Genetic characterization and phylogenetic study of Indonesian indigenous "Baung" catfish

[bekateen]

Megarani DV, Nugroho HA, Andarini ZP, Surbakti YDRBR, & Widayanti R. (2020). Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene. Veterinary World, 13(1): 96-103. doi: www.doi.org/10.14202/vetworld.2020.96-103
http://www.veterinaryworld.org/Vol.13/J ... 20/14.html

Abstract
Aim: This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences.
Materials and Methods: The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software.
Results: Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids).
Conclusion: Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with

Hemibagrus nemurus

and

Hemibagrus wyckioides

(Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with

Sperata seenghala

and

Hemibagrus spilopterus

(Bagridae family). Samples from Java (BSBJ) were clustered with

Pseudolais pleurotaenia

(Pangasiidae family). Samples EM (Java) were together with

Mystus cavasius

(Bagridae family). Samples from West Papua were clustered with

Potamosilurus latirostris

(Ariidae family).

• Keywords: cytochrome B, Indonesian indigenous catfish, mitochondrial DNA, phylogenetic study, Siluriformes.

[bekateen]

Not sure what to make of this paper, given that (1) it seems to ignore so many other Indonesian catfish, based on how many Indonesian species do not appear in this study, and (2) we were discussing previously how careful we need to be when tree- building with just one gene or protein (in this case, Cyt-B). Perhaps the answer lies in the fact that the authors targeted only those catfishes known as "Baung" catfishes to the locals.

According to GBIF.org, Pseudolais pleurotaenia, Hemibagrus wyckioides and Hemibagrus spilopterus have not been reported in Indonesia, but other Pseudolais have, including

Pseudolais micronemus

and several Hemibagrus have been found there.

[Silurus]

You know there is a problem when your Hemibagrus spilopterus clusters with Sperata seenghala with a 100% bootstrap probability in your NJ tree (NJ? Seriously?).

[bekateen]

Yes, there seem to be some serious gaps here.