorcontrib><creatorcontrib>Ma, Chuang</creatorcontrib><creatorcontrib>Guo, An-Yuan</creatorcontrib><creatorcontrib>Zhou, Yanhong</creatorcontrib><creatorcontrib>Chang, Junli</creatorcontrib><creatorcontrib>Yang, Guangxiao</creatorcontrib><creatorcontrib>He, Guangyuan</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Opposing Viewpoints in Context (Gale)</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>ProQuest Nursing and Allied Health Journals</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Health and Medical</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database (Proquest)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Database (1962 - 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Thus, a census of cyanobacterial gene recruits and a study of their function are presented to better understand the functional aspects of plastid symbiogenesis. From algae to angiosperms, the GO terms demonstrated a gradual expansion over functionally related genes in the nuclear genome, beginning with genes related to thylakoids and photosynthesis, followed by genes involved in metabolism, and finally with regulation-related genes, primarily in angiosperms. The results demonstrate that DNA is supplied to the nuclear genome on a permanent basis with no regard to function, and only what is needed is kept, which thereby expands on the GO space along the related genes.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25794152</pmid><doi>10.1371/journal.pone.0120527</doi><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; PubMed Central(OpenAccess); Public Library of Science; Free E-Journal (出版社公開部分のみ); Directory of Open Access Journals; Free Full-Text Journals in Chemistry |
subjects | Algae Analysis Angiosperms Arabidopsis thaliana Bioinformatics Biophysics Census Chlamydomonas reinhardtii Chloroplasts Cyanobacteria Cyanobacteria - classification Cyanobacteria - genetics Deoxyribonucleic acid DNA Education Evolution Gene expression Gene regulation Gene Transfer, Horizontal Genes Genetic engineering Genetic Variation Genome Genome, Mitochondrial Genome, Plastid Genomes Genomics Hypotheses International cooperation Laboratories Life sciences Metabolism Mitochondria Mitochondrial DNA Organelles Oryza sativa Ostreococcus tauri Photosynthesis Phylogeny Physcomitrella patens Physiological aspects Plants - genetics Plastids Plastids - genetics Populus balsamifera trichocarpa Proteins Selaginella moellendorffii Sorghum Sorghum bicolor Symbiosis Thylakoids |
title | A census of nuclear cyanobacterial recruits in the plant kingdom |
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