Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses

Abstract

In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.

Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

“…nucleotides, and a stem with complementary bases) were similar to the mitochondrial origins for replication of L-strand (OL) that existed in vertebrate mitogenomes [49,50]. This OL-like region is only observed in heptageniids, but not found in other families of Ephemeroptera.…”

“…As shown in Figure 5 , all IGSs could be folded into a stable stem–loop structure. The features mentioned above (stem–loop hairpin structure, a size of approximately 30 nucleotides, and a stem with complementary bases) were similar to the mitochondrial origins for replication of L-strand (OL) that existed in vertebrate mitogenomes [ 49 , 50 ]. This OL-like region is only observed in heptageniids, but not found in other families of Ephemeroptera.…”

Comparative Mitogenomes of Two Coreamachilis Species (Microcoryphia: Machilidae) along with Phylogenetic Analyses of Microcoryphia

“…In the A + T-rich region, it was reported that stem–loop structures could be formed. Also, it has been mentioned that conserved regions of single stem–loop structure (the 5′ flanking sequences with “TTATA”, while 3′ flanking sequences with a “G(A)nT” motif) have been observed in a variety of insect orders [ 24 , 26 ]. This stem–loop structure in the A + T-rich region was suggested as the site of the initiation of secondary strand synthesis [ 21 , 24 , 26 ].…”

“…Kim et al [ 25 ] suggested that hairpin structures are important for precise cleavage of the mature protein-coding genes. In addition, potential hairpin structures were also found in the A + T-rich region of insect mitogenomes, which was considered to be the initiation site of secondary strand synthesis [ 21 , 24 , 26 ]. However, the hairpin structures found in insects were relatively short (about 10 bp), and only a few studies have inferred an association between phylogenetic relationships and hairpin structures.…”

The complete mitochondrial genome sequence of Asclepios apicalis (Gerromorpha: Gerridae)

“…The characters of base composition and distribution were analyzed using Geneious Prime 2020 software (Kearse et al 2012). The mitogenome was annotated using MITOS web server (Yu et al 2019), and was manually checked and adjusted the annotation using Aquarius paludum (GenBank accession number: NC012841) as the reference sequence. The online tRNAscan-SE search server (Lowe and Chan 2016) was used to annotate the transfer RNA (tRNA) gene to determine its position, and the parameter settings were default.…”