Assembly and variation analyses of Clarias batrachus mitogenome retrieved from WGS data and its phylogenetic relationship with other catfishes.
ABSTRACT: Whole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequence the mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data of Clarias batrachus, generated from Roche 454 and Ion Torrent sequencing platforms, to assemble the complete mitogenome using both de novo and reference based approaches. Both the methods yielded almost similar results and the best assembled mitogenome was of 16,510 bp size (GenBank Acc. No. KM259918). The mitogenome annotation resulted in 13 coding genes, 22 tRNA genes, 2 rRNA genes and one control region, and the gene order was found to be identical with other catfishes. Variation analyses between assembled and the reference (GenBank Acc. No. NC_023923) mitogenome revealed 51 variations. The phylogenetic analysis of coding DNA sequences and tRNA supports the monophyly of catfishes. Two SSRs were identified in C. batrachus mitogenome, out of which one was unique to this species. Based on the relative rate of gene evolution, protein coding mitochondrial genes were found to evolve at a much faster pace than the d-loop, which in turn are followed by the rRNAs; the tRNAs showed wide variability in the rate of sequence evolution, and on average evolve the slowest. Among the coding genes, ND2 evolves most rapidly. The variations present in the coding regions of the mitogenome and their comparative analyses with other catfish species may be useful in species conservation and management programs.
Project description:The complete mitochondrial genome of stripped eel catfish, <i>Plotosus lineatus</i>, is sequenced in this study. The mitochondrial genome sequence is 16?480?bp in length, with the base composition of 24.7% A, 31.8% T, 27.8% G and 15.7% C. The G?+?C content is 43.5%. The mitochondria includes 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one D-loop region. Except for NAD6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. <i>Plotosus lineatus</i> was confirmed to be closely related to <i>P. japonicus</i> (GenBank: KR270437.1), based on our phylogenetic analysis on complete mitochondrial genome sequences of 13 species. Our complete mitogenome data are going to provide the basis for taxonomic and phylogenetic research of catfishes.
Project description:The complete mitogenome of <i>Idioscopus nitidulus</i> (Cicadellidae) was sequenced. It comprises 15,287 base pairs (bp), including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a control region. The phylogenetic analyses based on concatenated thirteen protein-coding genes of mitogenomes recover the monophyly of Auchenorrhyncha (Fulgoromorpha?+?Cicadomorpha) and Sternorrhyncha as a sister group to Auchenorrhyncha. The complete mitogenome sequence of <i>Idioscopus nitidulus</i>is available in the GenBank with accession number: KR024406.
Project description:The mitogenome of <i>Hyalella lucifugax</i> from Lake Titicaca, obtained using Illumina NGS technology, is described. The mitogenome attains 14,994?bp (although the control region could not be completed) and comprises the standard set of 2 rRNAs, 13 protein-coding genes, and 22 tRNA genes, plus two non-coding regions. A phylogenetic analysis based on the protein-coding mitochondrial genes from representatives from all amphipod genera with available sequences in GenBank recovers the monophyly of <i>H. lucifugax</i> with the superfamily Talitroidea.
Project description:The complete mitochondrial genome of the maize weevil <i>Sitophilus zeamais</i> (GenBank accession number: MN905575) from Guizhou Province consists of a circular DNA molecule of 18,421?bp (with 75.69% A?+?T content), which is longer by 316?bp than that of the mitogenome of <i>S. zeamais</i> from Nigeria. The mitogenome comprises 13 protein-coding, 22 tRNA, and two rDNA genes. The protein-coding genes have typical ATN (Met) initiation codons and are terminated by typical TAN stop codons.
Project description:We report for the first time the complete mitochondrial genome of <i>Sinopotamon xiushuiense</i>, which is found to be 18,460?bp in length, and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA), and 1 non-coding region known as the D-loop. In addition, the mitogenome has 18 intergenic regions ranging from 1 to 1221?bp in length. The complete mitogenome of <i>S. xiushuiense</i> is the longest among brachyurans reported in GenBank before November 2015, and its AT content is slightly lower than that in <i>Geotholphusa dehaani</i>. The mitogenome data provides a basis for further studies on population genetics and phylogenetics.
Project description:In this study, the near complete mitogenome sequence (15,469?bp) of <i>Oreolalax major</i> was determined using polymerase chain reaction (PCR). It includes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes and 19 transfer RNA (tRNA) genes (GenBank accession number KU310894). The features of <i>O. major</i> have one more tRNA gene (<i>tRNA<sup>Met</sup></i> ) behind the original one before <i>ND2</i> which is similar to <i>Leptobrachium boringii.</i> Phylogenetic analyses were based on the concatenated sequences of the 13 protein-encoding genes of <i>O. major</i> and other related species.
Project description:This data article presents the first complete mitochondrial genome (mitogenome) of an endangered slow loris subspecies, Nycticebus coucang insularis Robinson, 1917 from Tioman Island, Pahang. Once considered as extinct, an individual of the subspecies was captured alive from the island during the 2016 Biodiversity Inventory Programme as highlighted in the related research article entitled "Rediscovery of Nycticebus coucang insularis Robinson, 1917 (Primates: Lorisidae) at Tioman Island and its mitochondrial genetic assessment" Rovie-Ryan et al., 2018. Using MiSeq™ sequencing system, the entire mitogenome recovered is 16,765 bp in length, made up of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The mitogenome has been deposited at DDBJ/EMBL/GenBank under the accession number NC_040292.1/MG515246.
Project description:We generated the complete mitochondrial genome of the black paradise flycatcher (<i>Terpsiphone atrocaudata</i>; Family: Monarchidae), an ecologically important insectivorous bird in Asian forest ecosystems. The mitogenome was 16,984?bp in length and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. Gene composition and arrangement in the mitogenome were similar to those of related families Corvidae and Laniidae available in GenBank. However, <i>tRNA<sup>Ala</sup></i> was located between <i>COXII</i> and <i>ATP8</i> genes in the mitogenome of <i>T. atrocaudata</i> while <i>tRNA<sup>Lys</sup></i> , was in the same location in the mitogenomes of Corvidae and Laniidae. The phylogenetic tree based on the mitogenomes of <i>T. atrocaudata</i> and the related families supported that Monarchidae was the sister taxa to the clade of Laniidae and Corvidae. The mitogenome of <i>T. atrocaudata</i> will be a valuable genetic resource for phylogenetic analyses and implication of conservation and management of the species.
Project description:Using Illumina next-generation sequencing (NGS), the complete mitochondrial genome (mitogenome) of <i>Ducetia japonica</i> was sequenced in the present study. The mitogenome of <i>D. japonica</i> (Genbank accession no. KU885974) is 16,276?bp in size, had the typical invertebrate mitochondrial gene arrangement and containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and a control region. Except for the control region (868?bp), one novel larger intergenic (616?bp) was found between <i>nad2</i> and <i>trnW</i>. Phylogenetic results unambiguously support the monophyly of Phaneropterinae, although the gene order of two <i>Sinochlora</i> species different with other Tettigoniidae species. Using Illumina NGS platforms for mitogenome sequencing will provide rather essential and important DNA molecular data for the further phylogenetic analysis across major ensiferan lineages.
Project description:Here, we report the complete mitochondrial genome of a <i>Bombyx mori</i> strain BaiyuN, which is identified to be highly resistant to <i>Bombyx mori</i> nucleopolyhedrovirus (BmNPV). Its complete mitochondrial genome is 15,655?bp in length (GenBank accession no. MG797555), consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA, and 1 control region (494?bp). The complete mitogenome of the <i>B. mori</i> strain BaiyuN could provide a basic data for further phylogenetics and antivirus research.