Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos

Abstract

BackgroundThere are clear differences in embryo development between angiosperm and gymnosperm species. Most of the current knowledge on gene expression and regulation during plant embryo development has derived from studies on angiosperms species, in particular from the model plant Arabidopsis thaliana. The few published studies on transcript profiling of conifer embryogenesis show the existence of many putative embryo-specific transcripts without an assigned function. In order to extend the knowledge on the transcriptomic expression during conifer embryogenesis, we sequenced the transcriptome of zygotic embryos for several developmental stages that cover most of Pinus pinaster (maritime pine) embryogenesis.ResultsTotal RNA samples collected from five zygotic embryo developmental stages were sequenced with Illumina technology. A de novo transcriptome was assembled as no genome sequence is yet published for Pinus pinaster. The transcriptome of reference for the period of zygotic embryogenesis in maritime pine contains 67,429 transcripts, which likely encode 58,527 proteins. The annotation shows a significant percentage, 31%, of predicted proteins exclusively present in pine embryogenesis. Functional categories and enrichment analysis of the differentially expressed transcripts evidenced carbohydrate transport and metabolism over-representation in early embryo stages, as highlighted by the identification of many putative glycoside hydrolases, possibly associated with cell wall modification, and carbohydrate transport transcripts. Moreover, the predominance of chromatin remodelling events was detected in early to middle embryogenesis, associated with an active synthesis of histones and their post-translational modifiers related to increased transcription, as well as silencing of transposons.ConclusionsOur results extend the understanding of gene expression and regulation during zygotic embryogenesis in conifers and are a valuable resource to support further improvements in somatic embryogenesis for vegetative propagation of conifer species. Specific transcripts associated with carbohydrate metabolism, monosaccharide transport and epigenetic regulation seem to play an important role in pine early embryogenesis and may be a source of reliable molecular markers for early embryogenesis.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1564-2) contains supplementary material, which is available to authorized users.

Full-Length Transcriptome Analysis of the ABCB, PIN/PIN-LIKES, and AUX/LAX Families Involved in Somatic Embryogenesis of Lilium pumilum DC. Fisch.

“…Research in Arabidopsis has shown that carbohydrates play a role in the G2/M transition in cells via sugar signaling, which directly affects the proliferation of meristematic tissue [53]. A study in Pinus pinaster also reveals upregulation expression of genes involved in carbohydrate transport and metabolism in early stages of embryogenesis but downregulation expression toward the later stages of embryogenesis [54]. GO and KEGG pathway annotation analyses also revealed that many genes were involved in carbohydrate metabolism and signal transduction.…”

Transcriptome Analysis Identifies Genes Involved in the Somatic Embryogenesis of Eucalyptus

“…Furthermore, some other genes and proteins have been studied to relate to the vegetative propagation, like RP [47], HSP [48], and histone [49,50]. While very few studies have been demonstrated to investigate their functions and associations in the SE of Eucalyptus, our results indicate that the dysregulation of these genes or the known pathways like metabolisms involved by these genes might be related to the SE of Eucalyptus.…”

Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

“…Furthermore, RP [ 48 ], HSP [ 49 ], and histone [ 50 , 51 ] have been reported to function in the vegetative propagation in plants. While very few studies have been demonstrated to investigate their functions and associations in the SE of Eucalyptus, our results indicate that the dysregulation of these genes and pathways like metabolisms involved by these genes might play important roles in the SE of Eucalyptus.…”