Mitochondrial Genomes of Six Snakes (Lycodon) and Implications for Their Phylogeny

Abstract

Background: Colubridae, known to be one of the most species-rich snake families, remains relatively understudied in termshe context of complete mitochondrial genome research. This study provide the first systematic characterization of the mitochondrial genomes of six colubrid species: Lycodon subcinctus, Lycodon rosozonatus, Lycodon fasciatus, Lycodon gongshan, Lycodon futsingensis, and Lycodon aulicus.

Method: In this study, mitochondrial genomes were sequenced using Sanger sequencing. The raw data were subjected to quality- filtered withing using Fastp and subsequently assembled into complete mitochondrial genomes via SPAdes. Gene annotation was performed by Tblastn, Genewise (for CDS coding sequences), MiTFi (for transfer RNAs), and Rfam (for ribosomal RNAs). Sequence analyses were conducted with various tools, including MEGA, tRNAscan-SE, DnaSP, MISA, and REPuter. Finally, phylogenetic trees were reconstructed based on 13 protein-coding genes from 14 species.

Results: The mitogenomes of these six species ranged from 17,143 to 17,298 bp in length and con-sisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 2 control regions. The nucleotide composition of the Colu-bridae mitogenomes was comparable with an A + T composition ranging from 52.1% to 58.8% except for the trnS1 and trnC. All the tRNAs could fold into a stable secondary structure. The Pi and Ka/Ks values suggested that atp8 was the fastest-evolving gene, while cox1 was the most conserved gene. Bayesian inference and maximum likelihood phylogenetic analyses yielded consistent results, with the six sequenced species clus-tering together with their congeneric species. These findings will provide valuable references for further research on the phylogeny of Colubridae.

Keywords: Lycodon; comparative analysis; mitochondrial genome; phylogenetic relationships.

Figure 1

Circular maps of the mitogenomes of L. subcinctus (a), L. rosozonatus (b), L. fasciatus (c), L. gongshan (d), L. futsingensis (e), and L. aulicus (f). Genes are shown in different color blocks. Color blocks being outside the circle indicates that the genes are located on the heavy strand (H-strand); color blocks being within the circle indicates that the genes are located on the light strand (L-strand).

Figure 2

Relative synonymous codon usage (RSCU) values in protein-coding genes (PCGs) of the six Lycodon species.

Figure 3

Nucleotide diversity (a) and the Ka/Ks ratio (b) of PCGs in mitochondrial genomes of 14 species of Lycodon. The red line represent the trend of nucleotide diversity variation.

Figure 4

Phylogenetic estimate of relationships within the 14 Lycodon species based on the 13 PCGs using Bayesian inference (BI) and maximum likelihood (ML) analyses.