Complete mitochondrial genome characterization and exploratory mitochondrial DNA modification signals in square-head...

Area of Science:

• Genomics
• Evolutionary Biology
• Epigenetics

Background:

• Complete mitochondrial genomes are crucial for understanding fish evolution and epigenetics.
• The square-head catfish (Chaca chaca) mitogenome was previously uncharacterized.

Purpose of the Study:

• To sequence and annotate the first complete mitochondrial genome of Chaca chaca.
• To investigate mitochondrial DNA (mtDNA) methylation patterns in Chaca chaca.
• To establish a genomic resource for Chaca chaca for phylogenetic and conservation studies.

Main Methods:

• High-molecular-weight DNA was sequenced using Oxford Nanopore adaptive sampling.
• De novo assembly, annotation, and comparative genomic analyses were performed.
• Genome-wide methylation profiling identified 5-methylcytosine (5mC) and N6-methyladenine (6mA) signals.

Main Results:

• The complete Chaca chaca mitogenome is 16,591 bp, containing standard mitochondrial genes.
• Phylogenetic analysis placed Chaca chaca within Chacidae, near Pimelodidae and Pseudopimelodidae.
• Methylation analysis detected 5mC and 6mA, with strand-specific differences, particularly for 5mC.

Conclusions:

• This study presents the foundational mitogenome for Chaca chaca, enhancing phylogenetic resolution and conservation genetics.
• The findings highlight potential epigenetic regulation via mtDNA methylation in fishes.
• Further research is needed to validate the functional significance of mtDNA methylation signals in fish.