Complete mitochondrial genomes and phylogenetic relationships of the genera Nephila and Trichonephila (Araneae, Araneoidea)

Abstract

Spiders of the genera Nephila and Trichonephila are large orb-weaving spiders. In view of the lack of study on the mitogenome of these genera, and the conflicting systematic status, we sequenced (by next generation sequencing) and annotated the complete mitogenomes of N. pilipes, T. antipodiana and T. vitiana (previously N. vitiana) to determine their features and phylogenetic relationship. Most of the tRNAs have aberrant clover-leaf secondary structure. Based on 13 protein-coding genes (PCGs) and 15 mitochondrial genes (13 PCGs and two rRNA genes), Nephila and Trichonephila form a clade distinctly separated from the other araneid subfamilies/genera. T. antipodiana forms a lineage with T. vitiana in the subclade containing also T. clavata, while N. pilipes forms a sister clade to Trichonephila. The taxon vitiana is therefore a member of the genus Trichonephila and not Nephila as currently recognized. Studies on the mitogenomes of other Nephila and Trichonephila species and related taxa are needed to provide a potentially more robust phylogeny and systematics.

Figure 1

Complete mitogenomes of Nephila pilipes, Trichonephila antipodiana, T. vitiana (previously N. vitiana) and T. clavata with BRIG visualization showing the protein-coding genes, rRNAs and tRNAs. GC skew is shown on the outer surface of the ring whereas GC content is shown on the inner surface. The anticodon of each tRNAs is shown in parentheses. Figure generated by BRIG Development version (0.95-dev.0004) (http://brig.sourceforge.net/).

Figure 2

Amino acid frequency (A) and relative synonymous codon usage (B) of PCGs in the Nephila and Trichonephila mitogenomes generated using MEGAX (https://www.megasoftware.net/). NP, Nephila pilipes; TA, Trichonephila antipodiana; TV, Trichonephila vitiana (previously N. vitiana); TC, Trichonephila clavata.

Figure 3

Box plot for pairwise divergence of Ka/Ks ratio (mean ± SD, and range) for 13 PCGs of Nephila (n = 1) and Trichonephila (n = 3) mitogenomes generated using DnaSP6.0. (http://www.ub.edu/dnasp/).

Figure 4

Cloverleaf structure of the 22 inferred tRNAs in the mitogenomes of Nephila and Trichonephila mitogenomes obtained from MITOS web-server (http://mitos.bioinf.uni-leipzig.de/index.py).

Figure 5

Fifteen tandem repeats of ATAGA motif with TATATACATAT stretch (except one each with TAT, TATGTACATAT, and TATATACATAA) in the control region of Trichonephila clavata checked using Tandem Repeats Finder (http://tandem.bu.edu/trf/trf.html).

Figure 6

Bayesian inference phylogenetic tree based on (a) 13 PCGs and 2 rRNA genes, (b) 13 protein-coding genes, and (c) 2 rRNA genes of the whole mitogenomes of Nephila, Trichonephila and other araneid taxa with Tetragnatha taxa as outgroup. Trichonephila vitiana (previously Nephila vitiana); Numeric values at the nodes are Bayesian posterior probabilities. Figures generated by Mr Bayes v.3.1.2 (https://nbisweden.github.io/MrBayes/download.html).