Characterization of the complete mitochondrial genome of Orthaga olivacea Warre (Lepidoptera Pyralidae) and comparison with other Lepidopteran insects
Orthaga olivacea Warre (Lepidoptera: Pyralidae) is an important agricultural pest of camphor trees (Cinnamomum camphora). To further supplement the known genome-level features of related species, the complete mitochondrial genome of Orthaga olivacea is amplified, sequenced, annotated, analyzed, and...
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| Veröffentlicht in: | PloS one 2020-03, Vol.15 (3), p.e0227831-e0227831 |
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| creator | Yang, Liangli Dai, Junjun Gao, Qiuping Yuan, Guozhen Liu, Jiang Sun, Yu Sun, Yuxuan Wang, Lei Qian, Cen Zhu, Baojian Liu, Chaoliang Wei, Guoqing |
| description | Orthaga olivacea Warre (Lepidoptera: Pyralidae) is an important agricultural pest of camphor trees (Cinnamomum camphora). To further supplement the known genome-level features of related species, the complete mitochondrial genome of Orthaga olivacea is amplified, sequenced, annotated, analyzed, and compared with 58 other species of Lepidopteran. The complete sequence is 15,174 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative control region. Base composition is biased toward adenine and thymine (79.02% A+T) and A+T skew are slightly negative. Twelve of the 13 PCGs use typical ATN start codons. The exception is cytochrome oxidase 1 (cox1) that utilizes a CGA initiation codon. Nine PCGs have standard termination codon (TAA); others have incomplete stop codons, a single T or TA nucleotide. All the tRNA genes have the typical clover-leaf secondary structure, except for trnS(AGN), in which dihydrouridine (DHU) arm fails to form a stable stem-loop structure. The A+T-rich region (293 bp) contains a typical Lepidopter motifs 'ATAGA' followed by a 17 bp poly-T stretch, and a microsatellite-like (AT)13 repeat. Codon usage analysis revealed that Asn, Ile, Leu2, Lys, Tyr and Phe were the most frequently used amino acids, while Cys was the least utilized. Phylogenetic analysis suggested that among sequenced lepidopteran mitochondrial genomes, Orthaga olivacea Warre was most closely related to Hypsopygia regina, and confirmed that Orthaga olivacea Warre belongs to the Pyralidae family. |
| doi_str_mv | 10.1371/journal.pone.0227831 |
| format | Article |
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To further supplement the known genome-level features of related species, the complete mitochondrial genome of Orthaga olivacea is amplified, sequenced, annotated, analyzed, and compared with 58 other species of Lepidopteran. The complete sequence is 15,174 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative control region. Base composition is biased toward adenine and thymine (79.02% A+T) and A+T skew are slightly negative. Twelve of the 13 PCGs use typical ATN start codons. The exception is cytochrome oxidase 1 (cox1) that utilizes a CGA initiation codon. Nine PCGs have standard termination codon (TAA); others have incomplete stop codons, a single T or TA nucleotide. All the tRNA genes have the typical clover-leaf secondary structure, except for trnS(AGN), in which dihydrouridine (DHU) arm fails to form a stable stem-loop structure. The A+T-rich region (293 bp) contains a typical Lepidopter motifs 'ATAGA' followed by a 17 bp poly-T stretch, and a microsatellite-like (AT)13 repeat. Codon usage analysis revealed that Asn, Ile, Leu2, Lys, Tyr and Phe were the most frequently used amino acids, while Cys was the least utilized. Phylogenetic analysis suggested that among sequenced lepidopteran mitochondrial genomes, Orthaga olivacea Warre was most closely related to Hypsopygia regina, and confirmed that Orthaga olivacea Warre belongs to the Pyralidae family.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0227831</identifier><identifier>PMID: 32142522</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adenine ; Agricultural pests ; Amino acids ; Animals ; Base composition ; Base Sequence - genetics ; Biology and life sciences ; Camphor ; Characterization ; Cinnamomum camphora - parasitology ; Codons ; Computer and Information Sciences ; Cytochrome ; Cytochrome oxidase ; Cytochromes ; Deoxyribonucleic acid ; DNA ; Genes ; Genetic aspects ; Genome, Insect - genetics ; Genome, Mitochondrial ; Genomes ; Genomics ; Insect Control - methods ; Insects ; Lepidoptera ; Life sciences ; Mitochondria ; Mitochondrial DNA ; Moths - genetics ; Moths - pathogenicity ; Nucleotides ; Oxidases ; Pest Control, Biological - methods ; Phylogenetics ; Phylogeny ; Phylogeography ; Prejudice ; Protein structure ; Purines ; Pyralidae ; Pyrimidines ; Research and Analysis Methods ; Ribonucleic acid ; Ribosomal RNA ; RNA ; RNA, Ribosomal - genetics ; RNA, Transfer - genetics ; rRNA ; Secondary structure ; Sequence Analysis, DNA ; Thymine ; Transfer RNA ; tRNA</subject><ispartof>PloS one, 2020-03, Vol.15 (3), p.e0227831-e0227831</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Yang 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>2020 Yang et al 2020 Yang et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c593t-1b4fcae9a78c7ac7388134f45bf8d260d82b4fba233c0050680cd58a0e0767f13</citedby><cites>FETCH-LOGICAL-c593t-1b4fcae9a78c7ac7388134f45bf8d260d82b4fba233c0050680cd58a0e0767f13</cites><orcidid>0000-0001-8060-8742</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/PMC7059908/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059908/$$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/32142522$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Marcus, Jeffrey M.</contributor><creatorcontrib>Yang, Liangli</creatorcontrib><creatorcontrib>Dai, Junjun</creatorcontrib><creatorcontrib>Gao, Qiuping</creatorcontrib><creatorcontrib>Yuan, Guozhen</creatorcontrib><creatorcontrib>Liu, Jiang</creatorcontrib><creatorcontrib>Sun, Yu</creatorcontrib><creatorcontrib>Sun, Yuxuan</creatorcontrib><creatorcontrib>Wang, Lei</creatorcontrib><creatorcontrib>Qian, Cen</creatorcontrib><creatorcontrib>Zhu, Baojian</creatorcontrib><creatorcontrib>Liu, Chaoliang</creatorcontrib><creatorcontrib>Wei, Guoqing</creatorcontrib><title>Characterization of the complete mitochondrial genome of Orthaga olivacea Warre (Lepidoptera Pyralidae) and comparison with other Lepidopteran insects</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Orthaga olivacea Warre (Lepidoptera: Pyralidae) is an important agricultural pest of camphor trees (Cinnamomum camphora). To further supplement the known genome-level features of related species, the complete mitochondrial genome of Orthaga olivacea is amplified, sequenced, annotated, analyzed, and compared with 58 other species of Lepidopteran. The complete sequence is 15,174 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative control region. Base composition is biased toward adenine and thymine (79.02% A+T) and A+T skew are slightly negative. Twelve of the 13 PCGs use typical ATN start codons. The exception is cytochrome oxidase 1 (cox1) that utilizes a CGA initiation codon. Nine PCGs have standard termination codon (TAA); others have incomplete stop codons, a single T or TA nucleotide. All the tRNA genes have the typical clover-leaf secondary structure, except for trnS(AGN), in which dihydrouridine (DHU) arm fails to form a stable stem-loop structure. The A+T-rich region (293 bp) contains a typical Lepidopter motifs 'ATAGA' followed by a 17 bp poly-T stretch, and a microsatellite-like (AT)13 repeat. Codon usage analysis revealed that Asn, Ile, Leu2, Lys, Tyr and Phe were the most frequently used amino acids, while Cys was the least utilized. Phylogenetic analysis suggested that among sequenced lepidopteran mitochondrial genomes, Orthaga olivacea Warre was most closely related to Hypsopygia regina, and confirmed that Orthaga olivacea Warre belongs to the Pyralidae family.</description><subject>Adenine</subject><subject>Agricultural pests</subject><subject>Amino acids</subject><subject>Animals</subject><subject>Base composition</subject><subject>Base Sequence - genetics</subject><subject>Biology and life sciences</subject><subject>Camphor</subject><subject>Characterization</subject><subject>Cinnamomum camphora - parasitology</subject><subject>Codons</subject><subject>Computer and Information Sciences</subject><subject>Cytochrome</subject><subject>Cytochrome oxidase</subject><subject>Cytochromes</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genome, Insect - genetics</subject><subject>Genome, Mitochondrial</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Insect Control - methods</subject><subject>Insects</subject><subject>Lepidoptera</subject><subject>Life sciences</subject><subject>Mitochondria</subject><subject>Mitochondrial DNA</subject><subject>Moths - genetics</subject><subject>Moths - pathogenicity</subject><subject>Nucleotides</subject><subject>Oxidases</subject><subject>Pest Control, Biological - methods</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Phylogeography</subject><subject>Prejudice</subject><subject>Protein structure</subject><subject>Purines</subject><subject>Pyralidae</subject><subject>Pyrimidines</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>Ribosomal RNA</subject><subject>RNA</subject><subject>RNA, Ribosomal - genetics</subject><subject>RNA, Transfer - genetics</subject><subject>rRNA</subject><subject>Secondary structure</subject><subject>Sequence Analysis, DNA</subject><subject>Thymine</subject><subject>Transfer RNA</subject><subject>tRNA</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</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>eNptksuO0zAYhSMEYoaBN0Bgic2waPElcZwN0qjiMlKlYQFiaf31pXGV2MFOBw0PwvPitplRi0ZZOLK_c_6LTlG8JnhOWE0-bMI2eujmQ_BmjimtBSNPinPSMDrjFLOnR_9nxYuUNhhXTHD-vDhjlJS0ovS8-LtoIYIaTXR_YHTBo2DR2BqkQj90ZjSod2NQbfA6OujQ2vjQmx10E8cW1oBC525BGUA_IUaDLpdmcDoM2RHQt7sIndNg3iPweu8J0aVc5bcbWxRyoYiOBB45n4wa08vimYUumVfTeVH8-Pzp--LrbHnz5XpxtZypqmHjjKxKq8A0UAtVg6qZEISVtqxWVmjKsRY0EyugjKk8PeYCK10JwAbXvLaEXRRvD75DF5KcVpokZTUVFSmFyMT1gdABNnKIrod4JwM4ub8IcS0hjk51Rpqa1bkfoq21Zc1BVIwD0AbnB8V1k70-TtW2q95oZfyY93NievriXSvX4VbWuGoavGvmcjKI4dfWpFH2LinTdeBN2O77LhlpOK8y-u4_9PHpJmoNeQDnbch11c5UXnGSbSpW8kzNH6Hyp03vVM6fdfn-RFAeBCqGlKKxDzMSLHfpvW9G7tIrp_Rm2Zvj_TyI7uPK_gHdee-Y</recordid><startdate>20200306</startdate><enddate>20200306</enddate><creator>Yang, Liangli</creator><creator>Dai, Junjun</creator><creator>Gao, Qiuping</creator><creator>Yuan, Guozhen</creator><creator>Liu, Jiang</creator><creator>Sun, Yu</creator><creator>Sun, Yuxuan</creator><creator>Wang, Lei</creator><creator>Qian, Cen</creator><creator>Zhu, Baojian</creator><creator>Liu, Chaoliang</creator><creator>Wei, Guoqing</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>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><orcidid>https://orcid.org/0000-0001-8060-8742</orcidid></search><sort><creationdate>20200306</creationdate><title>Characterization of the complete mitochondrial genome of Orthaga olivacea Warre (Lepidoptera Pyralidae) and comparison with other Lepidopteran insects</title><author>Yang, Liangli ; Dai, Junjun ; Gao, Qiuping ; Yuan, Guozhen ; Liu, Jiang ; Sun, Yu ; Sun, Yuxuan ; Wang, Lei ; Qian, Cen ; Zhu, Baojian ; Liu, Chaoliang ; Wei, Guoqing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c593t-1b4fcae9a78c7ac7388134f45bf8d260d82b4fba233c0050680cd58a0e0767f13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Adenine</topic><topic>Agricultural pests</topic><topic>Amino acids</topic><topic>Animals</topic><topic>Base composition</topic><topic>Base Sequence - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yang, Liangli</au><au>Dai, Junjun</au><au>Gao, Qiuping</au><au>Yuan, Guozhen</au><au>Liu, Jiang</au><au>Sun, Yu</au><au>Sun, Yuxuan</au><au>Wang, Lei</au><au>Qian, Cen</au><au>Zhu, Baojian</au><au>Liu, Chaoliang</au><au>Wei, Guoqing</au><au>Marcus, Jeffrey M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization of the complete mitochondrial genome of Orthaga olivacea Warre (Lepidoptera Pyralidae) and comparison with other Lepidopteran insects</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2020-03-06</date><risdate>2020</risdate><volume>15</volume><issue>3</issue><spage>e0227831</spage><epage>e0227831</epage><pages>e0227831-e0227831</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Orthaga olivacea Warre (Lepidoptera: Pyralidae) is an important agricultural pest of camphor trees (Cinnamomum camphora). To further supplement the known genome-level features of related species, the complete mitochondrial genome of Orthaga olivacea is amplified, sequenced, annotated, analyzed, and compared with 58 other species of Lepidopteran. The complete sequence is 15,174 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative control region. Base composition is biased toward adenine and thymine (79.02% A+T) and A+T skew are slightly negative. Twelve of the 13 PCGs use typical ATN start codons. The exception is cytochrome oxidase 1 (cox1) that utilizes a CGA initiation codon. Nine PCGs have standard termination codon (TAA); others have incomplete stop codons, a single T or TA nucleotide. All the tRNA genes have the typical clover-leaf secondary structure, except for trnS(AGN), in which dihydrouridine (DHU) arm fails to form a stable stem-loop structure. The A+T-rich region (293 bp) contains a typical Lepidopter motifs 'ATAGA' followed by a 17 bp poly-T stretch, and a microsatellite-like (AT)13 repeat. Codon usage analysis revealed that Asn, Ile, Leu2, Lys, Tyr and Phe were the most frequently used amino acids, while Cys was the least utilized. Phylogenetic analysis suggested that among sequenced lepidopteran mitochondrial genomes, Orthaga olivacea Warre was most closely related to Hypsopygia regina, and confirmed that Orthaga olivacea Warre belongs to the Pyralidae family.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>32142522</pmid><doi>10.1371/journal.pone.0227831</doi><orcidid>https://orcid.org/0000-0001-8060-8742</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2020-03, Vol.15 (3), p.e0227831-e0227831 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2372851488 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Adenine Agricultural pests Amino acids Animals Base composition Base Sequence - genetics Biology and life sciences Camphor Characterization Cinnamomum camphora - parasitology Codons Computer and Information Sciences Cytochrome Cytochrome oxidase Cytochromes Deoxyribonucleic acid DNA Genes Genetic aspects Genome, Insect - genetics Genome, Mitochondrial Genomes Genomics Insect Control - methods Insects Lepidoptera Life sciences Mitochondria Mitochondrial DNA Moths - genetics Moths - pathogenicity Nucleotides Oxidases Pest Control, Biological - methods Phylogenetics Phylogeny Phylogeography Prejudice Protein structure Purines Pyralidae Pyrimidines Research and Analysis Methods Ribonucleic acid Ribosomal RNA RNA RNA, Ribosomal - genetics RNA, Transfer - genetics rRNA Secondary structure Sequence Analysis, DNA Thymine Transfer RNA tRNA |
| title | Characterization of the complete mitochondrial genome of Orthaga olivacea Warre (Lepidoptera Pyralidae) and comparison with other Lepidopteran insects |
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