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Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)
We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of...
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| Published in: | PloS one 2011-02, Vol.6 (2), p.e16444-e16444 |
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| creator | Margam, Venu M Coates, Brad S Hellmich, Richard L Agunbiade, Tolulope Seufferheld, Manfredo J Sun, Weilin Ba, Malick N Sanon, Antoine Binso-Dabire, Clementine L Baoua, Ibrahim Ishiyaku, Mohammad F Covas, Fernando G Srinivasan, Ramasamy Armstrong, Joel Murdock, Larry L Pittendrigh, Barry R |
| description | We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes. |
| doi_str_mv | 10.1371/journal.pone.0016444 |
| format | article |
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The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0016444</identifier><identifier>PMID: 21311752</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agriculture ; Analysis ; Animals ; Annotations ; Arginine ; Arthropoda ; Biology ; Borers ; Chromosome Mapping ; Chromosomes, Insect ; Codon - analysis ; Codon - genetics ; Codons ; CoxI gene ; Crambidae ; Deoxyribonucleic acid ; Diatraea saccharalis ; Divergence ; DNA ; DNA sequencing ; Drosophila ; Expressed Sequence Tags ; Fruit - parasitology ; Gene expression ; Gene Expression Profiling ; Gene mapping ; Gene sequencing ; Genes ; genome ; Genome, Insect - genetics ; Genome, Mitochondrial - genetics ; Genomes ; Genomics ; Insects ; Laboratories ; Legumes ; Lepidoptera ; Lepidoptera - genetics ; Lepidoptera - physiology ; Maruca testulalis ; Maruca vitrata ; messenger RNA ; microarray technology ; Midgut ; Mitochondria ; Mitochondrial DNA ; Molecular Sequence Annotation ; Molecular Sequence Data ; Nucleotide sequence ; nucleotide sequences ; Nucleotides ; Phylogeny ; Polyadenylation ; Proteins ; Proteomics ; ribosomal RNA ; rRNA ; Saccharum officinarum ; Salivary gland ; Sequence Analysis, DNA ; Stop codon ; Sugarcane ; Transcription ; transcription (genetics) ; Transcription factors ; Transfer RNA ; Translation (Genetics) ; tRNA</subject><ispartof>PloS one, 2011-02, Vol.6 (2), p.e16444-e16444</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011. This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c747t-ffce37c347d779284e966fa2375cc7bc3f4c4e6058b9ddd54453e4ce98bc64b13</citedby><cites>FETCH-LOGICAL-c747t-ffce37c347d779284e966fa2375cc7bc3f4c4e6058b9ddd54453e4ce98bc64b13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/1292671015/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/1292671015?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,315,733,786,790,891,25783,27957,27958,37047,37048,44625,53827,53829,75483</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21311752$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Smagghe, Guy</contributor><creatorcontrib>Margam, Venu M</creatorcontrib><creatorcontrib>Coates, Brad S</creatorcontrib><creatorcontrib>Hellmich, Richard L</creatorcontrib><creatorcontrib>Agunbiade, Tolulope</creatorcontrib><creatorcontrib>Seufferheld, Manfredo J</creatorcontrib><creatorcontrib>Sun, Weilin</creatorcontrib><creatorcontrib>Ba, Malick N</creatorcontrib><creatorcontrib>Sanon, Antoine</creatorcontrib><creatorcontrib>Binso-Dabire, Clementine L</creatorcontrib><creatorcontrib>Baoua, Ibrahim</creatorcontrib><creatorcontrib>Ishiyaku, Mohammad F</creatorcontrib><creatorcontrib>Covas, Fernando G</creatorcontrib><creatorcontrib>Srinivasan, Ramasamy</creatorcontrib><creatorcontrib>Armstrong, Joel</creatorcontrib><creatorcontrib>Murdock, Larry L</creatorcontrib><creatorcontrib>Pittendrigh, Barry R</creatorcontrib><title>Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes.</description><subject>Agriculture</subject><subject>Analysis</subject><subject>Animals</subject><subject>Annotations</subject><subject>Arginine</subject><subject>Arthropoda</subject><subject>Biology</subject><subject>Borers</subject><subject>Chromosome Mapping</subject><subject>Chromosomes, Insect</subject><subject>Codon - analysis</subject><subject>Codon - genetics</subject><subject>Codons</subject><subject>CoxI gene</subject><subject>Crambidae</subject><subject>Deoxyribonucleic acid</subject><subject>Diatraea saccharalis</subject><subject>Divergence</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Drosophila</subject><subject>Expressed Sequence Tags</subject><subject>Fruit - parasitology</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene mapping</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>genome</subject><subject>Genome, Insect - genetics</subject><subject>Genome, Mitochondrial - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Insects</subject><subject>Laboratories</subject><subject>Legumes</subject><subject>Lepidoptera</subject><subject>Lepidoptera - genetics</subject><subject>Lepidoptera - physiology</subject><subject>Maruca testulalis</subject><subject>Maruca vitrata</subject><subject>messenger RNA</subject><subject>microarray technology</subject><subject>Midgut</subject><subject>Mitochondria</subject><subject>Mitochondrial DNA</subject><subject>Molecular Sequence Annotation</subject><subject>Molecular Sequence Data</subject><subject>Nucleotide sequence</subject><subject>nucleotide sequences</subject><subject>Nucleotides</subject><subject>Phylogeny</subject><subject>Polyadenylation</subject><subject>Proteins</subject><subject>Proteomics</subject><subject>ribosomal RNA</subject><subject>rRNA</subject><subject>Saccharum officinarum</subject><subject>Salivary gland</subject><subject>Sequence Analysis, DNA</subject><subject>Stop codon</subject><subject>Sugarcane</subject><subject>Transcription</subject><subject>transcription (genetics)</subject><subject>Transcription factors</subject><subject>Transfer RNA</subject><subject>Translation 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Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</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>Margam, Venu M</au><au>Coates, Brad S</au><au>Hellmich, Richard L</au><au>Agunbiade, Tolulope</au><au>Seufferheld, Manfredo J</au><au>Sun, Weilin</au><au>Ba, Malick N</au><au>Sanon, Antoine</au><au>Binso-Dabire, Clementine L</au><au>Baoua, Ibrahim</au><au>Ishiyaku, Mohammad F</au><au>Covas, Fernando G</au><au>Srinivasan, Ramasamy</au><au>Armstrong, Joel</au><au>Murdock, Larry L</au><au>Pittendrigh, Barry R</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2011-02-02</date><risdate>2011</risdate><volume>6</volume><issue>2</issue><spage>e16444</spage><epage>e16444</epage><pages>e16444-e16444</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><notes>http://dx.doi.org/10.1371/journal.pone.0016444</notes><notes>http://hdl.handle.net/10113/48278</notes><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><notes>Conceived and designed the experiments: VMM BSC BRP. Performed the experiments: VMM BSC TA WS MNB. Analyzed the data: VMM BSC. Contributed reagents/materials/analysis tools: RLH MNB AS CLB IB MFI FGC RS JA LLM BRP. Wrote the paper: VMM BSC RLH TA MJS WS MNB AS CLB IB MFI FGC RS JA LLM BRP.</notes><abstract>We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>21311752</pmid><doi>10.1371/journal.pone.0016444</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2011-02, Vol.6 (2), p.e16444-e16444 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1292671015 |
| source | Publicly Available Content Database; PubMed Central |
| subjects | Agriculture Analysis Animals Annotations Arginine Arthropoda Biology Borers Chromosome Mapping Chromosomes, Insect Codon - analysis Codon - genetics Codons CoxI gene Crambidae Deoxyribonucleic acid Diatraea saccharalis Divergence DNA DNA sequencing Drosophila Expressed Sequence Tags Fruit - parasitology Gene expression Gene Expression Profiling Gene mapping Gene sequencing Genes genome Genome, Insect - genetics Genome, Mitochondrial - genetics Genomes Genomics Insects Laboratories Legumes Lepidoptera Lepidoptera - genetics Lepidoptera - physiology Maruca testulalis Maruca vitrata messenger RNA microarray technology Midgut Mitochondria Mitochondrial DNA Molecular Sequence Annotation Molecular Sequence Data Nucleotide sequence nucleotide sequences Nucleotides Phylogeny Polyadenylation Proteins Proteomics ribosomal RNA rRNA Saccharum officinarum Salivary gland Sequence Analysis, DNA Stop codon Sugarcane Transcription transcription (genetics) Transcription factors Transfer RNA Translation (Genetics) tRNA |
| title | Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae) |
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