The complete mitochondrial genome of Psolodesmus mandarinus McLachlan, 1870 (Odonata: Calopterygidae)

Abstract

In the present report, we describe the complete mitochondrial genome of Psolodesmus mandarinus, from the Hualien County, Taiwan. This mitogenome is 15,176 bp long, containing 13 protein-coding, 22 tRNA, and two rDNA genes. Nucleotide composition of the whole mitogenome was 41% for A, 25.92% for T, 19.06% for C, and 14.03% for G. The AT and GC skewness of mitogenome sequence was 0.225 and 0.152, showing the A-skew and C-skew. The reconstructed phylogenetic relationships of 23 Odonata species based on 13 protein-coding genes were highly supported. P. mandarinus grouped within the clade including the other three Calopterygidae genera, Mnais, Vestalis, and Atrocalopteryx was solid supported (100%). It was relatively close to Mnais costalis in the phylogenetic analysis. Our study will be useful for the population genetics, biogeography, and conservation of P. mandarinus in the future.

Keywords:

• Mitochondrial genome
• Psolodesmus mandarinus
• Odonata
• next-generation sequencing

There are only two species in the genus Psolodesmus McLachlan: Psolodesmus mandarinus in Taiwan and P. kuroiwae in Yaeyama islands in the Japanese Ryukyu Archipelago (Hämäläinen 2004; Karjalainen and Hämäläinen 2013). P. mandarinus is distributed in the streams up to 1500 m in Taiwan. The flight period is from March to December. The larval habitat is forest streams. Adults appear near water in the forest. Males often perch near females for courtship. Females usually oviposit on moss-covered stones, submerged leaves, and aquatic plants (Wang 2000). This is the first report of complete mitochondrial sequences for the genus Psolodesmus.

The specimen of Psolodesmus mandarinus, in this study, collected from Fuyuan, Hualien County, Taiwan in November 2015. Total genomic DNA was extracted from the adult’s thorax using the QuickExtract™ DNA Extraction Solution kit (Epicentre, Madison, WI) following the supplier’s instructions. The voucher specimen’s genome DNA and partial specimen were deposited in the Taiwan Forestry Research Institute, Taipei, Taiwan. The complete mitogenome of P. mandarinus was sequenced using the next-generation sequencing method (Illumina MiSeq, San Diego, CA). A total of 2.2 Gb next-generation sequencing paired-end reads were used to assemble the complete mitogenome sequence. The CLC Genomics Workbench (QIAGEN) was used for sequence quality analysis, data trimming, and de novo assembling. The locations of the protein-coding genes, ribosomal RNAs (rRNAs), and transfer RNAs (tRNAs) were predicted by using MITOS Web Server (Bernt et al. 2013) and identified by alignment with other mitogenomes of Odonata. The AT and CG skew was calculated according to the following formulas: AT skew = (A – T)/(A + T) and GC skew = (C – G)/(C + G) (Perna and Kocher 1995). The phylogenetic analysis was done by using MEGA6 (Tamura et al. 2013). The complete mitogenome of P. mandarinus is 15,176 bp in length (GenBank Accession No. MF150044), including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total nucleotide composition of the P. mandarinus mitogenome was 41% for A, 25.92% for T, 19.06% for C, and 14.03% for G. The AT and GC skewness of mitogenome sequence was 0.225 and 0.152, showing the A-skew and C-skew. The skew statistic of protein coding gene was 0.248 and 0.147, showing the same A-skew and C-skew. The gene rearrangement of the P. mandarinus mitogenome is identical to the ancestral insect type (Cameron 2014).

We reconstructed the phylogenetic relationships of 23 Odonata species and two species of outgroup (Pteronarcys princeps and Dinocras cephalotes) based on 13 protein-coding genes with Maximum Likelihood (ML) criteria by using MEGA6. Bootstrap values (1000 replications) greater than 70% are shown at the branch nodes (Figure 1). The majority of nodes had support values higher than 70% and 14 were 100% supported. P. mandarinus grouped within the clade including the other three Calopterygidae genera, Mnais, Vestalis, and Atrocalopteryx was solid supported (100%). P. mandarinus was relatively close to Mnais costalis in the phylogenetic analysis, consistent with the result of Dumont et al. (2005). Mitochondrial markers from our study will be useful for the population genetics, biogeography, and conservation of P. mandarinus in the future.

Figure 1. Phylogenetic tree of the 23 Odonata species based on the sequence of 13 protein-coding genes. The tree was reconstructed with the Maximum Likelihood (ML) criteria using MEGA v.6 (Tamura et al. 2013). Bootstrap values (1000 replications) greater than 70% are shown at the branch nodes. Anax imperator (NC031821) (Herzog et al. 2016), Atrocalopteryx atrata (NC027181), Brachythemis contaminate (NC026305) (Yu et al. 2016), Cordulia aenea (JX963627), Davidius lunatus (NC012644) (Lee et al. 2009), Epiophlebia superstes (NC023232) (Wang et al. 2015), Euphaea decorate (KF718294), Euphaea formosa (NC014493) (Lin et al. 2010), Euphaea ornate (KF718295), Euphaea yayeyamana (KF718293), Hydrobasileus croceus (NC025758), Ischnura elegans (NC031824) (Feindt et al. 2016a), Ischnura pumilio (KC878732) (Lorenzo-Carballa et al. 2014), Megaloprepus caerulatus (NC031823) (Feindt et al. 2016b), Mnais costalis (AP017642), Orthetrum chrysis (KU361233) (Yong et al. 2016), Orthetrum glaucum (KU361232) (Yong et al. 2016), Orthetrum sabina (KU361234) (Yong et al. 2016), Orthetrum testaceum (KU361235) (Yong et al. 2016), Platycnemis foliacea (NC027180), Pseudolestes mirabilis (NC020636), Psolodesmus mandarinus (in this study), Vestalis melania (NC023233) (Chen et al. 2015), Pteronarcys princeps (AY687866) (Stewart and Beckenbach 2006), Dinocras cephalotes (KF484757).

Acknowledgements

We are grateful to Chin-Hua Ai for his field work and Yen-Wei Chou for his assistance in DNA data downloading.

Disclosure statement

No potential conflict of interest was reported by the authors.