DNA barcoding of thrips (Thysanoptera: Thripidae) associated with selected vegetable crops of Kerala
| dc.contributor.advisor | Abida, P S | |
| dc.contributor.author | Namitha, T H | |
| dc.contributor.author | KAU | |
| dc.date.accessioned | 2021-04-13T07:08:05Z | |
| dc.date.available | 2021-04-13T07:08:05Z | |
| dc.date.issued | 2020 | |
| dc.description | MSc | en_US |
| dc.description.abstract | The study entitled “DNA barcoding of thrips (Thysanoptera: Thripidae) associated with selected vegetable crops of Kerala” was carried out at Regional Agricultural Research Station, Pattambi and Department of Agricultural Entomology, College of Horticulture, Kerala Agricultural University during the period 2019-2020. The primary objective of the study was to generate DNA barcodes for different species of thrips infesting selected vegetable crops of Kerala and to find out the variability among them. The family Thripidae insects are also known as thrips, a tiny sewing needle like complex plant pest in the size of 0.5-1.5 millimetres in length. Morphological identification of thrips species is very difficult because of their minute size, scarcity of solid morphological characters, high cryptic behaviour, sexual dimorphisms and overlapping host ranges and the need for taxonomic expertise. DNA barcoding is the most desirable tool to identify known and unknown species and phylogenetic analysis based on the nucleotide arrangement of sequence in DNA fragment by the use of a short-standardized DNA sequence of 658 bp fragment of the mitochondrial cytochrome cytochrome oxidase (COX I) gene. A total of 21 thrips specimens were collected from various locations of Thrissur and Palakkad districts of Kerala from vegetable crops like cucumber, coccinia, chilli, cowpea, brinjal and tomato. Morphological identification was done by Zoological Survey of India and identified four species which are Thrips florum, Thrips palmi, Thrips hawaiiensis and Ayyaria chaetophora. Total genomic DNA extraction of collected specimens were done using Qiagen DNeasy Blood and Tissue Kit. The extracted DNA was used to amplify the cytochrome oxidase subunit 1 gene, using the selected primers and gave amplicons in the size range 890 bp. The sequencing process was carried out at AgriGenome Lab. Pvt. Ltd., Cochin. Sequence homology analysis were done with the help of BLASTn tool of NCBI has resulted in a query coverage of 97% to 99% with the identified species. Barcode Gap Analysis helps to anticipate the distribution of distances within each species and the distance to the nearest neighbour of each species. Sequences were readily aligned using clustalW tool of MEGA7 software and the similarity in nitrogen bases of the sequences were identified. Multiple sequence alignment revealed highest similarity sequences between Thrips florum and Thrips hawaiiensis and showed difference only in the position of guanine in T. hawaiiensis in case of adenine in T. florum. Barcode gap analysis has shown the presence of cytosine in T.palmi but thymine in Ayyaria chaetophora. Data regarding specimens including taxonomy, specimen images, sequence information and trace files were deposited into BOLD database. Specific process IDs and barcodes were generated by BOLD for each specimen. The inter specific distance between species were computed using K2P (Kimura 2 parameter) from MEGA7 software. The “Distance|Compute Pair-wise” command created the pair wise distances. The range of distance within T. florum was 0% to 0.005%. Distance between T. florum and T. hawaiiensis was 0.003% to 0.005%. Distance between Ayyaria chaetophora and T.palmi was 0.259% to 0.267%. The phylogenetic tree constructed by using MEGA7 software (Maximum parsimony model) for COI sequences of thrips species has clearly shown that T. hawaiienesis and T. florum are closely related species. DNA sequences of 21 thrips species were deposited in the NCBI GenBank and accession numbers were generated could help the identification of species easily and specific barcodes generated for each species could be used for the species level allocation of thrips. The precise identification of thrips is the fundamental step to develop genetic and other biological information which is essential for effective management and quarantine measures. | en_US |
| dc.identifier.citation | 175048 | en_US |
| dc.identifier.uri | https://krishikosh.egranth.ac.in/handle/1/5810163448 | |
| dc.keywords | Plant Biotechnology | en_US |
| dc.language.iso | English | en_US |
| dc.pages | 77p. | en_US |
| dc.publisher | Department of Plant Biotechnology, College of Agriculture, Vellayani | en_US |
| dc.sub | Plant Biotechnology | en_US |
| dc.theme | Thrips (Thysanoptera: Thripidae) associated with selected vegetable crops of Kerala | en_US |
| dc.these.type | M.Sc | en_US |
| dc.title | DNA barcoding of thrips (Thysanoptera: Thripidae) associated with selected vegetable crops of Kerala | en_US |
| dc.type | Thesis | en_US |