Global scale transcriptome analysis reveal differentially expressed genes during early somatic embryogenesis in Dimocarpus longan Lour

Abstract

BackgroundSomatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to the totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as a model system for studying embryogenesis in woody plants, and some SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent.With the aim of understanding the molecular mechanisms underlying SE in longan, we examined the transcriptome changes by using Illumina HiSeq platform from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact proembryogenic cultures (ICpEC), globular embryos (GE). ResultsRNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to the reference genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22743, 19745, 21144, 21102 expressed transcripts and 1935, 1710, 1816, 1732 novel transcripts, and 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis revealed the important role of auxin and cytokinin during longan SE. The transcripts profiling of flavonoid and fatty acid biosynthesis related genes suggested that flavonoids were mainly accumulated in NEC, while fatty acid accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Transcript profiling combined with qRT-PCR performed on selected genes confirmed that 27 SE molecular markers (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC markers (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as potential molecular markers for longan early SE, respectively. ConclusionOur transcriptome reveals the transcription regulation of auxin, cytokinin and other hormones signaling pathway, flavonoids biosynthesis, fatty acid biosynthesis, extracelluar protein encoding genes, and other SE-related genes during early SE. Furthermore, we characterizes the potential

Genome-wide analysis of the GLP gene family and overexpression of GLP1-5–1 to promote lignin accumulation during early somatic embryo development in Dimocarpus longan

“…Except for DlGLP1-1, DlGLP3-8-2, and DlGLP3-8-3, all of the DlGLP genes contained at least one anaerobicity-inducible element. Drought-inducible elements (35) were also widely distributed in the promoter regions of the DlGLP genes. These results suggested that DlGLP genes play a wide range of roles in the response to hormones, drought stress and anaerobicity-induced adversity in longan.…”

“…POD can produce phenoxy radicals by decomposing H 2 O 2 , which is the raw material for lignin synthesis [34]. Previous studies have shown that DNA replication, cell cycle-related genes, and the extracellular protein-encoding genes LTP, CHI, GLP, and AGP were significantly differentially expressed during early SE in longan, and they may be involved in regulating SE in longan [35]. The GLP gene acts as an SOD or OXO to regulate the H 2 O 2 content in the process of plant growth and development, thus affecting the cross-linking of the cell wall [36].…”