Insights into Mitochondrial Rearrangements and Selection in Accipitrid Mitogenomes, with New Data on Haliastur indus and Accipiter badius poliopsis

Abstract

Background/objectives: Accipitridae mitogenomes exhibit unique structural variations, including duplicated control regions (CRs) that undergo gradual degeneration into pseudo-CRs, revealing a complex evolutionary landscape. However, annotation of this characteristic in a subset of accipitrid genomes is lacking. Due to the taxonomic diversity of Accipitridae and the presence of understudied species, comprehensive mitogenomic studies are essential. This study sought to expand and investigate the evolutionary characteristics of Accipitridae mitogenomes.

Methods: A comparative analysis was conducted using the newly acquired complete mitogenomes of Haliastur indus and Accipiter badius poliopsis along with 22 available accipitrid mitogenomes. Codon usage, selective pressure, phylogenetic relationships, and structural variations were comparatively analyzed.

Results: Accipitrid mitogenomes showed a strong AT bias with adenine preference. Most protein-coding genes (PCGs) were under purifying selection except for ND3, which underwent positive selection. The ATP8 gene exhibited relaxed purifying selection on codon usage patterns and showed high genetic variation. Selection for ATP8 and ND3 genes was specific to certain clades of accipitrids. Gene order re-examination revealed both non-degenerate CRs and highly degenerate CR2 fragments in the Accipitridae family. Non-degenerate CRs were found in early diverging species, such as Elanus caeruleus and Pernis ptilorhynchus orientalis, while more recent lineages had highly degenerate CR2 fragments with missing conserved element. Repeat motifs and sequence variations were observed in the functional CR.

Conclusions: These findings suggest that ATP8 and ND3 genes reflect metabolic adaptations, while CRs indicate potential diversification of these accipitrid species. This study provides valuable insights into mitochondrial genome evolution within the Accipitridae family.

Keywords: concerted evolution; duplication; evolution; phylogeny; raptors.

Figure 1

Circular maps of (a) H. indus and (b) A. badius poliopsis mitochondrial genomes.

Figure 2

Codon analysis results of 13 protein-coding genes (PCGs) from 24 species within the Accipitridae family: (a) neutrality plot; (b) effective number of codons (ENc) plot; and (c) box plot of ENc of 24 species in each PCGs.

Figure 3

Mitochondrial gene order and collections of DNA sequence motifs found in both CR1 and CR2 regions.

Figure 4

Nucleotide sequence alignment of the conserved sequence element in CR1. The upper schematic represents the avian control region, with conserved sequence boxes (F, E, D, C, and bird), CSBa, and CSBb in the central domain, shown in red. Conserved sequence elements in other domains are shown in grey. The boxed region highlights sequence variations with corresponding annotations.