Differentially expressed genes during the transition from early to late development phases in somatic embryo of banana (Musa spp. AAB group, Silk subgroup) cv. Manzano

Enríquez-Valencia, Adrián José; Vázquez‐Flota, Felipe; Ku-Cauich, José Roberto; Escobedo-GraciaMedrano, Rosa María

doi:10.1007/s11240-018-1514-6

Cited by 17 publications

(14 citation statements)

References 61 publications

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“…Chorismate gives rise to aromatic amino acids, including tryptophan, and through several reactions, including the conversion of tryptophan to indole-3-pyruvic acid by the tryptophan aminotransferase (TA); it can generate the auxin indole-3-acetic acid (IAA). TA has been proposed as a universal key enzyme to IAA biosynthesis not only in vegetative organs (Enríquez-Valencia et al, 2018) but also in the development of reproductive organs (Reyes-Olalde et al, 2017), including fruit growth and ripening (Estrada-Johnson et al, 2017). By contrast, when isochorismate synthase (ICS) is activated, chorismate can be converted into isochorismate and the latter can be transformed into SA.…”

Section: Chorismate-derived Phytohormonesmentioning

confidence: 99%

Biosynthesis, Metabolism and Function of Auxin, Salicylic Acid and Melatonin in Climacteric and Non-climacteric Fruits

et al. 2019

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Climacteric and non-climacteric fruits are differentiated by the ripening process, in particular by the involvement of ethylene, high respiration rates and the nature of the process, being autocatalytic or not, respectively. Here, we focus on the biosynthesis, metabolism and function of three compounds (auxin, salicylic acid and melatonin) sharing not only a common precursor (chorismate), but also regulatory functions in plants, and therefore in fruits. Aside from describing their biosynthesis in plants, with a particular emphasis on common precursors and points of metabolic diversion, we will discuss recent advances on their role in fruit ripening and the regulation of bioactive compounds accumulation, both in climacteric and non-climacteric fruits.

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Section: Chorismate-derived Phytohormonesmentioning

confidence: 99%

Biosynthesis, Metabolism and Function of Auxin, Salicylic Acid and Melatonin in Climacteric and Non-climacteric Fruits

et al. 2019

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“…Although little is known about the molecular mechanism that controls SE, NGS and RNA-seq have broadened the scope for studying the first stages of the SE process. Using the RNA-seq approach, it has been possible to identify a set of genes involved in the embryogenic response in species such as cotton (Cheng et al, 2016; Cao et al, 2017), conifers (Yakovlev et al, 2016), papaya (Jamaluddin, Mohd Noor & Goh, 2017), wheat (Chu et al, 2017), and banana (Enríquez-Valencia et al, 2019), among others like Arabidopsis, oil palm, soybean, carrot, grape, alfalfa, and maize (Cetz-Chel & Loyola-Vargas, 2016; Shi et al, 2016; Tao et al, 2016; Góngora-Castillo et al, 2018). Thus, the aim of this study is to provide a better understanding of the role of auxins during the induction of SE by identifying differentially expressed genes of Coffea canephora when analyzing different stages of SE induction.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes

Quintana-Escobar

Nic-Can

Avalos

et al. 2019

PeerJ

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Background Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Methods Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. Results A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. Discussion The results of this study allow a better understanding of the genes involved in the auxin signaling pathway as well as their expression profiles during the SE process.

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“…With the release of the C. canephora genome (Denoeud et al, 2014 The RNA-Seq technology has allowed us to have a complete picture of the genes expressed during SE induction. Transcriptomic studies have showed that the most important and determining changes begin at the start of the SE induction stage (1 DAI) and at the beginning of the development of the first structures (21 DAI) or, in other words, at the moment of the shift from a non-embryogenic state to an embryogenic one (Cheng et al, 2016;Shi et al, 2016;Tao et al, 2016;Cao et al, 2017;Chu et al, 2017;Enríquez-Valencia et al, 2019). Cao et al (2017) identified the main regulation phase of SE initiation in cotton to occur between three hours and three days after induction.…”

Section: Discussionmentioning

confidence: 99%

“…Using the RNA-seq approach, it has been possible to identify a set of genes involved in the embryogenic response in species such as cotton (Cheng et al, 2016;Cao et al, 2017), conifers (Yakovlev et al, 2016), papaya (Jamaluddin, Mohd Noor, Goh, 2017), wheat (Chu et al, 2017), and banana (Enríquez-Valencia et al, 2019), among others like Arabidopsis, oil palm, soybean, carrot, grape, alfalfa, and maize (Cetz-Chel & Loyola-Vargas, 2016;Shi et al, 2016;Tao et al, 2016;Góngora-Castillo et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #2 of "Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes (v0.1)"

Otoni¹

2019

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Background. Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Methods. Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. Results. A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. Discussion. The results of this study allow a better understanding of the genes involved in the auxin signaling pathway as well as their expression profiles during the SE process.

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Differentially expressed genes during the transition from early to late development phases in somatic embryo of banana (Musa spp. AAB group, Silk subgroup) cv. Manzano

Cited by 17 publications

References 61 publications

Biosynthesis, Metabolism and Function of Auxin, Salicylic Acid and Melatonin in Climacteric and Non-climacteric Fruits

Biosynthesis, Metabolism and Function of Auxin, Salicylic Acid and Melatonin in Climacteric and Non-climacteric Fruits

Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes

Peer Review #2 of "Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes (v0.1)"

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