ArticleMolecular biology reports2026
Sequence decoding and analysis of the first reference mitogenome of globally threatened clown-knife fish, Chitala chitala: witness of codon usage bias and intense purifying selection.
Article in Molecular biology reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundHumped featherback or clown-knife fish, Chitala chitala is an endangered and globally near threatened species. Mitochondrial genome or mitogenome and its bioinformatic analysis play important roles for the effective conservation of threatened fish species. METHODS AND
resultsNext generation sequencing decoded the complete circular mitochondrial genome of Chitala chitala which is endowed with typical organizational features of 13 protein coding genes (PCGs), 22 tRNA genes, two genes for ribosomal RNA subunits, and two non-coding regions. The mitochondrial genome of C. chitala displayed 92.87% homology with that of spotted knifefish, C. ornata (AP008923.1), followed by 91.4% homology with Indonesian featherback, C. lopis (AP008922.1). The phylogenetic analysis revealed that the mitogenome of C. chitala shares a close relationship with six other notopterids, which diverged in the Eocene period as a result of Gondwanan fragmentation and vicariant evolution of ancestral Osteoglossiform lineages. By applying bioinformatic tools, we elucidated several potential termination-associated sequence motifs, a tandem repeat array, and a short motif of conserved sequence block in the control region of C. chitala mitogenome. Consensus repeat motif and origin of light strand replication displayed predicted and potential secondary hairpin structures. The AT-GC skewness analysis exhibited a prominent negative GC-skew (-0.338) across all PCGs, revealing an "overrepresentation" of cytosine bases. The PCGs of C. chitala had the highest codon adaptation indices ranging from 0.707 to 0.816 compared to its congeners. Investigation of relative synonymous codon usage patterns revealed that a substantial set of codons in the C. chitala mitogenome were "overrepresented" and "underrepresented" indicating clear existence of codon usage bias. Comparative mutation rate analysis demonstrated that nearly all PCGs, excluding COX2, ND5, and CYTB of C. chitala mitogenome acquired non-synonymous to synonymous substitution rates (dN/dS) less than 0.1 proving the existence of intense purifying selection.
conclusionWe reported the first complete, verified, reference mitogenome of C. chitala and revealed distinct codon usage bias and strong purifying selection.
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