The mitochondrial genome of the first luminous click-beetle (Coleoptera: Elateridae) recorded in Asia

Abstract

The nearly complete mitochondrial genome (mitogenome) of Sinopyrophorus schimmeli Bi et Li, the luminous click beetle recorded in Asia, is described in this study. It totalizes 15,951 bp and contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and most part of AT-rich region. Thirteen PCGs totalize 11,136 bp, start with ATN, stop with TAA/G, except for cox2 and cox3 stopping with T. The rrnL and rrnS are 1280 and 862 bp, respectively. The AT-rich region contains several structures characteristic of the Coleoptera. The phylogenetic analyses of 13 PCGs confirm the position of S. schimmeli in Elateridae.

Keywords:

• Mitogenome
• the first luminous click beetle
• Asia
• phylogenetic implication
• next-generation sequencing

The cosmopolitan family Elateridae Leach currently contains almost 10,000 species in more than 400 genera (Kishii 1987; Costa et al. 2010), but its luminous taxa were previously reported to mainly distribute in the Agrypnine tribe Pyrophorini (approximately 200 species) from Neotropical region and Oceania, with two other Neotropical species in Thylacosterninae (Balgus schnusei Heller) and Campyloxeninae (Campyloxenus pyrothorax Fairmaire) (Costa 1975; Stibick 1979; Costa 1984; Costa et al. 2010; Oba et al. 2010; Amaral et al. 2012; Mitani et al. 2013). To date, only 11 Elateridae complete mitogenomes (including four luminous species) have been reported (Arnoldi et al. 2007; Amaral et al. 2016; Gerritsen et al. 2016; Linard et al. 2016) or deposited in GenBank.

Very interestingly, the first luminous click beetle recorded in Asia was found in China recently and named as Sinopyrophorus schimmeli Bi et Li (Bi et al. submitted to Zookey). Here, its nearly complete mitochondrial genomic sequence assembled using high-throughput next-generation sequencing technology is described. Male adults of S. schimmeli were collected from the vicinity of Husa (altitude, 1770 m), Longchuan County, Yunnan Province, China, during 15–25 June 2017 by Wenxuan Bi, and then stored in 75% alcohol at −20 °C. Total genomic DNA (gDNA) of one male was isolated using a Gentra Puregene Blood kit (Qiagen, Hilden, Germany). Library (150-bp insert size) was prepared and sequenced on the Illumina HisSeq4000. The mitochondrial genome assembly was performed as previously described (Tang et al. 2014), gene annotation was performed by MITOS webserver (Bernt et al. 2013) and Dual Organellar Genome Annotation (DOGMA) (Wyman et al. 2004) following indications by Cameron (2014) and corrected manually. Voucher specimens are deposited in Kunming Natural History Museum of Zoology, Chinese Academy of Sciences.

The nearly complete mitogenome of S. schimmeli totalizes 15,951 bp, with a gap region within control region (GenBank accession No. MH065615). S. schimmeli mitogenome contains 37 typical mitochondrial genes (13 PCGs, 22 tRNA genes, and two rRNA genes). The total length of all 13 PCGs was 11,136 bp, counting 69.81% of the whole mitogenome. A total of 22 tRNA genes fluctuate from 62 to 71 bp, with the classical clover-leaf structure except for trnS1 (AGN) lacking a dihydrouridine (DHU) arm that replaced by a simple loop. Such phenomenon is also observed in many metazoan mitogenomes (Wolstenholme 1992b ; Du et al. 2016). trnS (AGN) has ‘TCT’ anticodon instead of ‘GCT’, as in many other insects (Li et al. 2011; Wang et al. 2012; Du et al. 2016). The size of rrnL (1280 bp) and rrnS (862 bp) of S. schimmeli largely agree with those of other Elateridae species. The nearly complete AT-rich region (1242 bp) contains several structures characteristic of the Coleoptera.

Using Tribolium castaneum as outgroup, a phylogeny of 53 Elateroidea species, including S. schimmeli, was reconstructed based on nucleotide sequence of 13 PCGs with the maximum-likelihood (ML) method through RAxML version 7.0.4 (MÜnchen) (Stamatakis et al. 2008). The result indicated that S. schimmeli formed a clade with other click beetles (Figure 1).

Figure 1. Inferred phylogenetic relationships among Elateroidea based on the nucleotide sequence of concatenated 13 protein-coding genes (PCGs) using maximum-likelihood (ML) analysis. Tribolium castaneum was used as outgroup. Bootstrap values lower than 50% are not shown. Black square denotes luminous clades.

Acknowledgements

The authors would thank Mr. Xin Chen and Miss Ru Zhang for helping in data analysis. LXY and WW designed this study. HJW, LXY, and BWX wrote this manuscript. HJW made data analysis. DZW, LGC, and ZRP carried out experiments.

Disclosure statement

The authors declare no conflicts of interest.

Additional information

Funding

This work was funded by grants from the National Natural Science Foundation of China (No. 31472035) and Yunnan Provincial Science and Technology Department (No. 2014FB179) to LXY.