Dataset Information

Genome-enabled insights into the biology of thrips as crop pests.

ABSTRACT: BACKGROUND:The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. RESULTS:We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size?=?415.8?Mb, scaffold N50?=?948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~?10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. CONCLUSIONS:Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.

SUBMITTER: Rotenberg D

PROVIDER: S-EPMC7570057 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-enabled insights into the biology of thrips as crop pests.

Rotenberg Dorith D Baumann Aaron A AA Ben-Mahmoud Sulley S Christiaens Olivier O Dermauw Wannes W Ioannidis Panagiotis P Jacobs Chris G C CGC Vargas Jentzsch Iris M IM Oliver Jonathan E JE Poelchau Monica F MF Rajarapu Swapna Priya SP Schneweis Derek J DJ Snoeck Simon S Taning Clauvis N T CNT Wei Dong D Widana Gamage Shirani M K SMK Hughes Daniel S T DST Murali Shwetha C SC Bailey Samuel T ST Bejerman Nicolas E NE Holmes Christopher J CJ Jennings Emily C EC Rosendale Andrew J AJ Rosselot Andrew A Hervey Kaylee K Schneweis Brandi A BA Cheng Sammy S Childers Christopher C Simão Felipe A FA Dietzgen Ralf G RG Chao Hsu H Dinh Huyen H Doddapaneni Harsha Vardhan HV Dugan Shannon S Han Yi Y Lee Sandra L SL Muzny Donna M DM Qu Jiaxin J Worley Kim C KC Benoit Joshua B JB Friedrich Markus M Jones Jeffery W JW Panfilio Kristen A KA Park Yoonseong Y Robertson Hugh M HM Smagghe Guy G Ullman Diane E DE van der Zee Maurijn M Van Leeuwen Thomas T Veenstra Jan A JA Waterhouse Robert M RM Weirauch Matthew T MT Werren John H JH Whitfield Anna E AE Zdobnov Evgeny M EM Gibbs Richard A RA Richards Stephen S

BMC biology 20201019 1

<h4>Background</h4>The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.<h4>Results</h4>We report on the first genome ...[more]

PMID: 33070780

Similar Datasets

Project description:This study was conducted in Farta district, south Gondar from 2019 to 2020 cropping years to identify rodent pest species and estimate damage caused on barley crops. Four independent barley crop fields (40 x 40 m each) were sampled randomly to estimate the loss. Two were located near Alemsaga Priority State Forest and the other two were away from the forest. Four (2 x 2 m) rodent exclusion plots were established at 10 m interval as control units in each selected experimental barley fields using fine wire mesh. Rodent pest species were collected using both Sherman and snap traps throughout the different crop growing stages. The damaged and undamaged barley tillers by pest rodents were counted on five 1 x 1 m randomly sampled quadrats for each selected experimental fields. Variations on pest rodent population between cropping years and sites were analyzed using Chi square test. The mean crop damages between cropping years and experimental field sites were analyzed using two way ANOVA. Arvicanthis abyssinicus, Mastomys natalensis, Arvicanthis dembeensis, Mus musculus, Lophuromys simensis, Tachyoryctes splendens and Hystrix cristata were identified as pest rodents in the study area. A total of 968 individual rodents (427 in 2019 and 541 in 2020) were trapped during the study period. There was a statistical variation (χ2 = 13.42, df = 1 and P<0.05) between trapped individuals of the two successive years. The crop fields near the forest were more vulnerable than away from the forest during both cropping years. Statistical variations was observed on mean crop losses between cropping years and experimental barley crop sites. The highest crop damage was seen at maturity stage and the lowest during sowing in all experimental plots and cropping years. The percentage of barley yield loss due to rodent pests was 21.7 kg ha-1. The monetary value of this yield loss was equivalent to 4875 Birr (121.9 US$ h-1). Alemsaga Forest as shelter and conservation strategies like free of farmland from livestock and terracing for soil conservation have great role for the high rodent pest populations in the study area. Field sanitation, trapping and using restricted rodenticides like zinc phosphide are the possible recommendation to local farmers against rodent pests.

Project description: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.

Dataset Information

Genome-enabled insights into the biology of thrips as crop pests.

Publications

Genome-enabled insights into the biology of thrips as crop pests.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure