Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Abstract

Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.

Novel insight into lepidopteran phylogenetics from the mitochondrial genome of the apple fruit moth of the family Argyresthiidae

“…The largest PCG found in A. conjugella mitogenomes is nad5 (1732 bp), and the smallest one is atp8 (162 bp). These results are widely reported in various insect mitogenomes [ 49 , 50 ]. Overlap of the alginate sequences of atp6 and atp8 in A. conjugella (Fig.…”

Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae)

“…As was found in other insects [ 46 , 47 ], our results of the RSCU analyses also indicated that the third codon positions had a higher frequency in the usage of A and T relative to G and C, which may have led to the high codon bias observed. The negative correlation between CBI and ENC indicated that the reduced ENC could lead to high codon usage bias [ 48 ]. We proposed that differences in codon usage bias of Formica mitogenomes might be influenced by both natural selection and mutation pressure, as has also been reported in other insects [ 46 , 48 ].…”

“…The negative correlation between CBI and ENC indicated that the reduced ENC could lead to high codon usage bias [ 48 ]. We proposed that differences in codon usage bias of Formica mitogenomes might be influenced by both natural selection and mutation pressure, as has also been reported in other insects [ 46 , 48 ].…”

Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species.

“…Several studies have used tools to conduct comparative analysis, aiming to understand the correlations in terms of GC contents percentages, presence of complete or short gene repetition, protein-coding and non-coding regions, as well as the consistency between different regions (Ding et al, 2022, Kabiraj et al, 2022), which provides relevant information on proportions of changes in gene rearrangements within each class or family. These studies have provided valuable insights into the proportions of gene rearrangements within each class or family (Montaña-Lozano et al, 2022;Li et al, 2022).…”