First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications.

Zhi-Teng Chen,Yu-Zhou Du

doi:10.3390/ijms18050996

Zhi-Teng Chen, Yu-Zhou Du

Open Access

https://doi.org/10.3390/ijms18050996

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Abstract

The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer (AGN), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae.

Highlights

Nowadays, mitochondrial genome has been one of the most popular molecules widely used in insect taxonomy, population genetics, evolutionary biology and phylogenetics [1]
An insect mitogenome is a double strand circular molecule, ranging from 14–20 kb in length. It usually contains a typical set of 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA genes and two ribosomal RNA genes [2,3]
In N. nankinensis, the anticodons of the 22 transfer RNA (tRNA) were identical with other stoneflies, and the AGG codon was translated as Lys instead of Ser, which indicated the utilization of a variant of the

Summary

Introduction

Mitochondrial genome (mitogenome) has been one of the most popular molecules widely used in insect taxonomy, population genetics, evolutionary biology and phylogenetics [1]. An insect mitogenome is a double strand circular molecule, ranging from 14–20 kb in length. It usually contains a typical set of 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes [2,3]. Functional information on replication derived from these structures has been well discussed, but the transcription features of insect mitogenomes are still little known [6,7,8,9]. The Plecoptera (stoneflies) are a group of ancient insects, which are vital in the reconstruction of the TevhoelPulteicoonpatreyrah(issttoonreyflioefs)inarseecatgs,roaunpdotfhaenyciaernet iinmsepcotsr,tawnhticbhioairnedviictaatloinrsthoef rwecaotnesrtrquucatiloitnyo[f10]. DFinoanllPyC, tGhespehqyuleongceense.tic relationships of N. nankinensis and other stoneflies were reconstructed based on PCG sequences AFisntraullcyt,urthese, pahndylongoevneel tic relfaetaitounresshiopfsthoef eNlo. nngaantkeidneCnRsisinatnhde oNt.hnearnsktinoennesflisiemsitwogeerenormeceonwsetrreuacnteadlybzeadse. dFinoanllPyC, tGhespehqyuleongceense.tic relationships of N. nankinensis and other stoneflies were reconstructed based on PCG sequences

Genome Annotation and Base Composition

PCR Amplification and Sequencing

Phylogenetic Analyses

Conclusions