Complete mitochondrial DNA sequence of Silurus biwaensis

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Complete mitochondrial DNA sequence of Silurus biwaensis

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Kishimoto, Y., Okuyama, H., & Takahashi, J. I. (2021). Complete mitochondrial DNA sequence of the Japanese endemic catfish Silurus biwaensis (Siluriformes: Siluridae) from Lake Biwa. Mitochondrial DNA. Part B, Resources, 6(9), 2482.

https://dx.doi.org/10.1080/23802359.2021.1920487
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354177/
Abstract
The Japanese endemic catfish Silurus biwaensis is distributed only in Lake Biwa and Yodo river drainages. There are four species of the genus Silurus in Japan, of which S. biwaensis has a most limited distribution. This catfish needs to be collected for DNA data owing to the lack of information related to its phylogenetic relationship. Here, the complete mitochondrial genome of the S. biwaensis from Lake Biwa in Japan was analyzed using next-generation sequencing. The mitochondrial genome of S. biwaensis was identified as a 16,531 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with one A + T-rich control region. The AT content was 55.83%. The heavy (H)-strand was predicted to have 12 PCGs, 14 tRNA, and 2 rRNA genes, whereas the light (L)-strand was predicted to contain one PCG and eight tRNA genes. The start codons ATG, ATC, and GTG were found in 13 PCGs. The stop codons TAA, TAG, and AGA were observed in all PCGs, except CytB and COX3. All tRNA genes formed typical cloverleaf secondary structures. The molecular phylogenetic relationships estimated using 13 PCGs (maximum-likelihood method) indicated that S. biwaensis is genetically distinct from the sympatric species S. asotus and S. lithophilus. This result clearly indicated that S. biwaensis is a valid species.
  • Keywords: Next-generation sequencing, catfish, Lake Biwa, Silurus biwaensis, mitochondrial DNA
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Phylogenetic relationships (maximum likelihood) of the Siluridae based on the nucleotide sequences of the 13 protein-coding genes of the mitochondrial genome. Sequences from Kryptopterus bicirrhis and Ompok bimaculatus were used as an outgroups. These sequences were separated by codon positions, and for each partition, the optimal models of sequence evolution were used in the maximum likelihood method using MEGA X, based on the corrected Akaike information criterion. The numbers at the nodes indicate the bootstrap support inferred from 1000 bootstrap replicates. Alphanumeric terms indicate the DNA Database of Japan accession numbers.
Phylogenetic relationships (maximum likelihood) of the Siluridae based on the nucleotide sequences of the 13 protein-coding genes of the mitochondrial genome. Sequences from Kryptopterus bicirrhis and Ompok bimaculatus were used as an outgroups. These sequences were separated by codon positions, and for each partition, the optimal models of sequence evolution were used in the maximum likelihood method using MEGA X, based on the corrected Akaike information criterion. The numbers at the nodes indicate the bootstrap support inferred from 1000 bootstrap replicates. Alphanumeric terms indicate the DNA Database of Japan accession numbers.
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