Complete mitochondrial genomes of three skippers in the tribe Aeromachini (Lepidoptera: Hesperiidae: Hesperiinae) and their phylogenetic implications

Complete mitochondrial genome of Rectorisluxiensis (Teleostei, Cyprinidae): characterisation and phylogenetic implications

Mitochondrial genomes (mitogenomes) are widely used in scientific studies on phylogenetic relationships, molecular evolution and population genetics. Here, we sequenced and analysed the mitogenome of Rectorisluxiensis, a Yangtze River drainage endemic, but threatened cyprinid fish of Labeoninae. The complete mitogenome of R.luxiensis was 16,592 bp in length, encoding 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region. The mitogenome showed a high A+T content (58.2%) and a positive AT-skew (0.10) and negative GC-skew (-0.25) base composition pattern. All the 13 PCGs were found to start with ATG codons, except for the COXI, in which GTG was the start codon. The ratio of non-synonymous and synonymous substitutions (Ka/Ks) of all the 13 PCGs were less than 1, indicating negative or purifying selection evolved in these genes. Comparatively speaking, the evolutionary rate of ATP8 was the fastest and ND4L was the slowest. All tRNAs could fold into a typical cloverleaf secondary structure, except tRNA^Ser1 that lacked a dihydrouridine arm. Phylogenetic relationships, based on the PCGs dataset of 91 mitogenomes of Labeoninae, showed that R.luxiensis grouped with Rectorisposehensis and they formed a monophyletic Rectoris. However, many non-monophyletic genera were revealed in labeoninae fishes, such as Cirrhinus, Decorus, Garra, Labeo and Pseudocrossocheilus, which indicated that the validities of some traditional genera required a further check. This study reported the complete mitogenome of R.luxiensis for the first time, which provided valuable data for future molecular evolution and conservation related studies of Rectoris and other species in Labeoninae.

Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis

Rhodeuscyanorostris Li, Liao & Arai, 2020 is a freshwater fish that is endemic to China and restricted to Chengdu City in Sichuan Province. This study is the first to sequence and characterize the complete mitochondrial genome of R.cyanorostris. The mitogenome of R.cyanorostris is 16580 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the sequence is 28.5% A, 27.6% C, 26.4% T, and 17.5% G, with a bias toward A+T. The genome structure, nucleotide composition, and codon usage of the mitogenome of R.cyanorostris are consistent with those of other species of Rhodeus. To verify the molecular phylogeny of the genus Rhodeus, we provide new insights to better understand the taxonomic status of R.cyanorostris. The phylogenetic trees present four major clades based on 19 mitogenomic sequences from 16 Rhodeus species. Rhodeuscyanorostris exhibits the closest phylogenetic relationship with R.pseudosericeus, R.amarus, and R.sericeus. This study discloses the complete mitochondrial genome sequence of R.cyanorostris for the first time and provides the most comprehensive phylogenetic reconstruction of the genus Rhodeus based on whole mitochondrial genome sequences. The information obtained in this study will provide new insights for conservation, phylogenetic analysis, and evolutionary biology research.

Comparative Mitogenomic Analysis of Five Awl Skippers (Lepidoptera: Hesperiidae: Coeliadinae) and Their Phylogenetic Implications

Simple Summary

The subfamily Coeliadinae (Lepidoptera: Hesperiidae) is a unique group of over 70 species in the butterfly family, and its mitochondrial genome data still needs to be supplemented. This study sequenced and analyzed five additional complete mitochondrial genomes of the Coeliadinae species (Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis) and compared them in detail with those of the other known skipper mitogenomes. All five of these mitogenomes have the typical lepidopteran mitogenome characteristics of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding region. Our results indicate that their structure, nucleotide composition, codon usage, secondary structure of tRNAs, and so on, are highly conserved. Expanded sampling and gene data from the GenBank, phylogenetic analyses using maximum likelihood, and Bayesian inference methods indicate that Coeliadinae is monophyletic. These results contribute toward refining the phylogeny.

Abstract

To determine the significance of mitochondrial genome characteristics in revealing phylogenetic relationships and to shed light on the molecular evolution of the Coeliadinae species, the complete mitochondrial genomes (mitogenomes) of five Coeliadinae species were newly sequenced and analyzed, including Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis. The results show that all five mitogenomes are double-strand circular DNA molecules, with lengths of 15,340 bp, 15,295 bp, 15,304 bp, 15,295 bp, and 15,289 bp, respectively, and contain the typical 37 genes and a control region. Most protein-coding genes (PCGs) begin with ATN, with 3 types of stop codons including TAA, TAG, and an incomplete codon T-; most of the genes terminate with TAA. All of the transfer RNA genes (tRNAs) present the typical cloverleaf secondary structure except for the trnS1. Several conserved structural elements are found in the AT-rich region. Phylogenetic analyses based on three datasets (PCGs, PRT, and 12PRT) and using maximum likelihood (ML) and Bayesian inference (BI) methods show strong support for the monophyly of Coeliadinae, and the relationships of the five species are (B. exclamationis + ((B. harisa + (B. oedipodea + B. miracula)) + H. schoenherr)).