Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains
Ontology highlight
ABSTRACT:
SUBMITTER:
PROVIDER: S-EPMC10676084 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.
| S-EPMC4780788 | biostudies-literature
Project description:The first step toward marker-assisted selection is linking the phenotypes to molecular markers through quantitative trait loci (QTL) analysis. While the process is straightforward in self-pollinating diploid (2x) species, QTL analysis in polyploids requires unconventional methods. In this study, we have identified markers associated with weevil Cosmopolites sordidus (Germar) resistance in bananas using 138 triploid (2n = 3x) hybrids derived from a cross between a tetraploid "Monyet" (2n = 4x) and a 2x "Kokopo" (2n = 2x) banana genotypes. The population was genotyped by Diversity Arrays Technology Sequencing (DArTSeq), resulting in 18,009 polymorphic single nucleotide polymorphisms (SNPs) between the two parents. Marker-trait association was carried out by continuous mapping where the adjusted trait means for the corm peripheral damage (PD) and total cross-section damage (TXD), both on the logit scale, were regressed on the marker allele frequencies. Forty-four SNPs that were associated with corm PD were identified on the chromosomes 5, 6, and 8, with 41 of them located on chromosome 6 and segregated in "Kokopo." Eleven SNPs associated with corm total TXD were identified on chromosome 6 and segregated in "Monyet." The additive effect of replacing one reference allele with the alternative allele was determined at each marker position. The PD QTL was confirmed using conventional QTL linkage analysis in the simplex markers segregating in "Kokopo" (AAAA × RA). We also identified 43 putative genes in the vicinity of the markers significantly associated with the two traits. The identified loci associated with resistance to weevil damage will be used in the efforts of developing molecular tools for marker-assisted breeding in bananas.
| S-EPMC8667469 | biostudies-literature
Project description:Cosmopolites sordidus Genome sequencing and assembly
| PRJNA817621 | ENA
Project description:Cosmopolites sordidus Raw sequence reads
| PRJNA291033 | ENA
Project description:Understanding of ecological interactions is necessary for the application of biological control. Banana is the second most produced fruit worldwide and the banana weevil (Cosmopolites sordidus) is the most important pest of banana and plantain. Its biological control remains challenging because of the robustness and cryptic behaviour of the adult and the hidden development of larval stages. Researchers therefore tend to favour conservation biological control of this pest. The commonly used methods for measuring the effects of natural enemies on the regulation of this pest focus on invertebrates and may underestimate the role of vertebrates on biological control. Using cameras, we recorded the predation of sentinel adult weevils in banana plots in La Réunion island that differed in weevil infestation levels and in animal biodiversity. To facilitate image analysis, we used background subtraction to isolate moving parts of image sequences and thus detect predators and predation events. Our cameras recorded only vertebrates as predators of adult banana weevils. The most important predator appeared to be the Asian shrew (Suncus murinus), which was responsible for 67% of the predation events. Other predators included the house mouse (Mus musculus), the oriental garden lizard (Calotes versicolor), and the guttural toad (Sclerophrys gutturalis). The exact time of predation events were determined from the images metadata. It was thus possible to identify predator foraging periods that coincided with activity of adult weevils. Our results confirm that images provide useful information for biological and ecological studies. Along with other recent studies, our results suggest that the role of vertebrates in biological control may be underestimated. Based on these results, we advocate for several management implications such as the installation of hedges, grasslands, and ponds to favour these vertebrate predators of the banana weevil, possibly also favouring other vertebrate and invertebrate natural enemies.
| S-EPMC9488773 | biostudies-literature
Project description:Fungal Volatile Organic Compounds (VOCs) repel banana black weevil (BW), Cosmopolites sordidus (Germar, 1824), the key-pest of banana [Musa sp. (Linnaeus, 1753)]. The entomopathogens Beauveria bassiana (Bb1TS11) and Metarhizium robertsii (Mr4TS04) were isolated from banana plantation soils using an insect bait. Bb1TS11 and Mr4TS04 were pathogenic to BW adults. Bb1TS11, Bb203 (from infected palm weevils), Mr4TS04 and the nematophagous fungus Pochonia clamydosporia (Pc123), were tested for VOCs production. VOCs were identified by Gas Chromatography/Mass Spectrometry-Solid-Phase Micro Extraction (GC/MS-SPME). GC/MS-SPME identified a total of 97 VOCs in all strains tested. Seven VOCs (styrene, benzothiazole, camphor, borneol, 1,3-dimethoxy-benzene, 1-octen-3-ol and 3-cyclohepten-1-one) were selected for their abundance or previous record as insect repellents. BW-starved adults in the dark showed the highest mobility to banana corm in olfactometry bioassays. 3-cyclohepten-1-one (C7), produced by all fungal strains, is the best BW repellent (p < 0.05), followed by 1,3-dimethoxy-benzene (C5). The rest of the VOCs have a milder repellency to BW. Styrene (C1) and benzothiazole (C2) (known to repel palm weevil) block the attraction of banana corm and BW pheromone to BW adults in bioassays. Therefore, VOCs from biocontrol fungi can be used in future studies for the biomanagement of BW in the field.
| S-EPMC7469225 | biostudies-literature
Project description:The data presented in this article are related to the research article entitled "Ant abundance and Cosmopolites sordidus damage in plantain fields as affected by intercropping" (A.G. Dassou, D. Carval, S. Dépigny, G.H Fansi, P. Tixier, 2015) [1]. This article describes how associated crops maize (Zea mays), cocoyam (Xanthosoma sagittifolium) and bottle gourd (Lagenaria siceraria) intercropped in the plantain fields in Cameroun modify ant community structure and damages of banana weevil Cosmopolites sordidus. The field data set is made publicly available to enable critical or extended analyzes.
| S-EPMC5008051 | biostudies-literature
Project description:Gene conversions are broadly defined as the transfer of genetic material from a "donor" to an "acceptor" sequence and can happen both in meiosis and mitosis. They are a subset of noncrossover (NCO) events and, like crossover (CO) events, gene conversion can generate new combinations of alleles and counteract mutation load by reverting germline mutations through GC-biased gene conversion. Estimating gene conversion rate and the distribution of gene conversion tract lengths remains challenging. We present a new method for estimating tract length, rate, and detection probability of NCO events directly in HiFi PacBio long read data. The method can be used to make inference from sequencing of gametes from a single individual. The method is unbiased even under low single nucleotide variant (SNV) densities and does not necessitate any demographic or evolutionary assumptions. We test the accuracy and robustness of our method using simulated datasets where we vary length of tracts, number of tracts, the genomic SNV density, and levels of correlation between SNV density and NCO event position. Our simulations show that under low SNV densities, like those found in humans, only a minute fraction (∼2%) of NCO events are expected to become visible as gene conversions by moving at least 1 SNV. We finally illustrate our method by applying it to PacBio sequencing data from human sperm.
| S-EPMC11844249 | biostudies-literature
Project description:The complete mitogenome of Ips calligraphus was sequenced, the length was 19,144 bp which consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a major non-coding AT-rich region (GenBank accession no. MW589547). All of 13 protein-coding genes (PCGs) started with ATN. 12 PCGs used the typical stop codon 'TAA,' while ATP8 terminated with stop codon 'TAG.' Phylogenetic analyses were performed using mitochondrial PCGs for the I. calligraphus and other 18 species within the Scolytinae. The I. calligraphus was clustered together with the other two Ips species in tribe Ipini which were closely related to Xyleborini and Dryocoetini.
| S-EPMC8330781 | biostudies-literature