Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population
The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of t...
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| description | The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome in a group of Maoris in an effort to characterise genome variation in this Polynesian population for use in future disease association studies. We sequenced the complete mitochondrial genomes of 20 non-admixed Maori subjects using Affymetrix technology. DNA diversity analyses showed the Maori group exhibited reduced mitochondrial genome diversity compared to other worldwide populations, which is consistent with historical bottleneck and founder effects. Global phylogenetic analysis positioned these Maori subjects specifically within mitochondrial haplogroup--B4a1a1. Interestingly, we identified several novel variants that collectively form new and unique Maori motifs--B4a1a1c, B4a1a1a3 and B4a1a1a5. Compared to ancestral populations we observed an increased frequency of non-synonymous coding variants of several mitochondrial genes in the Maori group, which may be a result of positive selection and/or genetic drift effects. In conclusion, this study reports the first complete mitochondrial genome sequence data for a Maori population. Overall, these new data reveal novel mitochondrial genome signatures in this Polynesian population and enhance the phylogenetic picture of maternal ancestry in Oceania. The increased frequency of several mitochondrial coding variants makes them good candidates for future studies aimed at assessment of metabolic disease risk in Polynesian populations. |
| doi_str_mv | 10.1371/journal.pone.0035026 |
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The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome in a group of Maoris in an effort to characterise genome variation in this Polynesian population for use in future disease association studies. We sequenced the complete mitochondrial genomes of 20 non-admixed Maori subjects using Affymetrix technology. DNA diversity analyses showed the Maori group exhibited reduced mitochondrial genome diversity compared to other worldwide populations, which is consistent with historical bottleneck and founder effects. Global phylogenetic analysis positioned these Maori subjects specifically within mitochondrial haplogroup--B4a1a1. Interestingly, we identified several novel variants that collectively form new and unique Maori motifs--B4a1a1c, B4a1a1a3 and B4a1a1a5. Compared to ancestral populations we observed an increased frequency of non-synonymous coding variants of several mitochondrial genes in the Maori group, which may be a result of positive selection and/or genetic drift effects. In conclusion, this study reports the first complete mitochondrial genome sequence data for a Maori population. Overall, these new data reveal novel mitochondrial genome signatures in this Polynesian population and enhance the phylogenetic picture of maternal ancestry in Oceania. The increased frequency of several mitochondrial coding variants makes them good candidates for future studies aimed at assessment of metabolic disease risk in Polynesian populations.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0035026</identifier><identifier>PMID: 22514703</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Archaeology ; Biology ; Cladistic analysis ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DNA, Mitochondrial - genetics ; Energy metabolism ; Environmental science ; Evolution ; Gene sequencing ; Genes ; Genetic diversity ; Genetic drift ; Genetic variance ; Genetics ; Genetics, Population ; Genome, Mitochondrial - genetics ; Genomes ; Genomics ; Haplotypes ; Haplotypes - genetics ; Health risks ; Humans ; Maoris ; Medical research ; Medicine ; Medicine, Experimental ; Metabolic disorders ; Metabolism ; Migration ; Mitochondria ; Mitochondrial DNA ; Molecular biology ; Native peoples ; Nucleotide sequence ; Nucleotide sequencing ; Phylogenetics ; Phylogeny ; Population ; Population genetics ; Populations ; Positive selection ; Sequence Analysis, DNA ; Studies ; Technology assessment ; Type 2 diabetes</subject><ispartof>PloS one, 2012-04, Vol.7 (4), p.e35026</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Benton et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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>Benton et al. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-60a189bb2611975aef3cd93db55ccab207cf4b36733863aafc21e757f51f80ad3</citedby><cites>FETCH-LOGICAL-c692t-60a189bb2611975aef3cd93db55ccab207cf4b36733863aafc21e757f51f80ad3</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/PMC3325929/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325929/$$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/22514703$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Kayser, Manfred</contributor><creatorcontrib>Benton, Miles</creatorcontrib><creatorcontrib>Macartney-Coxson, Donia</creatorcontrib><creatorcontrib>Eccles, David</creatorcontrib><creatorcontrib>Griffiths, Lyn</creatorcontrib><creatorcontrib>Chambers, Geoff</creatorcontrib><creatorcontrib>Lea, Rod</creatorcontrib><title>Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome in a group of Maoris in an effort to characterise genome variation in this Polynesian population for use in future disease association studies. We sequenced the complete mitochondrial genomes of 20 non-admixed Maori subjects using Affymetrix technology. DNA diversity analyses showed the Maori group exhibited reduced mitochondrial genome diversity compared to other worldwide populations, which is consistent with historical bottleneck and founder effects. Global phylogenetic analysis positioned these Maori subjects specifically within mitochondrial haplogroup--B4a1a1. Interestingly, we identified several novel variants that collectively form new and unique Maori motifs--B4a1a1c, B4a1a1a3 and B4a1a1a5. Compared to ancestral populations we observed an increased frequency of non-synonymous coding variants of several mitochondrial genes in the Maori group, which may be a result of positive selection and/or genetic drift effects. In conclusion, this study reports the first complete mitochondrial genome sequence data for a Maori population. Overall, these new data reveal novel mitochondrial genome signatures in this Polynesian population and enhance the phylogenetic picture of maternal ancestry in Oceania. The increased frequency of several mitochondrial coding variants makes them good candidates for future studies aimed at assessment of metabolic disease risk in Polynesian populations.</description><subject>Analysis</subject><subject>Archaeology</subject><subject>Biology</subject><subject>Cladistic analysis</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Energy metabolism</subject><subject>Environmental science</subject><subject>Evolution</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic diversity</subject><subject>Genetic drift</subject><subject>Genetic variance</subject><subject>Genetics</subject><subject>Genetics, Population</subject><subject>Genome, Mitochondrial - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Haplotypes</subject><subject>Haplotypes - genetics</subject><subject>Health 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Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Benton, Miles</au><au>Macartney-Coxson, Donia</au><au>Eccles, David</au><au>Griffiths, Lyn</au><au>Chambers, Geoff</au><au>Lea, Rod</au><au>Kayser, Manfred</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-04-13</date><risdate>2012</risdate><volume>7</volume><issue>4</issue><spage>e35026</spage><pages>e35026-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome in a group of Maoris in an effort to characterise genome variation in this Polynesian population for use in future disease association studies. We sequenced the complete mitochondrial genomes of 20 non-admixed Maori subjects using Affymetrix technology. DNA diversity analyses showed the Maori group exhibited reduced mitochondrial genome diversity compared to other worldwide populations, which is consistent with historical bottleneck and founder effects. Global phylogenetic analysis positioned these Maori subjects specifically within mitochondrial haplogroup--B4a1a1. Interestingly, we identified several novel variants that collectively form new and unique Maori motifs--B4a1a1c, B4a1a1a3 and B4a1a1a5. Compared to ancestral populations we observed an increased frequency of non-synonymous coding variants of several mitochondrial genes in the Maori group, which may be a result of positive selection and/or genetic drift effects. In conclusion, this study reports the first complete mitochondrial genome sequence data for a Maori population. Overall, these new data reveal novel mitochondrial genome signatures in this Polynesian population and enhance the phylogenetic picture of maternal ancestry in Oceania. The increased frequency of several mitochondrial coding variants makes them good candidates for future studies aimed at assessment of metabolic disease risk in Polynesian populations.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22514703</pmid><doi>10.1371/journal.pone.0035026</doi><tpages>e35026</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Archaeology Biology Cladistic analysis Deoxyribonucleic acid DNA DNA sequencing DNA, Mitochondrial - genetics Energy metabolism Environmental science Evolution Gene sequencing Genes Genetic diversity Genetic drift Genetic variance Genetics Genetics, Population Genome, Mitochondrial - genetics Genomes Genomics Haplotypes Haplotypes - genetics Health risks Humans Maoris Medical research Medicine Medicine, Experimental Metabolic disorders Metabolism Migration Mitochondria Mitochondrial DNA Molecular biology Native peoples Nucleotide sequence Nucleotide sequencing Phylogenetics Phylogeny Population Population genetics Populations Positive selection Sequence Analysis, DNA Studies Technology assessment Type 2 diabetes |
| title | Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population |
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