Mitogenome of Tachysurus nudiceps and review of Bagrid phylogeny

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Mitogenome of Tachysurus nudiceps and review of Bagrid phylogeny

Post by bekateen »

Hashimoto, S., Kakehashi, R., Mori, T., Kambayashi, C., Kanao, S., & Kurabayashi, A. (2022). The complete mitochondrial genome of a bagrid catfish, Tachysurus nudiceps, and its phylogenetic implications for the classification of the bagrid genera. Mitochondrial DNA Part B, 7(4), 606-608.

https://doi.org/10.1080/23802359.2022.2057253
https://www.tandfonline.com/doi/full/10 ... 22.2057253
Abstract
The complete sequence of the mitochondrial genome (mitogenome) of (family Bagridae; order Siluriformes) was determined using next-generation sequencing. The composition of its mitogenome is the same as that observed in most other vertebrates and consists of 37 genes, an L-strand replication origin and a control region. As in previous studies, our phylogenetic analyses revealed that many of the bagrid genera are not monophyletic, emphasizing the necessity for reviewing and revising the taxonomy of this family at the genus level.
Keywords: Mitogenome, next-generation sequencing, Tachysurus nudiceps, Bagridae
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Figure 1. Phylogenetic tree of bagrid catfishes based on mitochondrial protein-coding gene sequences. The ML tree of 41 bagrids reconstructed from the 13 PCG sequences with the best-fit partitioning scheme is shown. *indicates Tachysurus nudiceps of which mtDNA was sequenced in this study. The partitioning scheme and optimal substitution models for the selected partitions were estimated by IQ-tree (partition 1 = ATP6 + Cytb + ND1-5 with substitution model GTR + F+G + I, partition 2 = ATP8 + CO1-3 with GTR + F+G + I, and partition 3 = ND6 with HKY + F+I + G4). The numbers at the nodes indicate nonparametric ML Bootstrap values (left) calibrated by 1,000 pseudo replicates and Bayesian Post Probabilities (right) calibrated by four independent MCMC runs for 10 million generations (sampling frequency is one per 1,000 generations) without first one million samples (i.e. 10% burn-in). Two Pangasianodon species (family Pangasiidae) were used as the outgroup. The scientific names were followed to FishBase (Froese and Pauly 2021).
Figure 1. Phylogenetic tree of bagrid catfishes based on mitochondrial protein-coding gene sequences. The ML tree of 41 bagrids reconstructed from the 13 PCG sequences with the best-fit partitioning scheme is shown. *indicates Tachysurus nudiceps of which mtDNA was sequenced in this study. The partitioning scheme and optimal substitution models for the selected partitions were estimated by IQ-tree (partition 1 = ATP6 + Cytb + ND1-5 with substitution model GTR + F+G + I, partition 2 = ATP8 + CO1-3 with GTR + F+G + I, and partition 3 = ND6 with HKY + F+I + G4). The numbers at the nodes indicate nonparametric ML Bootstrap values (left) calibrated by 1,000 pseudo replicates and Bayesian Post Probabilities (right) calibrated by four independent MCMC runs for 10 million generations (sampling frequency is one per 1,000 generations) without first one million samples (i.e. 10% burn-in). Two Pangasianodon species (family Pangasiidae) were used as the outgroup. The scientific names were followed to FishBase (Froese and Pauly 2021).
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Re: Mitogenome of Tachysurus nudiceps and review of Bagrid phylogeny

Post by Silurus »

This is what happens when you let molecular biologists who have no idea of taxonomy conduct a study. Non-monophyletic, my ass.
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Re: Mitogenome of Tachysurus nudiceps and review of Bagrid phylogeny

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Is there any valid species of Pelteobagrus or Pseudobagrus remaining?

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Re: Mitogenome of Tachysurus nudiceps and review of Bagrid phylogeny

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bekateen wrote: 13 Apr 2022, 06:03 Is there any valid species of Pelteobagrus or Pseudobagrus remaining?
None. All East Asian bagrids are Tachysurus.
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Re: Mitogenome of Tachysurus nudiceps and review of Bagrid phylogeny

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Thanks HH. And Coreobagrus? I see C. brevicorpus is treated on Planetcatfish as , but still exists in our database as Coreobagrus. Is that just an oversight on our part?

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Re: Mitogenome of Tachysurus nudiceps and review of Bagrid phylogeny

Post by Silurus »

Coreobagrus=Tachysurus
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Re: Mitogenome of Tachysurus nudiceps and review of Bagrid phylogeny

Post by bekateen »

Okay. Thanks. I've renamed C. ichikawai to .

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