International Journal of Aquaculture, 2025, Vol.15, No.2, 88-98 http://www.aquapublisher.com/index.php/ija 90 combine mitochondrial data with nuclear gene data to obtain more comprehensive and reliable conclusions (Santos et al., 2019). In the study of catfish phylogeny, in addition to the commonly used genes such as Cyt b, COI, and 16S, in recent years, more emphasis has been placed on using the complete mitochondrial genome sequence or its extracted hypervariable regions (such as control regions and ND2 genes) as reconstruction tools to improve the resolution and support rate of the phylogenetic tree. The mitochondrial genome has played a huge role as molecular evidence in the study of fish phylogeny and classification, and has become one of the core tools for the study of the evolution of Siluriformes fish. 3 Mitochondrial Genome Characteristics in Siluriformes 3.1 Gene content, rearrangements, and gene loss The size and gene composition of the mitochondrial genome of Siluriformes fish are generally similar to those of most bony fish, generally about 16.5 Kb, encoding 13 proteins, 22 tRNAs and 2 rRNAs, a total of 37 genes, and a control region (D-loop). For example, the mitochondrial genome of yellow catfish (Pelteobagrus fulvidraco) is about 16,540 bp long, containing a typical 37 genes and a control region (Liu et al., 2019). Another example is the mitochondrial genome of the marine catfish Arius maculatus, which is 16,710 bp long, and its gene composition and arrangement are similar to those of other reported Siluriformes fish. The gene arrangement of the mitochondrial genome of most Siluriformes fish follows the standard order of bony fish, and no major rearrangement events have occurred. In terms of protein-coding genes, the promoters of each gene are usually ATG, and only the COI gene often uses GTG as the start codon. Some stop codons are incomplete (such as "T-" or "TA-"), and complete stop signals are formed by tailing after transcription. For example, in the mitochondrial genomes of some Siluriformes fish, up to 7 protein genes end with incomplete terminators (Yang et al., 2022). All 22 mitochondrial tRNA genes can fold into a typical cloverleaf secondary structure, except that tRNA-Ser (AGY) lacks the DHU arm, which is a common feature of vertebrate mitochondrial genomes. 3.2 Control region variation and replication origin features The length of the control region varies slightly among different species, such as the control region of the Amazon giant catfish, which is as long as 911 bp. The base composition of the mitochondrial genome of Siluriformes fish usually shows a high A+T content, with a GC content ranging from about 37% to 45%. Taking the Piraíba giant catfish (B. filamentosum) as an example, the GC content of its mitochondrial genome is 42.21% (Formiga et al., 2021). 3.3 Selective pressures and adaptive changes in coding regions In terms of functional sequence evolution, each protein-coding gene is subject to strong purifying selection, and its nonsynonymous/synonymous substitution ratio (K_a/K_s) is far below 1. This indicates that mitochondrial protein genes are highly conserved in function, and the accumulated amino acid changes in these genes in different catfish species are limited by selection pressure. It is worth noting that there are also some differences in the details of the mitochondrial genomes of catfish from different families. For example, a study compared the mitochondrial codon usage frequency of spotted catfish and closely related species and found that the preference was basically the same, but there were lineage-specific differences in the relative usage frequency of a few codons. The mitochondrial genome structure of Siluriformes fish is conservative and the functional genes evolve slowly, which provides a reliable basis for reconstructing their phylogenetic relationships using mitochondrial genome data. However, small differences such as control region length variation and codon usage patterns can still be used as molecular features between different evolutionary lineages, providing additional information for classification and evolutionary studies (Yang et al., 2022). 4 Phylogenetic Relationships within Siluriformes 4.1 Branching structure and topology of major families and genera Phylogenetic analysis based on a large amount of mitochondrial genome data has made the relationship between fish families in the order Siluriformes increasingly clear. In general, molecular phylogenetic evidence supports that the order Siluriformes originated in the Southern Hemisphere and differentiated into two main branches in the
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