A study on climatic adaptation of dipteran mitochondrial protein coding genes

Diptera, the true flies are frequently found in nature and their habitat is found all over the world including Antarctica and Polar Regions. The number of documented species for order diptera is quite high and thought to be 14% of the total animal present in the earth [1]. Most of the study in diptera has focused on the taxa of economic and medical importance, such as the fruit flies Ceratitis capitata and Bactrocera spp. (Tephritidae), which are serious agricultural pests; the blowflies (Calliphoridae) and oestrid flies (Oestridae), which can cause myiasis; the anopheles mosquitoes (Culicidae), are the vectors of malaria; and leaf-miners (Agromyzidae), vegetable and horticultural pests [2]. Insect mitochondrion consists of 13 protein coding genes, 22 tRNAs and 2 rRNAs, are the remnant portion of alpha-proteobacteria is responsible for simultaneous function of energy production and thermoregulation of the cell through the bi-genomic system thus different adaptability in different climatic condition might have compensated by complementary changes is the both genomes [3,4]. In this study we have collected complete mitochondrial genome and occurrence data of one hundred thirteen such dipteran insects from different databases and literature survey. Our understanding of the genetic basis of climatic adaptation in diptera is limited to the basic information on the occurrence location of those species and mito genetic factors underlying changes in conspicuous phenotypes. To examine this hypothesis, we have taken an approach of Nucleotide substitution analysis for 13 protein coding genes of mitochondrial DNA individually and combined by different software for monophyletic group as well as paraphyletic group of dipteran species. Moreover, we have also calculated codon adaptation index for all dipteran mitochondrial protein coding genes. Following this work, we have classified our sample organisms according to their location data from GBIF (https://www.gbif.org). Finally, result suggests that dipteran insects from different regions are gone through distinct selection process and even our outcome also indicate that dipteran mitochondrial genes from different climatic condition shows differential efficacy in their translation process

<i>A</i>. <i>assamensis</i> mitochondrial genome.

<p><b>(A) Circular map (B) Characteristic features of the mitogenome.</b><i>tRNAs</i> are represented as <i>trn</i> followed by the IUPAC-IUB single letter amino acid codes e.g. <i>trnM</i> denote <i>tRNA</i>^<i>Met</i>. IGN represents (+) values as intergenic nucleotides and (-) values as overlapping regions.</p

Codon usage in <i>A</i>. <i>assamensis</i> mitogenome.

<p><b>(A) Codon distribution where CDspT = codons per thousand codons (B) Relative synonymous codon usage (RSCU).</b> Termination codons were excluded in the study.</p

The mitochondrial genome of Muga silkworm (<i>Antheraea assamensis</i>) and its comparative analysis with other lepidopteran insects

<div><p>Muga (<i>Antheraea assamensis</i>) is an economically important silkmoth endemic to the states of Assam and Meghalaya in India and is the producer of the strongest known commercial silk. However, there is a scarcity of genomic and proteomic data for understanding the organism at a molecular level. Our present study is on decoding the complete mitochondrial genome (mitogenome) of <i>A</i>. <i>assamensis</i> using next generation sequencing technology and comparing it with other available lepidopteran mitogenomes. Mitogenome of <i>A</i>. <i>assamensis</i> is an AT rich circular molecule of 15,272 bp (A+T content ~80.2%). It contains 37 genes comprising of 13 protein coding genes (PCGs), 22 tRNA and 2 rRNA genes along with a 328 bp long control region. Its typical <i>tRNA</i>^<i>Met</i><i>-tRNA</i>^<i>Ile</i><i>-tRNA</i>^<i>Gln</i> arrangement differed from ancestral insects (<i>tRNA</i>^<i>Ile</i><i>-tRNA</i>^<i>Gln</i><i>-tRNA</i>^<i>Met</i>). Two PCGs <i>cox1</i> and <i>cox2</i> were found to have CGA and GTG as start codons, respectively as reported in some lepidopterans. Interestingly, <i>nad4l</i> gene showed higher transversion mutations at intra-species than inter-species level. All PCGs evolved under strong purifying selection with highest evolutionary rates observed for <i>atp8</i> gene while lowest for <i>cox1</i> gene. We observed the typical clover-leaf shaped secondary structures of tRNAs with a few exceptions in case of <i>tRNA</i>^<i>Ser1</i> and <i>tRNA</i>^<i>Tyr</i> where stable DHU and TΨC loop were absent. A significant number of mismatches (35) were found to spread over 19 tRNA structures. The control region of mitogenome contained a six bp (CTTAG<u>A/G</u>) deletion atypical of other <i>Antheraea</i> species and lacked tandem repeats. Phylogenetic position of <i>A</i>. <i>assamensis</i> was consistent with the traditional taxonomic classification of Saturniidae. The complete annotated mitogenome is available in GenBank (Accession No. KU379695). To the best of our knowledge, this is the first report on complete mitogenome of <i>A</i>. <i>assamensis</i>.</p></div

Phylogenetic tree inferred from nucleotide sequences of 13 PCGs of 34 organisms using bayesian inference (BI) method in MrBayes v3.2.6.

<p>The tree is drawn to scale with bayesian posterior probability values indicated along with the branches.</p

Phylogenetic tree inferred from nucleotide sequences of 13 PCGs of 34 organisms using maximum likelihood (ML) method in RaxmlGUI v1.3 (1000 bootstrap replicates).

<p>The tree is drawn to scale with bootstrap values indicated along with the branches.</p

A pictorial overview of the methodologies used for sequencing and analysis of <i>A</i>. <i>assamensis</i> mitogenome.

<p>A pictorial overview of the methodologies used for sequencing and analysis of <i>A</i>. <i>assamensis</i> mitogenome.</p

List of species considered for comparative mitogenome study.

<p>(Highlighted ones are the organisms of Bombycoidea superfamily used for comparative mitogenome analysis with respect to <i>A</i>. <i>assamensis</i>).</p

Evolutionary rates (Ka/Ks) of individual PCG of <i>A</i>. <i>assamensis</i> with selected species.

<p>w.r.t. here denotes with reference to-.</p