The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae): Comparative analysis

The melon thrips, Thrips palmi is a serious pest and vector for plant viruses on a wide range of economically important crops. DNA barcoding evidenced the presence of cryptic diversity in T. palmi and that warrants exhaustive molecular studies. Our present study is on decoding the first complete mitochondrial genome of T. palmi (15,333 bp) through next-generation sequencing (NGS). The T. palmi mt genome contains 37 genes, including 13 Protein coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA (tRNAs), and two control regions (CRs). The majority strand of T. palmi revealed 78.29% A+T content, and 21.72% G+C content with positive AT skew (0.09) and negative GC skew (-0.06). The ATN initiation codons were observed in 12 PCGs except for cox1 which have unique start codon (TTG). The relative synonymous codon usage (RSCU) analysis revealed Phe, Leu, Ile, Tyr, Asn, Lys and Met were the most frequently used amino acids in all PCGs. The codon (CGG) which is assigned to Arginine in most insects but absent in T. palmi. The Ka/Ks ratio ranges from 0.078 in cox1 to 0.913 in atp8. We observed the typical cloverleaf secondary structure in most of the tRNA genes with a few exceptions; absence of DHU stem and loop in trnV and trnS, absence of DHU loop in trnE, lack of T-arm and loop in trnN. The T. palmi gene order (GO) was compared with ancestral GO and observed an extensive gene arrangement in PCGs, tRNAs and rRNAs. The cox2 gene was separated from the gene block 'cox2-trnL2' in T. palmi as compared with the other thrips mt genomes, including ancestor GO. Further, the nad1, trnQ, trnC, trnL1, trnV, trnF, rrnS, and rrnL were inversely transpositioned in T. palmi GO. The gene blocks 'trnQ-trnS2-trnD' and 'trnN-trnE-trnS1-trnL1' seems to be genus specific. The T. palmi mt genome contained 24 intergenic spacer regions and 12 overlapping regions. The 62 bp of CR2 shows the similarity with CR1 indicating a possible duplication. The occurrence of multiple CRs in thrips mt genomes seems to be a derived trait which needs further investigation. Although, the study depicted extensive gene rearrangements in T. palmi mt genome, but the negative GC skew reflects only strand asymmetry. Both the ML and BI phylogenetic trees revealed the close relationships of Thrips with Scirtothrips as compared to Frankliniella. Thus, more mt genomes of the diverse thrips species are required to understand the in-depth phylogenetic and evolutionary relationships.