Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

Abstract

A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorpha coarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae) and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae) were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of A. coarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida) and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY) could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes.

The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes

“…(Table 1). The variation of the Chilopoda mitogenome size was relatively conserved, which was consistent with that reported in Diplopoda, an animal class close to Chilopoda (Dong et al 2016). The gene distribution was mainly presented on the plus strand of the S. mutilans mitogenome, and only four PCGs and two rRNA genes were located on the minus strand (Figure 1).…”

Complete mitochondrial genome ofSellanucheza jaegeriGolovatch, 2013 by next generation sequencing (Polydesmida: Paradoxosomatidae) and phylogenetic analysis in Diplopoda

“…Its genes' arrangement and orientation are matched known Polydesmida mtDNA pattern (Dong et al 2016). The typical ATG start codon is present in all PCGs except for ND1 and ND2 being with ATA and TTG, respectively.…”

The complete mitochondrial genome of the millipede Epanerchodus koreanus Verhoeff, 1937 collected in limestone cave of Korea (Polydesmidae: Polydesmida)

“…Raw sequences from Illumina NovaSeq6000 (Macrogen, Korea) were filtered by Trimmomatic v0.33 (Bolger et al 2014) and de novo assembled by Velvet v1.2.10 (Zerbino and Birney 2008), SOAPGapCloser v1.12 (Zhao et al 2011), BWA v0.7.17 (Li 2013, and SAMtools v1.9 (Li et al 2009) under the environment of Genome Information System (GeIS; http://geis.infoboss.co.kr/). Geneious R11 v11.1.5 (Biomatters Ltd, Auckland, New Zealand) was used to annotate based on three mitochondrial genomes of Appalachioria falcifera (NC_021933; Brewer et al 2013), Asiomorpha coarctata (KU721885; Dong et al 2016), and Xystodesmus sp. (KU721886; Dong et al 2016).…”

“…Geneious R11 v11.1.5 (Biomatters Ltd, Auckland, New Zealand) was used to annotate based on three mitochondrial genomes of Appalachioria falcifera (NC_021933; Brewer et al 2013), Asiomorpha coarctata (KU721885; Dong et al 2016), and Xystodesmus sp. (KU721886; Dong et al 2016).…”

“…Figure1. Bayesian inference (1,000,000 generations), maximum-likelihood (10,000 bootstrap repeats), and neighbor-joining (10,000 bootstrap repeats) phylogenetic trees of eleven Diplopoda, and one Symphlya mitochondrial genomes as an out group: Epanerchodus koreanus (MT898420; This study), Asiomorpha coarctata (KU721885;Dong et al 2016), Xystodesmus sp. (KU721886; Dong et al 2016), Appalachioria falcifera (NC_021933; Brewer et al 2013), Anaulaciulus koreanus (NC_034656; Woo HJ et al 2017), Antrokoreana gracilipes (NC_010221; Woo H-J et al 2007), Narceus annularus (NC_003343; Lavrov et al 2002), Brachycybe lecontii (NC_021934; Brewer et al 2013), Sphaerotheriidae sp.…”