Thrips are one of the major sucking pest and vector of plant viruses causing huge economic loss in agriculture. The accurate identification of thrips is crucial for effective pest management strategies. However, morphology based identification has limitations and warrants integration of molecular data. We attempted the largest DNA barcoding initiative on 370 sequences of 89 thrips morphospecies including 104 novel sequences from 39 morphospecies, including the type specimens of four species. The results of multiple species delimitation methods (BIN, ABGD, GMYC and bPTP) were consistent for 73 species (82%) with their morphological identifications. A total of 107 molecular operational taxonomic units (MOTUs) was recovered for 89 morphospecies by superimposing multiple methods and applying a three level nomenclature system. We detected more than one MOTU in 14 morphospecies indicating to have cryptic diversity including, two major vector species (Frankliniella schultzei and Thrips palmi). However, four morphospecies (Thrips moundi, Thrips carthami, Haplothrips andersi and Haplothrips gowdeyi) showed low genetic distances between them with overlapping in barcode gap that requires further analysis with multiple molecular markers and more specimens from wide geographical areas for better taxonomic judgment. We also presented the advantage of simultaneous use of multiple delimitation methods for detection and identification of cryptic species.

prior to this study, complete mitochondrial genomes from order thysanoptera were restricted to a single family, the thripidae, resulting in a biased view of their evolution. Here we present the sequences for the mitochondrial genomes of four additional thrips species, adding three extra families and an additional subfamily, thus greatly improving taxonomic coverage. thrips mitochondrial genomes are marked by high rates of gene rearrangement, duplications of the control region and tRnA mutations. Derived features of mitochondrial tRnAs in thrips include gene duplications, anticodon mutations, loss of secondary structures and high gene translocation rates. Duplicated control regions are found in the Aeolothripidae and the 'core' thripinae clade but do not appear to promote gene rearrangement as previously proposed. phylogenetic analysis of thrips mitochondrial sequence data supports the monophyly of two suborders, a sister-group relationship between Stenurothripidae and thripidae, and suggests a novel set of relationships between thripid genera. Ancestral state reconstructions indicate that genome rearrangements are common, with just eight gene blocks conserved between any thrips species and the ancestral insect mitochondrial genome. Conversely, 71 derived rearrangements are shared between at least two species, and 24 of these are unambiguous synapomorphies for clades identified by phylogenetic analysis. While the reconstructed sequence of genome rearrangements among the protein-coding and ribosomal RnA genes could be inferred across the phylogeny, direct inference of phylogeny from rearrangement data in MLGo resulted in a highly discordant set of relationships inconsistent with both sequence-based phylogenies and previous morphological analysis. Given the demonstrated rates of genomic evolution within thrips, extensive sampling is needed to fully understand these phenomena across the order.Complete mitochondrial genomes have been shown to be useful for phylogenetic and evolutionary studies at various taxonomic scales, as they provide more phylogenetic information than individual genes alone 1-4 . The mitochondrial genome of metazoans is typically a circular molecule 14-19 kilobases (kb) in length, that contains a conserved set of 37 genes: 13 protein-coding genes (PCGs), ATPase subunits 6 and 8 (atp6 and atp8), Cytochrome oxidase subunits 1 to 3 (cox1-cox3), cytochrome b (cob), NADH dehydrogenase subunits 1-6 and 4 L (nad1-6 and nad4L); the small and large subunit rRNAs (rrnL and rrnS), 22 transfer RNA (tRNA) genes, and a non-coding control region (CR) which contains initiation sites for transcription and replication 1,5 . In addition to sequence variation, metazoan mitochondrial genomes also exhibit variation in a number of features, such as length, tRNA secondary structure, gene order, and the number and internal structure of control regions 6-8 . These features can provide evidence for evolutionary relationships among taxa at high and/or low taxonomic levels beyond that provided by analysis of mitochondrial seq...

Rajasree chakraborty, priya prasad, Shantanu Kundu, inderjeet tyagi & Kailash chandra the complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the pcGs used Atn start codon except cox3, and nad4 with ttG. comparative studies indicated the use of ttG, ttA, ttt, GtG, ctG, ctA as start codons by few pcGs. Most of the tRnAs were truncated and do not fold into the typical cloverleaf structure. further, the motif (cAtAtA) was detected in cR of nine species including L. crotalus. the gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block c was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and pholcidae) and other Mygalomorphae species. The order Araneae is classified into two infra-orders Mesothelae (primitive spiders) and Opisthothelae (modern spiders). The infra-order Opisthothelae is further classified into two suborders Mygalomorphae and Araneomorphae with 117 families. The family Theraphosidae belongs to suborder Mygalomorphae of infra-order Opisthothelae with 992 species. Out of 992 species, 52 species are known from India 1. The members of family Theraphosidae are commonly known as tarantulas or giant spiders for their huge body size. These giant spiders play an important role in controlling the insects 2 and also predators on vertebrates and invertebrates 3. The venom of these tarantulas is the main source of pharmacological research 3. The Pet trade of tarantulas across the globe is in great demand due to their body size, attractiveness, longitivity and for economic point of view 4. So far, 13 species in three genera (Poecilotheria, Thrigmopoeus and Lyrognathus) from India have been reported in the pet trade 4. The species Lyrognathus crotalus is endemic to India restricted to northeast region and frequently traded. The correct identification of these tarantulas is the basic need due to their economical and medicinal values and involvement in the pet trade. However, identification of species in the absence of well-preserved specimens is not possible through morphology ...

South East Asia pest thrips species, Thrips parvispinus (Karny), is a serious pest on a number of agricultural and horticultural crops in a number of plant families. Based on an integrated approach of morphology and DNA barcoding, invasion of this serious pest is reported first time from India on papaya plantations. Molecular data have corroborated with the morphological identification. Haplotyping data suggested that the Indonesia may be a probable source of invasion of this pest to India.

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.