EST Sequencing from Embryogenic Cyclamen persicum Cell Cultures Identifies a High Proportion of Transcripts Homologous to Plant Genes Involved in Somatic Embryogenesis

Rensing, Stefan A.; Lang, Daniel; Schumann, Eik; Reski, Ralf; Hohe, Annette

doi:10.1007/s00344-005-0033-y

Cited by 34 publications

(36 citation statements)

References 24 publications

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“…These analyses showed that the EST libraries cover a wide range of biological functions. A majority of the GO terms in molecular function ontology were comprised with proteins involved in binding or catalytic activity, which is comparable with the observations made previously in both embryogenesis related EST data (Rensing et al, 2005) and developing seeds (Costa et al, 2010). However, no major differences were observed in highly represented GO term associated categories between the leaf library and the other embryo tissue library, suggesting that a major portion of transcripts of different tissues are involving in similar functions.…”

Section: December 2015supporting

confidence: 87%

“…Chitinases affect the early phases of embryo development and it could rescue somatic embryo development in mutant lines (De Jong et al, 1992), play a crucial role in embryogenesis by exhibiting higher expression mainly in transcriptome analysis in different species [e.g. Cyclamen persicum (Rensing et al, 2005); oil palm (Ho et al, 2007) . The abundance levels of chitinase in the embryo libraries were suggestive of its involvement in embryo development and should be considered as a candidate gene for further studies.…”

Section: December 2015mentioning

confidence: 99%

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Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

Bandupriya¹,

Dunwell²

2015

J. Natn. Sci. Foundation Sri Lanka

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Coconut, Cocos nucifera L. is a major plantation crop, which ensures income for millions of people in the tropical region. Detailed molecular studies on zygotic embryo development would provide valuable clues for the identification of molecular markers to improve somatic embryogenesis. Since there is no ongoing genome project for this species, coconut expressed sequence tags (EST) would be an interesting technique to identify important coconut embryo specific genes as well as other functional genes in different biochemical pathways. The goal of this study was to analyse the ESTs by examining the transcriptome data of the different embryo tissue types together with one somatic tissue. Here, four cDNA libraries from immature embryo, mature embryo, microspore derived embryo and mature leaves were constructed. cDNA was sequenced by the Roche-454 GS-FLX system and assembled into 32621 putative unigenes and 155017 singletons. Of these unigenes, 18651 had significant sequence similarities to non-redundant protein database, from which 16153 were assigned to one or more gene ontology categories. Homologue genes, which are responsible for embryo development such as chitinase, beta-1,3-glucanase, ATP synthase CF0 subunit, thaumatin-like protein and metallothionein-like protein were identified among the embryo EST collection. Of the unigenes, 6694 were mapped into 139 KEGG pathways including carbohydrate metabolism, energy metabolism, lipid metabolism, amino acid metabolism and nucleotide metabolism. This collection of 454-derived EST data generated from different tissue types provides a significant resource for genome wide studies and gene discovery of coconut, a non-model species.

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Section: December 2015supporting

confidence: 87%

Section: December 2015mentioning

confidence: 99%

Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

Bandupriya¹,

Dunwell²

2015

J. Natn. Sci. Foundation Sri Lanka

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“…In accordance, auxin-related TFs have been found to be the most frequent among the hormone-related genes that are involved in SE induction (Yang et al 2012;Gliwicka et al 2013;Wickramasuriya and Dunwell 2015). The TF genes that have a regulatory role in SE include the core regulators of auxin signalling, AUX/IAA and ARF genes (Rensing et al 2005;Su et al 2007;Wu et al 2009;Yang et al 2012;Gliwicka et al 2013). A differential expression of IAA16, IAA29, IAA30, IAA31 and ARF1, ARF2, ARF3, ARF5, ARF6, ARF8 and ARF11 was observed during SE induction in Arabidopsis and the mutants in these genes were substantially defective in the embryogenic response (Gliwicka et al 2013;Wójcikowska and MDG, in preparation for publication).…”

Section: Global Characteristics Of the Se-associated Tf Transcriptomesmentioning

confidence: 85%

Transcription Factors in the Regulation of Somatic Embryogenesis

Nowak

Gaj

2016

Somatic Embryogenesis: Fundamental Aspects and Applications

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Somatic embryogenesis (SE), the process through which already differentiated cells reverse their developmental programme and become embryogenic, requires drastic changes in the transcriptome of the explant cells. Among the various factors that underlie this developmental switch, genes encoding transcription factors (TFs), which constitute the sequence-specific DNA-binding proteins, are widely accepted as playing a central function in the gene expression regulation. In recent years, intensive analysis of the global transcriptomes of plant cells that are undergoing embryogenic transition and the use of Arabidopsis (a model in plant genomics) in studies on the genetic control of SE have substantially contributed to the identification of SE regulators. A survey of SE-associated transcriptomes illustrated the combinational effects of stress and hormone signalling that are related to the in vitro environment that is imposed during a culture. Accordingly, among the TFs that are considered to be essential in SE induction, those that are involved in stress and hormone plant responses and especially flower development were found to be most frequent. This chapter provides a comprehensive review of the current knowledge about the TFs that are involved in the induction of SE in plant explants that are cultured in vitro. In addition to a general characterisation of the TF transcriptomes that are associated with SE induction in different plants, the individual TF genes with documented functions in the regulation of SE are presented with a special reference to their possible targets and the TF-controlled molecular mechanisms that underlie SE induction.

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“…However, Rensing et al (2005) reported enhanced expression of WRKY during somatic embryogenesis in Cyclamen persicum. Embryogenic calli of both WCT and COD showed increased expression of WUS compared to somatic embryo.…”

Section: Discussionmentioning

confidence: 99%

Comparative gene expression profiling during in vitro regeneration in two coconut cultivars

Udyawar

Edathil

Jayaraj

et al. 2016

Emir. J. Food Agric

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EST Sequencing from Embryogenic Cyclamen persicum Cell Cultures Identifies a High Proportion of Transcripts Homologous to Plant Genes Involved in Somatic Embryogenesis

Cited by 34 publications

References 24 publications

Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

Transcription Factors in the Regulation of Somatic Embryogenesis

Comparative gene expression profiling during in vitro regeneration in two coconut cultivars

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