Characterization of the nearly complete mitochondrial genome of a Chinese endemic stonefly species, Caroperla siveci (Plecoptera: Perlidae)

Abstract

The stonefly Caroperla Siveci, an unusual and endemic new species, only distributed to the Wuyi Mountain, Fujian Province, China. Here, we sequenced and determined the complete mitochondrial (mt) genome of C. Siveci representing the genus Caroperla for the first time. The total genome size is 15,353 bp in length. The nucleotide composition is A (35.2%), T (32.3%), C (20.5%), and G (11.9%). Mostly PCGs use the typical start codon ATN, except ND1, ND2, and ND5, which start with TTG, GTG, and GTG. The COI, COIII, and ND5 genes stopped with incomplete stop codon T and the rest use stop codon TAN. C. siveci was recovered as a sister-group to the clade ((Acroneuria + Dinocras) + (Togoperla + Kamimuria)). This mitogenome will assist a variety of biodiversity researches, especially in taxonomy and phylogeny of stoneflies.

Keywords:

• Mitochondrial genome
• phylogenetics
• Caroperla Siveci

ptPerlidae consist of about 400 species which are widely distributed in the northern hemisphere with a few genera extending into the southern hemisphere in Africa and South America (DeWalt et al. 2018). Up till now, there are only three species in the genus Caroperla (Perlidae) in the world. Kohno (1946) proposed the first species C. pacifica only from Japan, and later the second species C. longiseta from Thailand was described, the genus Caroperla was remained as enigmatic and unique genus among Perlidae (Sivec and Stark 2010). The stonefly C. Siveci was rare and limited from the Fujian Province of China, was considered as the third species in the small genus Caroperla (Li and Wang 2013). In this study, we assembled and characterized the mitochondrial genome of C. siveci by high-throughput sequencing method for the first time. The sequence had been deposited in GenBank with accession number MG677942.

The specimen of C. siveci was collected by Weihai Li at Wuyi Mountains, Fujian Province, China in 2016. Samples and voucher specimens were deposited in Henan institute of Science and Technology, China. Whole genomic DNA was extracted from the thorax muscle using QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). The mitogenomes were amplified and sequenced as described in previous studies (Li et al. 2017; Wang et al. 2017; Liu et al. 2018; Wang et al. 2018). Sequence reads were assembled into contigs with BioEdit version 7.0.5.3 (Hall 1999).

The nearly complete C. siveci mitogenome was 15,353 bp in length. The nucleotide composition of mitogenome of C. siveci was clearly biased towards A/T nucleotides (A = 35.2%, T = 32.3%, G = 11.9%, C = 20.5%). The A + T content of PCGs (Protein coding genes), tRNAs, and rRNAs was 65.7%, 70.5%, and 72.8%, respectively. Ten PCGs used ATN as the start codon, while ND1, ND2, and ND5 used TTG, GTG, and GTG, respectively. The stop codons mostly used were TAN, while three PCGs (COII, COIII, and ND5) stopped with the incomplete stop codon T. All 22 typical tRNAs found in the invertebrate mitogenomes were found in C. siveci, ranging in size from 65 to 72 bp. The length of rrnS and rrnL was determined to be 824 bp and 1345 bp with A + T content as 70.5% and 74.3%, respectively.

Sequences of 13 PCGs and 2 rRNAs from 6 available Perlid species and 2 species (Styloperla spinicercia and Cryptoperla stilifera as outgroups) were used in the present phylogenetic analysis. In this study, the Bayesian (BI) and maximum likelihood analyses based on the PCGR matrices generated the phylogenic trees with the same topologies (Figure 1). C. siveci was recovered as a sister-group to the clade ((Acroneuria + Dinocras) + (Togoperla + Kamimuria)). While in traditional morphology-based classification, the relationship of these five genera was (Acroneuria + Caroperla) + (Dinocras + (Togoperla + Kamimuria)) (Sivec et al. 1988). Our result was partially differed from those results due to lack of data. Additional taxon sampling will be required to resolve this problem.

Figure 1. Bayesian inference and maximum likelihood phylogenetic trees for 8 species based on the mitogenomic sequence data of 13 PCGs and 2 rRNAs.

Disclosure statement

The authors report no conflict of interest.

Additional information

Funding

This work was supported by the Initial Project of Henan Institute of Science and Technology [No. 2015026], and the Landmark Innovative Project of Henan Institute of Science and Technology [No. 2015BZ04].