Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein‐coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncod...
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| Veröffentlicht in: | Ecology and evolution 2020-12, Vol.10 (23), p.12817-12837 |
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| creator | Jiang, Lichun Zhang, Min Deng, Lu Xu, Zhongwen Shi, Hongyan Jia, Xiaodong Lai, Zhenli Ruan, Qiping Chen, Wei |
| description | The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein‐coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6‐trnE‐Cytb‐D‐loop‐trnL2 (CUN)‐ND5‐D‐loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6‐ trnE‐ Cytb‐ D‐ loop‐ trnL2 (CUN) ‐ ND5‐ D‐ loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species. |
| doi_str_mv | 10.1002/ece3.6824 |
| format | Article |
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The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6‐ trnE‐ Cytb‐ D‐ loop‐ trnL2 (CUN) ‐ ND5‐ D‐ loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.</description><identifier>ISSN: 2045-7758</identifier><identifier>EISSN: 2045-7758</identifier><identifier>DOI: 10.1002/ece3.6824</identifier><identifier>PMID: 33304496</identifier><language>eng</language><publisher>HOBOKEN: Wiley</publisher><subject>Amphibians ; Base composition ; control region ; Deoxyribonucleic acid ; DNA ; Ecology ; Endangered & extinct species ; Environmental Sciences & Ecology ; Evolutionary Biology ; Frogs ; Gene rearrangement ; gene rearrangements ; Genes ; Genetic variability ; Genomes ; Life Sciences & Biomedicine ; Mitochondria ; Mitochondrial DNA ; mitochondrial genome ; Original Research ; Phylogenetics ; Phylogeny ; protein‐coding genes ; Rana chaochiaoensis ; Rana omeimontis ; Ranidae ; rRNA ; Science & Technology ; Software ; Species ; tRNA</subject><ispartof>Ecology and evolution, 2020-12, Vol.10 (23), p.12817-12837</ispartof><rights>2020 The Authors. published by John Wiley & Sons Ltd.</rights><rights>2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.</rights><rights>2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>5</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000582978800001</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c4434-944e3e8bd4d7d566831626f4beb326f402e4114e5baf8d88cd0090a9d5037363</citedby><cites>FETCH-LOGICAL-c4434-944e3e8bd4d7d566831626f4beb326f402e4114e5baf8d88cd0090a9d5037363</cites><orcidid>0000-0001-7437-3238 ; 0000-0002-0150-3000</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7713938/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7713938/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,1418,2115,11566,27928,27929,45578,45579,46056,46480,53795,53797</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33304496$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Jiang, Lichun</creatorcontrib><creatorcontrib>Zhang, Min</creatorcontrib><creatorcontrib>Deng, Lu</creatorcontrib><creatorcontrib>Xu, Zhongwen</creatorcontrib><creatorcontrib>Shi, Hongyan</creatorcontrib><creatorcontrib>Jia, Xiaodong</creatorcontrib><creatorcontrib>Lai, Zhenli</creatorcontrib><creatorcontrib>Ruan, Qiping</creatorcontrib><creatorcontrib>Chen, Wei</creatorcontrib><title>Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships</title><title>Ecology and evolution</title><addtitle>ECOL EVOL</addtitle><addtitle>Ecol Evol</addtitle><description>The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein‐coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6‐trnE‐Cytb‐D‐loop‐trnL2 (CUN)‐ND5‐D‐loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6‐ trnE‐ Cytb‐ D‐ loop‐ trnL2 (CUN) ‐ ND5‐ D‐ loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.</description><subject>Amphibians</subject><subject>Base composition</subject><subject>control region</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecology</subject><subject>Endangered & extinct species</subject><subject>Environmental Sciences & Ecology</subject><subject>Evolutionary Biology</subject><subject>Frogs</subject><subject>Gene rearrangement</subject><subject>gene rearrangements</subject><subject>Genes</subject><subject>Genetic variability</subject><subject>Genomes</subject><subject>Life Sciences & Biomedicine</subject><subject>Mitochondria</subject><subject>Mitochondrial DNA</subject><subject>mitochondrial genome</subject><subject>Original Research</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>protein‐coding genes</subject><subject>Rana chaochiaoensis</subject><subject>Rana omeimontis</subject><subject>Ranidae</subject><subject>rRNA</subject><subject>Science & 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Inc</general><scope>24P</scope><scope>WIN</scope><scope>AOWDO</scope><scope>BLEPL</scope><scope>DTL</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7X2</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M0K</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>SOI</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-7437-3238</orcidid><orcidid>https://orcid.org/0000-0002-0150-3000</orcidid></search><sort><creationdate>202012</creationdate><title>Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships</title><author>Jiang, Lichun ; Zhang, Min ; Deng, Lu ; Xu, Zhongwen ; Shi, Hongyan ; Jia, Xiaodong ; Lai, Zhenli ; Ruan, Qiping ; Chen, Wei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4434-944e3e8bd4d7d566831626f4beb326f402e4114e5baf8d88cd0090a9d5037363</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Amphibians</topic><topic>Base composition</topic><topic>control region</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Ecology</topic><topic>Endangered & extinct species</topic><topic>Environmental Sciences & Ecology</topic><topic>Evolutionary Biology</topic><topic>Frogs</topic><topic>Gene rearrangement</topic><topic>gene rearrangements</topic><topic>Genes</topic><topic>Genetic variability</topic><topic>Genomes</topic><topic>Life Sciences & Biomedicine</topic><topic>Mitochondria</topic><topic>Mitochondrial DNA</topic><topic>mitochondrial genome</topic><topic>Original Research</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>protein‐coding genes</topic><topic>Rana chaochiaoensis</topic><topic>Rana omeimontis</topic><topic>Ranidae</topic><topic>rRNA</topic><topic>Science & Technology</topic><topic>Software</topic><topic>Species</topic><topic>tRNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jiang, Lichun</creatorcontrib><creatorcontrib>Zhang, Min</creatorcontrib><creatorcontrib>Deng, Lu</creatorcontrib><creatorcontrib>Xu, Zhongwen</creatorcontrib><creatorcontrib>Shi, Hongyan</creatorcontrib><creatorcontrib>Jia, Xiaodong</creatorcontrib><creatorcontrib>Lai, Zhenli</creatorcontrib><creatorcontrib>Ruan, Qiping</creatorcontrib><creatorcontrib>Chen, Wei</creatorcontrib><collection>Wiley Online Library 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Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Ecology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jiang, Lichun</au><au>Zhang, Min</au><au>Deng, Lu</au><au>Xu, Zhongwen</au><au>Shi, Hongyan</au><au>Jia, Xiaodong</au><au>Lai, Zhenli</au><au>Ruan, Qiping</au><au>Chen, Wei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships</atitle><jtitle>Ecology and evolution</jtitle><stitle>ECOL EVOL</stitle><addtitle>Ecol Evol</addtitle><date>2020-12</date><risdate>2020</risdate><volume>10</volume><issue>23</issue><spage>12817</spage><epage>12837</epage><pages>12817-12837</pages><issn>2045-7758</issn><eissn>2045-7758</eissn><abstract>The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein‐coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6‐trnE‐Cytb‐D‐loop‐trnL2 (CUN)‐ND5‐D‐loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6‐ trnE‐ Cytb‐ D‐ loop‐ trnL2 (CUN) ‐ ND5‐ D‐ loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.</abstract><cop>HOBOKEN</cop><pub>Wiley</pub><pmid>33304496</pmid><doi>10.1002/ece3.6824</doi><tpages>21</tpages><orcidid>https://orcid.org/0000-0001-7437-3238</orcidid><orcidid>https://orcid.org/0000-0002-0150-3000</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Wiley Online Library - AutoHoldings Journals; PubMed Central Free; DOAJ Directory of Open Access Journals; Wiley Online Library Open Access; EZB-FREE-00999 freely available EZB journals |
| subjects | Amphibians Base composition control region Deoxyribonucleic acid DNA Ecology Endangered & extinct species Environmental Sciences & Ecology Evolutionary Biology Frogs Gene rearrangement gene rearrangements Genes Genetic variability Genomes Life Sciences & Biomedicine Mitochondria Mitochondrial DNA mitochondrial genome Original Research Phylogenetics Phylogeny protein‐coding genes Rana chaochiaoensis Rana omeimontis Ranidae rRNA Science & Technology Software Species tRNA |
| title | Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships |
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