Different mitogenomic codon usage patterns between damselflies and dragonflies and nine complete mitogenomes for odonates

The complete mitochondrial genome of Chlorogomphus shanicus Wilson, 2002 (Anisoptera: Chlorogomphidae), an endemic species in South China

In this study, the complete mitochondrial genome of Chlorogomphus shanicus Wilson, 2002 was reported, and the maximum-likelihood (ML) phylogenetic tree was constructed using 13 protein-coding genes (PCGs). The total length of the mitogenome of C. shanicus was 15,497 bp. Twelve PCGs started with ATN codons, except cox1 began with TTG codon. Most transfer RNA genes (tRNAs) were predicted to fold in a typical cloverleaf structure, except the trnS1 (gct), which lacked a dihydrouridine arm that had been simplified to a loop. The phylogenetic tree showed that Anisoptera was split into two clades, and revealed that C. shanicus was closely related to Cordulegaster boltonii (Donovan, 1807) which is endemic to Europe.

Comparative analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial genome of Thrips parvispinus

Thrips parvispinus is a serious sucking pest on a number of economically important crops in the oriental region. It has gained importance recently for its drastic range extension distribution as an invasive pest. Here, the complete mitochondrial genome (15,067 bp) of Thrips parvispinus was sequenced and characterized. It possesses 37 genes and the putative noncoding region is duplicated. Comparative analyses of nucleotide diversity, skewness, codon usage bias, and selection pressure in mitochondrial protein-coding genes of the available 31 thrips mitogenomes (24 Terebrantia + 7 Tubulifera) were performed. Phylogenetic analysis showed a sister relationship of T. parvispinus to the clade (T. florum + T. hawaiiensis). Phylogenetic analyses formed the monophyly of subfamilies Phlaeothripinae and Idolothripinae within the family Phlaeothripidae (Suborder Tubulifera). Low nucleotide diversity was indicative of reversal of strand asymmetry in the Tubulifera. Neutrality analysis showed that directional mutation plays a major role in shaping codon usage bias in both suborders. Principal component analysis indicated distinct codon usage patterns in each suborder. Our data suggested weaker selection constrains on Terebrantia than in the Tubulifera. More tubuliferan mitogenomes are required to resolve previous classification hypotheses and elucidate genome evolution in these two suborders.

Comparative genome and phylogenetic analysis revealed the complex mitochondrial genome and phylogenetic position of Conopomorpha sinensis Bradley

Conopomorpha sinensis Bradley is a destructive pest that causes severe economic damage to litchi and longan. Previous C. sinensis research has focused on population life tables, oviposition selectivity, pest population prediction, and control technology. However, there are few studies on its mitogenome and phylogenetic evolution. In this study, we sequenced the whole mitogenome of C. sinensis by the third-generation sequencing, and analyzed the characteristics of its mitogenome by comparative genome. The complete mitogenome of C. sinensis is a typical circular and double-stranded structure. The ENC-plot analyses revealed that natural selection could affect the information of codon bias of the protein-coding genes in the mitogenome of C. sinensis in the evolutionary process. Compared with 12 other Tineoidea species, the trnA-trnF gene cluster of tRNA in the C. sinensis mitogenome appears to have a new arrangement pattern. This new arrangement has not been found in other Tineoidea or other Lepidoptera, which needs further exploration. Meanwhile, a long AT repeated sequence was inserted between trnR and trnA, trnE and trnF, ND1 and trnS in the mitogenome of C. sinensis, and the reason for this sequence remains to be further studied. Furthermore, the results of phylogenetic analysis showed that the litchi fruit borer belonged to Gracillariidae, and Gracillariidae was monophyletic. The results will contribute to an improved understanding of the complex mitogenome and phylogeny of C. sinensis. It also will provide a molecular basis for further research on the genetic diversity and population differentiation of C. sinensis.

Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

BACKGROUND

Soft scales (Hemiptera: Coccidae), including important agricultural and forestry pests, are difficult to identify directly by morphological characters. Mitochondrial genomes (mitogenomes) have been widely used in species identification and phylogenetic research. However, only three complete mitogenomes, and very few mitochondrial genes of scale insects (Hemiptera: Coccoidea) can be searched in GenBank. Mitogenome comparisons between scale insects or between scale insects and other hemipteran species have not yet been reported.

RESULTS

In this study, detailed annotation of three new mitogenomes and comparative analysis of scale insects were completed, as well as comparative analysis of the gene composition, gene arrangement, codon usage and evolutionary forces between scale insects and 488 other hemipteran species for the first time. We found that high A + T content, gene rearrangement and truncated tRNAs are common phenomena in soft scales. The average A + T content and codon usage bias of scale insects are higher and stronger than those of other hemipteran insects, respectively. The atp8 gene of Hemiptera and nine other protein-coding genes of scale insects are under positive selection with higher evolutionary rates.

CONCLUSIONS

The study revealed the particularity of the scale insect mitogenomes, which will provide a good reference for future research on insect phylogenetic relationships, insect pest control, biogeography and identification.

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.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Neurothemis fulvia (Odonata: Anisoptera: Libellulidae)

Neurothemis fulvia is a dragonfly of wet forests and usually perches on fallen logs and shrubs. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of N. fulvia. This mitogenome was 15,459 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA unit genes (rRNAs). The nucleotide composition of the mitogenome was biased toward A and T, with 70.5% of A + T content (A 38.8%, T 31.7%, C 16.6%, and G 12.9%). Gene order was conserved and identical to most other previously sequenced Libellulidae dragonflies. Most PCGs of N. fulvia have the conventional start codons ATN (six ATG, three ATT, and two ATC), with the exception of cox1 and nad1 (TTG). Except for four PCGs (cox1, cox2, cox3, and nad5) end with the incomplete stop codon T––, all other PCGs terminated with the stop codon TAA or TAG. Phylogenetic analysis showed that N. fulvia got together with Tramea virginia with high support value. Libellulidae had a close relationship with Corduliidae, the relationships ((Hydrobasileus + Brachythemis) + (Orthetrum + (Acisoma + (Neurothemis + Tramea)))) were supported in Libellulidae.

Understanding the codon usage patterns of mitochondrial CO genes among Amphibians

A universal phenomenon of using synonymous codons unequally in coding sequences known as codon usage bias (CUB) is observed in all forms of life. Mutation and natural selection drive CUB in many species but the relative role of evolutionary forces varies across species, genes and genomes. We studied the CUB in mitochondrial (mt) CO genes from three orders of Amphibia using bioinformatics approach as no work was reported yet. We observed that CUB of mt CO genes of Amphibians was weak across different orders. Order Caudata had higher CUB followed by Gymnophiona and Anura for all genes and CUB also varied across genes. Nucleotide composition analysis showed that CO genes were AT-rich. The AT content in Caudata was higher than that in Gymnophiona while Anura showed the least content. Multiple investigations namely nucleotide composition, correspondence analysis, parity plot analysis showed that the interplay of mutation pressure and natural selection caused CUB in these genes. Neutrality plot suggested the involvement of natural selection was more than the mutation pressure. The contribution of natural selection was higher in Anura than Gymnophiona and the lowest in Caudata. The codons CGA, TGA, AAA were found to be highly favoured by nature across all genes and orders.

Complete mitochondrial genome sequence of Anax parthenope (Odonata: Anisoptera: Aeshnidae) and phylogenetic analysis

Anax parthenope (Odonata: Aeshnidae) is a big dragonfly which can be seen patrolling around ponds, lakes and other still water. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of A. parthenope. This mitogenome was 15,366 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA unit genes (rRNAs). The nucleotide composition of the mitogenome was biased toward A and T, with 74.8% of A + T content (A 40.1%, T 34.7%, C 14.0%, G 11.2%). Gene order was conserved and identical to most other previously sequenced Aeshnidae dragonflies. Most PCGs of A. parthenope have the conventional start codons ATN (six ATG, three ATT, and two ATC), with the exception of cox1 and nad1 (TTG). Except for three genes (cox1, cox2, and nad5) end with the incomplete stop codon T--, all other PCGs terminated with the stop codon TAA. Phylogenetic analysis showed that A. parthenope is sister to Anax imperator with high support value. All 15 Anisoptera species constituted a major clade with well support, and Aeshnidae had a close relationship with Gomphidae and Libellulidae.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Pseudothemis zonata (Odonata: Anisoptera: Libellulidae)

Pseudothemis zonata is a commonly seen dragonfly with a big yellow or white ringlike spot on the third and fourth segments of its abdomen. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of P. zonata. This mitogenome was 15,434 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA unit genes (rRNAs). Gene order was conserved and identical to most other previously sequenced Libellulidae dragonflies. The whole mitogenome exhibited heavy AT nucleotide bias (74.6%). Most PCGs of P. zonata have the conventional start codons ATN (six ATG, three ATT, and two ATC), with the exception of cox1 and nad1 (TTG). Except for four genes (cox1, cox2, cox3, and nad5) end with the incomplete stop codon T−, all other PCGs terminated with the stop codon TAA or TAG. Phylogenetic analysis showed that P. zonata got together with Brachythemis contaminata with high support value, and the relationships ((Brachythemis + Psolodesmus) + ((Hydrobasileus + Trigomphus) + (Orthetrum + Acisoma))) were supported in Libellulidae.

Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family

Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.

Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens

Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.

Analysis of codon usage pattern of mitochondrial ND genes in Platyhelminthes

Codon usage bias (CUB) is the nonrandom usage of synonymous codons in which some codons are more preferred to others.CUB can be determined by mutation pressure and selection. Various approaches have been used to understand the pattern of CUB in the mitochondrial ND (MT-ND or ND) genes involved in complex I of respiratory chain in five different classes of Platyhelminthes as no work was reported yet. The present study revealed that the CUB varies across MT-ND genes and the coding sequences showed the richness of A and T. Correspondence analysis implied the effect of mutational pressure and also the pattern of codon usage was different in different classes of platyhelminthes for MT-ND genes. Highly significant correlation was observed between overall nucleotide composition and its 3rd codon position in most of the homogeneous nucleotides such as A% and A3%, T% and T3%, G% and G3%, C% and C3%, GC% and GC3% and also some significant correlations observed among heterogeneous nucleotides in all the five classes for MT-ND genes suggested the role of mutational pressure as well as natural selection in affecting the CUB. Neutrality plot suggested that the contributions of natural selection and mutational pressure varied across different classes of platyhelminthes and also differed in different MT-ND genes.

Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes

Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly correlated with codon usage. In general, both mitochondrial genomes favor codons that end in A or U, with a secondary preference for pyrimidine rich codons. These observations are similar to previous reports of codon usage in cotton nuclear genomes, possibly suggestive of a general bias spanning genomic compartment. Although evidence for codon usage bias is weak for most genes, we identified six genes (i.e. atp8, atp9, sdh3, sdh4, mttB and rpl2) with significant nonrandom codon usage. In general, we find multiple factors that influence cotton mitochondrial genome codon usage, which may include selection in a subset of genes.