New mitochondrial genomes of three whip spider species from the Amazon (Arachnida, Amblypygi) with phylogenetic relationships and comparative analysis

Abstract

The complete mitochondrial genomes of the whip spiders Charinus carajas, C. ferreus, and Heterophrynus longicornis were sequenced, annotated, and compared with other mitogenomes of whip spiders and arachnids. The three new mitogenomes have the 37 genes usually observed in Metazoa: 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs), plus a non-coding control region (CR). Most PCGs presented an ATN start codon, except cox1 in both Charinus species, initiating with TTA. Most PCGs terminated with stop codons TAA or TAG, except nad5 of C. carajas and cox3 of H. longicornis, which presented an incomplete stop codon (T). The Ka/Ks ratios were less than one for all the PCGs, indicating these genes are under purifying selection. All the tRNAs, except for serine 1 (trnS1), had the typical cloverleaf-shaped secondary structure. All the phylogenetic analyses resolved Charinus carajas and C. ferreus as monophyletic groups. Nonetheless, we did not recover the monophyly of Heterophrynus longicornis. The phylogenies under partitioned models did not recover suprageneric taxonomic groups as clades, but the Bayesian inference under the CAT infinite mixture model recovered the family Phrynidae and the superfamily Phrynoidea as monophyletic groups.

Keywords: Charinus; Heterophrynus; Cave species; Ka/Ks ratio.

Fig. 1

Circular maps of the complete mitochondrial genomes of Charinus carajas, C. ferreus, and Heterophrynus longicornis, showing the PCGs (CDS), rRNAs, tRNAs, and the control region. The images were generated using the CGView/Proksee online server (https://proksee.ca/)

Fig. 2

Box plot for pairwise divergence of Ka/Ks ratio of the 13 PCGs in the mitogenomes of Amblypygi (n = 5: Charinus carajas, C. ferreus; Damon diadema, Heterophrynus longicornis and Phrynus sp.). The analysis was computed in DnaSP v6

Fig. 3

Phylogenetic trees showing the relationship among the species herein sequenced with other arachnids using maximum likelihood (ML) (a–c) and Bayesian analyses (d–f). Branches in blue represent the genus Charinus; branches in green represent the genus Heterophrynus. Numbers on nodes are SH-aLRT/UFBoot supports in ML analyses and posterior probabilities (PP) in percentage in Bayesian analyses; asterisks indicate full node supports (i.e., SH-aLRT, UFBoot and PP = 100). Boldface terminals indicate novel mitogenomic data from this study. The three-gene matrix (a, d) with only cox1 and rRNA sequences has a more extensive taxonomic sampling. The complete datasets, with the mitogenomes of Damon diadema, Phrynus sp., Mastigoproctus giganteus, Schizomus zhensis, and Trichonephila clavata, used nucleotide sequences of 14 genes (12 PCGs and rRNAs) (b, e) or amino acid sequences of the 12 PCGs (c, f). The monophyly of Phrynidae and Phrynoidea was only obtained in the PhyloBayes tree under the CAT-GTR model on amino acids (f).