Gaining insights into the compositional constraints and molecular phylogeny of five silkworms mitochondrial genome

Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae)

To elucidate phylogenetic relationships within the leafhopper's subfamily Megophthalminae (Hemiptera: Cicadellidae), mitogenomes of 12 species of the subfamily were sequenced and assembled. These were added to the mitogenomes of the eight other species that are currently available. Mitogenome size ranged from 15,193 bp in Onukigallia onukii (Matsumura, 1912) to 15,986 bp in Multinervis guangxiensis (Li and Li, 2013), they all contained 37 genes, and gene order was similar to that in other leafhoppers. Nucleotide composition analysis showed that the AT content was higher than that of GC, and the protein-coding genes usually ended with A/T at the 3rd codon position. The Ka/Ks ratio showed that the CYTB gene has the slowest evolutionary rate, while ND4 is the gene with the fastest evolutionary rate. Relative synonymous codon usage analysis revealed the most frequently used codon was UUA (L), followed by CGA (R), and the least frequently used codon was CCG (P). Parity plot and neutrality plot analyses showed that the codon usage bias of mitochondrial genes was influenced by natural selection and mutation pressure. However, natural selection plays a major role, while the effect of mutation pressure was small. Effective number of codons values were 40.15-49.17, which represented relatively low codon bias. Phylogenetic analyses based on three datasets (AA, 13PCG, 13PCG_2rRNA) using two methods (maximum likelihood and Bayesian inference). In the obtained topology, the Megophthalminae species were clustered into a monophyletic group. In conclusion, our results clarify structural modules of the mitochondrial genes and confirm the monophyly of Megophthalminae within Cicadellidae.

Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae)

Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)

Japanagallia is a genus of Cicadomorpha in the family of leafhoppers that are plant piercing-sucking insects, and it is difficult to distinguish by morphological characteristics. So far, only one complete mitochondrial genome data has been reported for the genus Japanagallia. Therefore, in order to better understand this group, we assembled and annotated the complete mitochondrial genomes of five Japanagallia species, and analyzed their codon usage patterns. Nucleotide composition analysis showed that AT content was higher than GC content, and the protein-coding sequences preferred to end with A/T at the third codon position. Relative synonymous codon usage analysis revealed most over-represented codon ends with A or T. Parity plot analysis revealed the codon usage bias of mitochondrial genes was influenced by both natural selection and mutation pressure. In the neutrality plot, the slopes of regression lines were < 0.5, suggesting that natural selection was playing a major role while mutation pressure was of minor importance. The effective number of codons showed that the codon usage bias between genes and genomes was low. Correspondence analysis revealed that the codon usage pattern differed among 13 protein-coding genes. Phylogenetic analyses based on three datasets using two methods (maximum likelihood and Bayesian inference), restored the Megophthalminae monophyly with high support values (bootstrap support values (BS) = 100, Bayesian posterior probability (PP) = 1). In the obtained topology, the seven Japanagallia species were clustered into a monophyletic group and formed a sister group with Durgade. In conclusion, our study can provide a reference for the future research on organism evolution, identification and phylogeny relationships of Japanagallia species.

Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of Four Krisna Species (Hemiptera: Cicadellidae: Iassinae)

Krisna species are insects that have piercing-sucking mouthparts and belong to the Krisnini tribe in the Iassinae subfamily of leafhoppers in the Cicadellidae family. In this study, we sequenced and compared the mitochondrial genomes (mitogenomes) of four Krisna species. The results showed that all four mitogenomes were composed of cyclic double-stranded molecules and contained 13 protein-coding genes (PCGs) and 22 and 2 genes coding for tRNAs and rRNAs, respectively. Those mitogenomes exhibited similar base composition, gene size, and codon usage patterns for the protein-coding genes. The analysis of the nonsynonymous substitution rate (Ka)/synonymous substitution rate (Ks) showed that evolution occurred the fastest in ND4 and the slowest in COI. 13 PCGs that underwent purification selection were suitable for studying phylogenetic relationships within Krisna. ND2, ND6, and ATP6 had highly variable nucleotide diversity, whereas COI and ND1 exhibited the lowest diversity. Genes or gene regions with high nucleotide diversity can provide potential marker candidates for population genetics and species delimitation in Krisna. Analyses of parity and neutral plots showed that both natural selection and mutation pressure affected the codon usage bias. In the phylogenetic analysis, all subfamilies were restored to a monophyletic group; the Krisnini tribe is monophyletic, and the Krisna genus is paraphyletic. Our study provides novel insights into the significance of the background nucleotide composition and codon usage patterns in the CDSs of the 13 mitochondrial PCGs of the Krisna genome, which could enable the identification of a different gene organization and may be used for accurate phylogenetic analysis of Krisna species.

Nutritional aspects and dietary benefits of "Silkworms": Current scenario and future outlook

In the current scenario, it is estimated that by 2050, there will be an additional 2.5 billion people and a 70% increase in food demand. Crop yields are not increasing fast enough to support global needs, and world agriculture is facing several serious challenges. Therefore, insects can be a nutritious alternative to meet the ever-increasing food demand in the present and future. The majority of insect consumption occurs in developing countries, with approximately 1,900 insect species consumed worldwide. Food and feed derived from them are of high quality, have a high feed conversion ratio and emit a low level of greenhouse gases. Among insects silkworms are beneficial to humans, not only because of their high nutritional value, but also because of their several pharmacological properties. Silkworm eggs, larvae, and pupae contains high amount of proteins, oils, minerals, vitamins, and several other beneficial components which are nutritious as well as have positive effect on human health. Studies have shown that silkworm pupae protect the liver, enhance immunity, inhibit apoptosis, inhibit cancer, inhibit tumor growth, inhibit microbial growth, regulate blood glucose and blood lipids, and lower blood pressure. This review paper summerized the nutritional value of different life stages of silkworm, nutritional comparison of silkworm with the major human foods, and the effects of silkworm consumption on human health, thus ittargets to generate interest toward in sericulture and improve human health by using silkworm as a nutritious food and attain sustainability in food and nutritional security.

Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications

The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea.

Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae)

The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.

Silkworm Pupae: A Functional Food with Health Benefits for Humans

Silkworm pupae are insects that are beneficial to human health, not only for their high nutritional value but, more importantly, for the variety of pharmacological functions they can perform when consumed. Currently, there is a lot of interest in the pharmaceutical applications of silkworm pupae. In recent years, the biological functions of domestic silkworm pupae have gradually been identified and confirmed, especially for their beneficial effects on human health. Studies have found that silkworm pupae have positive effects on liver protection, immune enhancement, antiapoptosis, antitumour, antibacterial, regulation of blood glucose and blood lipids, and lowering of blood pressure. However, the pharmacological mechanisms and systemic safety of silkworm pupae have not been systematically evaluated. In this paper, the nutritional composition of the pupae of the domestic silkworm is first summarised. The pharmacological functions of silkworm pupae and their components are then classified, and their mechanisms of occurrence are described. In addition, we provide a preliminary evaluation of the safety of silkworm pupae, analyse their application prospects, and suggest future directions for further pharmacological function studies. The aim is to generate interest in the promotion of human health through the use of silkworm pupae.