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Dataset of transcriptome assembly of date palm embryogenic calli and functional annotation.

ABSTRACT: Date palm (Phoenix dactylifera L.; 2n?=?36; Arecaceae), cultivated in tropical and sub-tropical regions worldwide, is a staple food for people in the Middle East region and has economic value throughout the world. Tissue culture is considered as a feasible technique for the large-scale multiplication of elite date palm varieties. In this article, we report the transcriptome assembly from the embryogenic calli of Khalas variety of date palm. A total of 50,852,331 paired-end (PE) raw reads were acquired using an Illumina sequencing platform. Reference-based assembly, with date palm genome, resulted in 53251 transcripts. A total of 63888 Gene Ontology (GO) terms could be annotated from the assembled transcriptome. Also, transcription factor families and small RNAs were annotated from the assembled transcriptome. Results of the pathway analysis revealed that a total of 2584 transcripts were involved in various metabolic pathways. Transcripts with possible roles in somatic embryogenesis were also identified. The dataset provides insights into the expression pattern of various genes during early somatic embryogenesis in date palm.

SUBMITTER: Naganeeswaran S

PROVIDER: S-EPMC7270187 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Dataset of transcriptome assembly of date palm embryogenic calli and functional annotation.

Naganeeswaran S S Fayas T P TP Rajesh M K MK

Data in brief 20200525

Date palm (<i>Phoenix dactylifera</i> L.; 2n = 36; Arecaceae), cultivated in tropical and sub-tropical regions worldwide, is a staple food for people in the Middle East region and has economic value throughout the world. Tissue culture is considered as a feasible technique for the large-scale multiplication of elite date palm varieties. In this article, we report the transcriptome assembly from the embryogenic calli of Khalas variety of date palm. A total of 50,852,331 paired-end (PE) raw reads ...[more]

PMID: 32518810

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Project description:The coconut rhinoceros beetle, Oryctes rhinoceros L. (Insecta: Coleoptera: Scarabaeidae: Dynastinae) is one of the world's most important endemic and incessant pests of coconut (particularly in India and Southeast Asia), causing an estimated 10% yield loss in the crop. Various management strategies formulated and implemented to control this pest include bioagents, insecticide sprays, liquid formulations, pheromone traps, and botanical formulations. Also, potential microbial bioagents viz., Oryctes rhinoceros nudivirus (OrNV) and Metarhizium anisopliae have been implemented as biological control agents and this has led to a beneficial reduction of the pest population unless significant immigration occurs. To date, research and development activities are still on-going for the successful management of the pest; yet advances in understanding at the molecular level have been limited because basic genomic information is lacking for this cosmopolitan pest. Transcriptome approach has been proved extremely useful in finding potential genes for pest control. Transcriptome analysis aids in gaining insights into the transcriptional changes which occur during different developmental stages of an organism. We have performed RNA sequencing of certain different developmental stages of O. rhinoceros viz., early instar larva, late instar larva, pupa, and adult, in an Illumina HiSeq™ 2500 platform. Due to the unavailability of O. rhinoceros genome, the RNA-seq data generated were assembled de novo using Trinity and annotated following redundancy removal. A dataset of 87,451 transcripts, which resulted after redundancy removal, were annotated using the NCBI non-redundant (nr) protein and Uniprot databases. The data furnished could be used by others working in the development of pest management strategies, especially the identification of molecular targets for effective pest control. This information allows a better understanding of O. rhinoceros biology which would contribute to outlining a new generation of stage-specific, environmentally friendly pest management techniques.

Dataset Information

Dataset of transcriptome assembly of date palm embryogenic calli and functional annotation.

Publications

Dataset of transcriptome assembly of date palm embryogenic calli and functional annotation.

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