title: Next-generation sequencing and comparative analysis of Pyrrhocorax pyrrhocorax and Pyrrhocorax graculus (Passeriformes: Corvidae) mitochondrial genomes.
abstract: The complete mitochondrial genomes of Red-billed Chough (Pyrrhocorax pyrrhocorax) and Yellow-billed Chough (Pyrrhocorax graculus) were sequenced using the Ion Torrent PGM platform. These mitogenomes contain 16,889 bp (Red-billed Chough) and 16,905 bp (Yellow-billed Chough), including 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (D-loop). The gene content, orientation, and structure are similar to a wide range of other vertebrate species and the nucleotide composition is very similar to other Passeriformes. All PCGs start with ATG, except for COX1 that starts with GTG, and four stop codons and one incomplete stop codon are used (TAA, TAG, AGG, AGA, and T-). The size of PCGs is the same in both mitogenomes, except for ND6 that has one codon less in the Yellow-billed Chough. All the tRNAs can fold into a typical cloverleaf secondary structure. These mitogenomic data can be of great value in complementing forthcoming approaches on molecular ecology, comparative and functional genomics.
authors.affiliation: a Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD) , Vila Real , Portugal .|b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal .
authors.forename: Francisco
authors.initials: F
authors.lastname: Morinha
authors.affiliation: c STAB VIDA, Madan Parque, Rua dos Inventores , Caparica , Portugal .
authors.forename: Carla
authors.initials: C
authors.lastname: Clemente
authors.affiliation: b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal .
authors.forename: João A
authors.initials: JA
authors.lastname: Cabral
authors.affiliation: c STAB VIDA, Madan Parque, Rua dos Inventores , Caparica , Portugal .
authors.forename: Magdalena M
authors.initials: MM
authors.lastname: Lewicka
authors.affiliation: b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal .
authors.forename: Paulo
authors.initials: P
authors.lastname: Travassos
authors.affiliation: b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal .
authors.forename: Diogo
authors.initials: D
authors.lastname: Carvalho
authors.affiliation: d Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC, UCLM, JCCM) , Ciudad Real , Spain , and.
authors.forename: José A
authors.initials: JA
authors.lastname: Dávila
authors.affiliation: b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal .
authors.forename: Mário
authors.initials: M
authors.lastname: Santos
authors.affiliation: e Museo Nacional de Ciencias Naturales (CSIC) , Madrid , Spain.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Blanco
authors.affiliation: a Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD) , Vila Real , Portugal .
authors.forename: Estela
authors.initials: E
authors.lastname: Bastos
mesh_terms: D000818:Animals; D018387:Codon, Initiator; D018388:Codon, Terminator; D055028:Comparative Genomic Hybridization; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D003576:Electron Transport Complex IV / Q000737:chemistry / Q000235:genetics; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D009245:NADH Dehydrogenase / Q000737:chemistry / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D046109:Passeriformes / Q000235:genetics*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D018387:Codon, Initiator; D018388:Codon, Terminator; D004272:DNA, Mitochondrial; D012335:RNA, Ribosomal; D012343:RNA, Transfer; D009245:NADH Dehydrogenase; D003576:Electron Transport Complex IV
keywords: Gene annotation; Pyrrhocorax graculus; Pyrrhocorax pyrrhocorax; mitochondrial genome; next-generation sequencing