Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree
The cachara ( Pseudoplatystoma reticulatum ) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to dom...
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creator | Villela, Luciana Cristine Vasques Alves, Anderson Luis Varela, Eduardo Sousa Yamagishi, Michel Eduardo Beleza Giachetto, Poliana Fernanda da Silva, Naiara Milagres Augusto Ponzetto, Josi Margarete Paiva, Samuel Rezende Caetano, Alexandre Rodrigues |
description | The cachara (
Pseudoplatystoma reticulatum
) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to domesticate and raise the species in commercial systems. The complete cachara mitochondrial genome was obtained by assembling Illumina RNA-seq data from pooled samples. The full mitogenome was found to be 16,576 bp in length, showing the same basic structure, order, and genetic organization observed in other Pimelodidae, with 13 protein-coding genes, 2 rNA genes, 22 trNAs, and a control region. Observed base composition was 24.63% T, 28.47% C, 31.45% A, and 15.44% G. With the exception of
NAD6
and eight tRNAs, all of the observed mitochondrial genes were found to be coded on the H strand. A total of 107 SNPs were identified in
P. reticulatum
mtDNA, 67 of which were located in coding regions. Of these SNPs, 10 result in amino acid changes. Analysis of the obtained sequence with 94 publicly available full Siluriformes mitogenomes resulted in a phylogenetic tree that generally agreed with available phylogenetic proposals for the order. The first report of the complete
Pseudoplatystoma reticulatum
mitochondrial genome sequence revealed general gene organization, structure, content, and order similar to most vertebrates. Specific sequence and content features were observed and may have functional attributes which are now available for further investigation. |
doi_str_mv | 10.1007/s10709-016-9945-7 |
format | Article |
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Pseudoplatystoma reticulatum
) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to domesticate and raise the species in commercial systems. The complete cachara mitochondrial genome was obtained by assembling Illumina RNA-seq data from pooled samples. The full mitogenome was found to be 16,576 bp in length, showing the same basic structure, order, and genetic organization observed in other Pimelodidae, with 13 protein-coding genes, 2 rNA genes, 22 trNAs, and a control region. Observed base composition was 24.63% T, 28.47% C, 31.45% A, and 15.44% G. With the exception of
NAD6
and eight tRNAs, all of the observed mitochondrial genes were found to be coded on the H strand. A total of 107 SNPs were identified in
P. reticulatum
mtDNA, 67 of which were located in coding regions. Of these SNPs, 10 result in amino acid changes. Analysis of the obtained sequence with 94 publicly available full Siluriformes mitogenomes resulted in a phylogenetic tree that generally agreed with available phylogenetic proposals for the order. The first report of the complete
Pseudoplatystoma reticulatum
mitochondrial genome sequence revealed general gene organization, structure, content, and order similar to most vertebrates. Specific sequence and content features were observed and may have functional attributes which are now available for further investigation.</description><identifier>ISSN: 0016-6707</identifier><identifier>EISSN: 1573-6857</identifier><identifier>DOI: 10.1007/s10709-016-9945-7</identifier><identifier>PMID: 28160169</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Amino acids ; Animal Genetics and Genomics ; Animals ; Aquaculture products ; Base Composition ; Base Sequence ; Biomedical and Life Sciences ; Catfishes - classification ; Catfishes - genetics ; Codon ; Computational Biology - methods ; Economic importance ; Evolutionary Biology ; Genes, Mitochondrial ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Human Genetics ; Indigenous species ; Life Sciences ; Microbial Genetics and Genomics ; Molecular Sequence Annotation ; Original Paper ; Phylogeny ; Plant Genetics and Genomics ; Polymorphism, Single Nucleotide</subject><ispartof>Genetica, 2017-02, Vol.145 (1), p.51-66</ispartof><rights>Springer International Publishing Switzerland 2017</rights><rights>Genetica is a copyright of Springer, 2017.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c405t-ee59d785749c8868e51b6435b5ab373725bf722d5740691c1d68c39d8ea4e0e43</citedby><cites>FETCH-LOGICAL-c405t-ee59d785749c8868e51b6435b5ab373725bf722d5740691c1d68c39d8ea4e0e43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10709-016-9945-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10709-016-9945-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28160169$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Villela, Luciana Cristine Vasques</creatorcontrib><creatorcontrib>Alves, Anderson Luis</creatorcontrib><creatorcontrib>Varela, Eduardo Sousa</creatorcontrib><creatorcontrib>Yamagishi, Michel Eduardo Beleza</creatorcontrib><creatorcontrib>Giachetto, Poliana Fernanda</creatorcontrib><creatorcontrib>da Silva, Naiara Milagres Augusto</creatorcontrib><creatorcontrib>Ponzetto, Josi Margarete</creatorcontrib><creatorcontrib>Paiva, Samuel Rezende</creatorcontrib><creatorcontrib>Caetano, Alexandre Rodrigues</creatorcontrib><title>Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree</title><title>Genetica</title><addtitle>Genetica</addtitle><addtitle>Genetica</addtitle><description>The cachara (
Pseudoplatystoma reticulatum
) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to domesticate and raise the species in commercial systems. The complete cachara mitochondrial genome was obtained by assembling Illumina RNA-seq data from pooled samples. The full mitogenome was found to be 16,576 bp in length, showing the same basic structure, order, and genetic organization observed in other Pimelodidae, with 13 protein-coding genes, 2 rNA genes, 22 trNAs, and a control region. Observed base composition was 24.63% T, 28.47% C, 31.45% A, and 15.44% G. With the exception of
NAD6
and eight tRNAs, all of the observed mitochondrial genes were found to be coded on the H strand. A total of 107 SNPs were identified in
P. reticulatum
mtDNA, 67 of which were located in coding regions. Of these SNPs, 10 result in amino acid changes. Analysis of the obtained sequence with 94 publicly available full Siluriformes mitogenomes resulted in a phylogenetic tree that generally agreed with available phylogenetic proposals for the order. The first report of the complete
Pseudoplatystoma reticulatum
mitochondrial genome sequence revealed general gene organization, structure, content, and order similar to most vertebrates. Specific sequence and content features were observed and may have functional attributes which are now available for further investigation.</description><subject>Amino acids</subject><subject>Animal Genetics and Genomics</subject><subject>Animals</subject><subject>Aquaculture products</subject><subject>Base Composition</subject><subject>Base Sequence</subject><subject>Biomedical and Life Sciences</subject><subject>Catfishes - classification</subject><subject>Catfishes - genetics</subject><subject>Codon</subject><subject>Computational Biology - methods</subject><subject>Economic importance</subject><subject>Evolutionary Biology</subject><subject>Genes, Mitochondrial</subject><subject>Genome, Mitochondrial</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Human Genetics</subject><subject>Indigenous species</subject><subject>Life Sciences</subject><subject>Microbial Genetics and Genomics</subject><subject>Molecular Sequence Annotation</subject><subject>Original Paper</subject><subject>Phylogeny</subject><subject>Plant Genetics and Genomics</subject><subject>Polymorphism, Single Nucleotide</subject><issn>0016-6707</issn><issn>1573-6857</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</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><recordid>eNqNkcuKFDEUhoMoTjv6AG4kIMi4KE2qKrfl0IwXGFAYXRep1KnpDJWkzGXRT-OrmqLHQQTBVRL-L9_h8CP0kpJ3lBDxPlEiiGoI5Y1SPWvEI7SjTHQNl0w8RjuyJVwQcYaepXRHCFGCq6forJWU10zt0M99cOsCGbCzOZhD8FO0esG34IMDPMfg8E0o-YAvHURrtMdG59mmA_6aoExhXXQ-phycxhGyNaW-i8MXV7YqnPYev8EP97dY-wnbnLB1qzYZW49v7FKinUN0kPB6OC6hwpsJ5wjwHD2Z9ZLgxf15jr5_uPq2_9Rcf_n4eX953ZiesNwAMDWJunWvjJRcAqMj7zs2Mj12ohMtG2fRtlMFCFfU0IlL06lJgu6BQN-do4uTd43hR4GUB2eTgWXRHkJJA5VCyE4Syf8D5Yx1quWioq__Qu9Cib4uslFCtYK3m5CeKBNDShHmYY3W6XgcKBm2oodT0UOtbNiKHjbzq3tzGR1MDz9-N1uB9gSkGvlbiH-M_qf1F61ItSw</recordid><startdate>20170201</startdate><enddate>20170201</enddate><creator>Villela, Luciana Cristine Vasques</creator><creator>Alves, Anderson Luis</creator><creator>Varela, Eduardo Sousa</creator><creator>Yamagishi, Michel Eduardo Beleza</creator><creator>Giachetto, Poliana Fernanda</creator><creator>da Silva, Naiara Milagres Augusto</creator><creator>Ponzetto, Josi Margarete</creator><creator>Paiva, Samuel Rezende</creator><creator>Caetano, Alexandre Rodrigues</creator><general>Springer International Publishing</general><general>Springer Nature B.V</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>7QL</scope><scope>7SN</scope><scope>7SS</scope><scope>7T7</scope><scope>7TK</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</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>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20170201</creationdate><title>Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree</title><author>Villela, Luciana Cristine Vasques ; Alves, Anderson Luis ; Varela, Eduardo Sousa ; Yamagishi, Michel Eduardo Beleza ; Giachetto, Poliana Fernanda ; da Silva, Naiara Milagres Augusto ; Ponzetto, Josi Margarete ; Paiva, Samuel Rezende ; Caetano, Alexandre Rodrigues</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c405t-ee59d785749c8868e51b6435b5ab373725bf722d5740691c1d68c39d8ea4e0e43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Amino acids</topic><topic>Animal Genetics and Genomics</topic><topic>Animals</topic><topic>Aquaculture products</topic><topic>Base Composition</topic><topic>Base Sequence</topic><topic>Biomedical and Life Sciences</topic><topic>Catfishes - classification</topic><topic>Catfishes - genetics</topic><topic>Codon</topic><topic>Computational Biology - methods</topic><topic>Economic importance</topic><topic>Evolutionary Biology</topic><topic>Genes, Mitochondrial</topic><topic>Genome, Mitochondrial</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Human Genetics</topic><topic>Indigenous species</topic><topic>Life Sciences</topic><topic>Microbial Genetics and Genomics</topic><topic>Molecular Sequence Annotation</topic><topic>Original Paper</topic><topic>Phylogeny</topic><topic>Plant Genetics and Genomics</topic><topic>Polymorphism, Single Nucleotide</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Villela, Luciana Cristine Vasques</creatorcontrib><creatorcontrib>Alves, Anderson Luis</creatorcontrib><creatorcontrib>Varela, Eduardo Sousa</creatorcontrib><creatorcontrib>Yamagishi, Michel Eduardo Beleza</creatorcontrib><creatorcontrib>Giachetto, Poliana Fernanda</creatorcontrib><creatorcontrib>da Silva, Naiara Milagres Augusto</creatorcontrib><creatorcontrib>Ponzetto, Josi Margarete</creatorcontrib><creatorcontrib>Paiva, Samuel Rezende</creatorcontrib><creatorcontrib>Caetano, Alexandre Rodrigues</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech 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>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genetica</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Villela, Luciana Cristine Vasques</au><au>Alves, Anderson Luis</au><au>Varela, Eduardo Sousa</au><au>Yamagishi, Michel Eduardo Beleza</au><au>Giachetto, Poliana Fernanda</au><au>da Silva, Naiara Milagres Augusto</au><au>Ponzetto, Josi Margarete</au><au>Paiva, Samuel Rezende</au><au>Caetano, Alexandre Rodrigues</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree</atitle><jtitle>Genetica</jtitle><stitle>Genetica</stitle><addtitle>Genetica</addtitle><date>2017-02-01</date><risdate>2017</risdate><volume>145</volume><issue>1</issue><spage>51</spage><epage>66</epage><pages>51-66</pages><issn>0016-6707</issn><eissn>1573-6857</eissn><abstract>The cachara (
Pseudoplatystoma reticulatum
) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to domesticate and raise the species in commercial systems. The complete cachara mitochondrial genome was obtained by assembling Illumina RNA-seq data from pooled samples. The full mitogenome was found to be 16,576 bp in length, showing the same basic structure, order, and genetic organization observed in other Pimelodidae, with 13 protein-coding genes, 2 rNA genes, 22 trNAs, and a control region. Observed base composition was 24.63% T, 28.47% C, 31.45% A, and 15.44% G. With the exception of
NAD6
and eight tRNAs, all of the observed mitochondrial genes were found to be coded on the H strand. A total of 107 SNPs were identified in
P. reticulatum
mtDNA, 67 of which were located in coding regions. Of these SNPs, 10 result in amino acid changes. Analysis of the obtained sequence with 94 publicly available full Siluriformes mitogenomes resulted in a phylogenetic tree that generally agreed with available phylogenetic proposals for the order. The first report of the complete
Pseudoplatystoma reticulatum
mitochondrial genome sequence revealed general gene organization, structure, content, and order similar to most vertebrates. Specific sequence and content features were observed and may have functional attributes which are now available for further investigation.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>28160169</pmid><doi>10.1007/s10709-016-9945-7</doi><tpages>16</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Amino acids Animal Genetics and Genomics Animals Aquaculture products Base Composition Base Sequence Biomedical and Life Sciences Catfishes - classification Catfishes - genetics Codon Computational Biology - methods Economic importance Evolutionary Biology Genes, Mitochondrial Genome, Mitochondrial High-Throughput Nucleotide Sequencing Human Genetics Indigenous species Life Sciences Microbial Genetics and Genomics Molecular Sequence Annotation Original Paper Phylogeny Plant Genetics and Genomics Polymorphism, Single Nucleotide |
title | Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree |
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