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.
Highlights
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
We report the transcriptome assembly from the embryogenic calli of Khalas variety of date palm
Agriculture and Biological Sciences Plant transcriptomics Tables, figure, text file Illumina HiSeq TM 2000 sequencing platform Raw, filtered, analyzed Embryogenic calli were generated from juvenile leaf explants of Khalas variety of date palm on Murashige and Skoog (MS) medium [1] supplemented with 2,4-D (100 mg/L), 2iP (3 mg/L) and sucrose (60 g/L)
Summary
Annotated Gene Ontology (GO) terms in date palm embryogenic calli transcriptome are given in Fig. 1 and Supplementary table S2. The details of transcription factors and small RNAs, annotated from the assembled transcriptome, are provided in Supplementary tables S3 and S4 respectively. A total of 63,888 GO terms (Fig. 1) were annotated from the assembled transcriptome (Supplementary table S2). Results of the pathway analysis revealed that 2,584 transcripts were involved in various metabolic pathways (Supplementary table S5). The transcripts possessing possible roles in date palm somatic embryogenesis include APETALA2 (AP2) class of transcription factors, auxin responsive factors (ARFs), leafy cotyledon (LEC), late embryogenesis-abundant protein (LEA), mitogen-activated protein kinase (MAPK), somatic embryogenesis receptor kinase (SERK), small auxin up RNA-like (SAUR-like) auxin-responsive family, WRKY and WUSCHEL (WUS) transcription factors (Supplementary table S6)
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