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Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia.

ABSTRACT: Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia.

PROVIDER: PRJNA611085 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11266554_1.fastq.gz	Fastqsanger.gz
	SRR11266554_2.fastq.gz	Fastqsanger.gz
	SRR11266555_1.fastq.gz	Fastqsanger.gz
	SRR11266555_2.fastq.gz	Fastqsanger.gz
	SRR11266556_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia.

Project description:Objective: To provide genetic resources for future research on developing RNAi as a strategy for management of this pest Methods: We sequenced the transcriptome of C. cramerella representing the three stages of development, larva, pupa and adult moth using Illumina NovaSeq6000. Transcriptome assembly was performed by Trinity for all the samples. Results: A total number of 147,356,088 high quality reads were obtained. Of these, 285,882 contigs were assembled. The mean contig size was 374 bp. Additionally, we identified a number of genes that are involved in reproduction and development such as genes involved in general function processes in the insect. Genes found to be involved in reproduction such as porin, dsx, bol and fruitless were associated with sex determination, spermatogenesis and pheromone binding. Conclusions: The transcriptomes data would be a valuable genetic resource for identification of genes in C. cramerella and the study will provide putative targets for RNAi pest control.

2021-03-08 | GSE146610 | GEO

Data on RNA-seq analysis of the cocoa pod borer pest <i>Conopomorpha cramerella</i> (Snellen) (Lepidoptera: Gracillariidae).

Project description:Cocoa bean (Theobroma cacao L.) is part of the global cocoa and chocolate industry valued at 44 billion US dollars in 2019. Cocoa pod borer (CPB), Conopomorpha cramerella is a major pest of cocoa in Malaysia and Indonesia that is responsible for the decline for cocoa production. They have been detected since 1980s. Unfortunately, current control strategies are inefficient for CPB management. Although biotechnological alternatives, including RNA interference (RNAi), have been proposed in recent years to control insect pests, characterizing the genetics of the target pest is essential for successful application of these emerging technologies. We generated a comprehensive RNA-seq dataset (135,915,430 clean reads) for larva and adult stages of CPB by using the Illumina HiseqTM 4000 system to increase the understanding of CPB in relation to molecular features. The CPB transcriptome was assembled de novo and annotated. The final assembled produced 249,280 unigenes, of which 75,929 unigenes annotated against NCBI NR database and were distributed among 156 KEGG pathways. The raw data were uploaded to SRA database and the BioProject ID is PRJNA553611. The transcriptomic dataset we present are the first reports of transcriptome information in CPB that is valuable for further exploration and understanding of CPB molecular pathways.

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Transcriptome analysis of the litchi fruit borer (Conopomorpha sinensis)

Project description:Purpose: transcriptome sequencing of Conopomorpha sinensis Methods: high-through Illumina HiSeqTM 2000 Results:66017 transcripts,35383 unigenes Conclusions:This study provided valuable transcriptome data for the litchi fruit borer, which was the first fundamental genomic basis for exploiting gene resources from the litchi fruit borer

2018-03-03 | GSE67194 | GEO

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Conopomorpha sinensis

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Conopomorpha sinensis

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Project description:Transcriptome analysis of the litchi fruit borer (Conopomorpha sinensis)

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Population Prehistory in Island Southeast Asia

Project description:Affymetrix single nucleotide polymorphism (SNP) array data were collected to study genome-wide patterns of genomic variation across a broad geographical range of Island Southeast Asian populations. This region has experienced an extremely complex admixture history. Initially settled ~50,000 years ago, Island Southeast Asia has since been the recipient of multiple waves of population movements, most recently by Austronesian-speaking groups ultimately from Neolithic mainland Asia and later arrivals during the historic era from India and the Middle East. We have genotyped SNPs in ~500 individuals from 30 populations spanning this entire geographical region, from communities close to mainland Asia through to New Guinea. Particular attention has been paid to genomic data that are informative for population history, including the role of recent arrivals during the historic era and admixture with archaic hominins.

2017-08-02 | GSE80534 | GEO

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