Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using Illumina paired-end sequencing

Abstract

BackgroundLongan is a tropical/subtropical fruit tree of great economic importance in Southeast Asia. Progress in understanding molecular mechanisms of longan embryogenesis, which is the primary influence on fruit quality and yield, is slowed by lack of transcriptomic and genomic information. Illumina second generation sequencing, which is suitable for generating enormous numbers of transcript sequences that can be used for functional genomic analysis of longan.ResultsIn this study, a longan embryogenic callus (EC) cDNA library was sequenced using an Illumina HiSeq 2000 system. A total of 64,876,258 clean reads comprising 5.84 Gb of nucleotides were assembled into 68,925 unigenes of 448-bp mean length, with unigenes ≥1000 bp accounting for 8.26% of the total. Using BLASTx, 40,634 unigenes were found to have significant similarity with accessions in Nr and Swiss- Prot databases. Of these, 38,845 unigenes were assigned to 43 GO sub-categories and 17,118 unigenes were classified into 25 COG sub-groups. In addition, 17,306 unigenes mapped to 199 KEGG pathways, with the categories of Metabolic pathways, Plant-pathogen interaction, Biosynthesis of secondary metabolites, and Genetic information processing being well represented. Analyses of unigenes ≥1000 bp revealed 328 embryogenesis-related unigenes as well as numerous unigenes expressed in EC associated with functions of reproductive growth, such as flowering, gametophytogenesis, and fertility, and vegetative growth, such as root and shoot growth. Furthermore, 23 unigenes related to embryogenesis and reproductive and vegetative growth were validated by quantitative real time PCR (qPCR) in samples from different stages of longan somatic embryogenesis (SE); their differentially expressions in the various embryogenic cultures indicated their possible roles in longan SE.ConclusionsThe quantity and variety of expressed EC genes identified in this study is sufficient to serve as a global transcriptome dataset for longan EC and to provide more molecular resources for longan functional genomics.

De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing

“…Transcriptome analysis of somatic embryogenesis have been undertaken using microarray analyses in soybean (Thibaud-Nissen et al 2003), maize (Che et al 2006), and rape seed (Joosen et al 2007) and suppression subtractive hybridization in oil palm (Lin et al 2009). With the advent of next-generation sequencing (NGS) technologies, which possess high-throughput and accuracy and are cost-effective, RNA-Seq technique has been implemented to study the gene expression patterns during somatic embryogenesis in cotton (Yang et al 2012), longan (Lai and Lin 2013), cocoa (Maximova et al 2014), and maize (Salvo et al 2014). These studies have provided a fillip to the understanding of genomic factors which are involved in somatic embryogenesis in these crops.…”

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.

“…After removing the low-quality reads, such as those containing poly-N, 5′ adapter contaminants, no 3′ adapter or insert tag, or those containing poly(A), (T), (G) or (C), from the raw data, the clean data were obtained. The clean tags were mapped to the longan genome (NCBI accession number: BioProject PRJNA305337) 29 and longan embryogenic callus transcriptional database (SRA050205) 30 by SOAP or Bowtie 31 . The expression and distribution of sRNA in the genome were analysed.…”

Somatic Embryogenesis: Fundamental Aspects and Applications

“…De novo transcriptomes from Larix leptolepis, Dimocarpus longan Lour., Cinnamomum camphora, Cocus nucifera, Araucaria angustifolia, Zea mays, and G. hirsitum showed an increasing number of genes involved at the early or late stages of SE (Elbl et al 2015;Lai and Lin 2013;Shi et al 2016;Xu et al 2013;Zhang et al 2012). In cotton (Gossypium hirsutum), the Illumina digital gene expression platform was used to analyze the transcriptional profile during SE.…”