Use of Non‐Normalized, Non‐Amplified cDNA for 454‐Based RNA Sequencing of Fleshy Melon Fruit

Diber, Alex; Pollock, Sarah; Karchi, Hagai; Lev, Shery; Tzuri, Galil; Harel-Beja, Rotem; Forer, Relly; Portnoy, Vitaly; Lewinsohn, Efraim; Tadmor, Yaakov; Burger, Joseph; Schaffer, Arthur A.; Katzir, Nurit

doi:10.3835/plantgenome2010.11.0026

Cited by 29 publications

(31 citation statements)

References 72 publications

(88 reference statements)

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“…454 Pyrosequencing was performed on Genome Sequencer FLX by DYN G.S. Ltd, Israel, according to the procedure described by Margulies et al (2005) and is described in Portnoy et al (2011). Each library ran on one quarter of a 70 9 75 PicoTiterPlate (PTP) except for the 40 DAA library that was run twice, as described.…”

Section: Pyrosequencingmentioning

confidence: 99%

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Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation

et al. 2011

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The sweet melon fruit is characterized by a metabolic transition during its development that leads to extensive accumulation of the disaccharide sucrose in the mature fruit. While the biochemistry of the sugar metabolism pathway of the cucurbits has been well studied, a comprehensive analysis of the pathway at the transcriptional level allows for a global genomic view of sugar metabolism during fruit sink development. We identified 42 genes encoding the enzymatic reactions of the sugar metabolism pathway in melon. The expression pattern of the 42 genes during fruit development of the sweet melon cv Dulce was determined from a deep sequencing analysis performed by 454 pyrosequencing technology, comprising over 350,000 transcripts from four stages of developing melon fruit flesh, allowing for digital expression of the complete metabolic pathway. The results shed light on the transcriptional control of sugar metabolism in the developing sweet melon fruit, particularly the metabolic transition to sucrose accumulation, and point to a concerted metabolic transition that occurs during fruit development.

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Section: Pyrosequencingmentioning

confidence: 99%

“…Preparation of mRNA and non-amplified cDNA Total RNA was isolated as described (Portnoy et al 2011). PolyA-mRNA was purified from 1 mg of total RNA using the PolyATtract mRNA isolation system (Promega, WI, USA).…”

Section: Pcr Based Cloningmentioning

confidence: 99%

Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation

et al. 2011

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“…The International Cucurbit Genomics Initiative (ICuGI) database (available at http://www.icugi.org [verified Apr 8, 2012]) comprises approximately 8,144,030 expressed sequence tags (ESTs) and 611,438 unigenes, nearly onethird of which were derived from fruit libraries (Portnoy and others 2011). In addition, MELONOMICS (https:// melonomics.net) is available for genomic database which includes CM_ protein_v3.5 (verified May 4, 2011), melon_genome_pseudomolecules v3.5 (verified Jun 21, 2012), CM_assembly_scaffold_and_ unscaffold_contigs_v3.5 (verified May 4, 2011.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Phylogenetic Analysis of the ERF Gene Family in Melon

Zhang

Bade

et al. 2014

J Plant Growth Regul

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Members of the ERF transcription factor family have significant functions in regulating gene expression in response to biotic and abiotic stresses. In melon (Cucumis melo L.), however, few ERF genes have been studied. In this study, we performed a comprehensive computational analysis of 119 ERF family genes and identified 136 ERF superfamily genes in melon. We present a complete overview of ERF family gene in melon, including the phylogeny, gene structures, and putative conserved motifs of melon ERF family proteins, as well as a comparative analysis between ERF subfamily genes in cucumber. The AP2/ERF gene superfamily in melon can be classified into three families, ERF (ethylene-responsive factor), RAV (related to ABI3/VP1), and AP2 (APETALA2), which comprise 119, 4, and 13 members, respectively. The ERF family in melon was divided into 11 groups, designated I to XI, as in tomato. Our motif analysis indicated that most conserved motifs outside of the AP2/ERF domain are distributed between different clades in the phylogenetic tree. Most ERF family genes have no introns. Based on the observation that 11 of these groups existed in melon, we concluded that the chief functional diversification in the ERF family predated the divergence between monocots and dicots. In our analysis of expression patterns, ERF subfamily genes were distributed widely throughout melon plant tissues and most of the ERF subfamily genes were detected in all seven types of tissues. Some ERF subfamily genes show expression patterns characteristic of tissuespecific expression, implying their probability of performing various roles in growth and development in melon.

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“…Fruit rind RNA extraction for RNA-Seq analysis was performed according to the work by Portnoy et al (2011). Twelve samples (two replicates of three developmental stages: 10 DAA, 20 DAA, and mature fruit rind of yellow and white F 3 families) were used to construct RNA-Seq libraries following the standard Illumina protocol.…”

Section: Rna-seq Data Processing and De Novo Assemblymentioning

confidence: 99%

A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in Cucumis melo L.

Feder

Burger²,

Gao

et al. 2015

Plant Physiol.

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The flavonoids are phenylpropanoid-derived metabolites that are ubiquitous in plants, playing many roles in growth and development. Recently, we observed that fruit rinds of yellow casaba muskmelons (Cucumis melo 'Inodorous Group') accumulate naringenin chalcone, a yellow flavonoid pigment. With RNA-sequencing analysis of bulked segregants representing the tails of a population segregating for naringenin chalcone accumulation followed by fine mapping and genetic transformation, we identified a Kelch domain-containing F-box protein coding (CmKFB) gene that, when expressed, negatively regulates naringenin chalcone accumulation. Additional metabolite analysis indicated that downstream flavonoids are accumulated together with naringenin chalcone, whereas CmKFB expression diverts the biochemical flux toward coumarins and general phenylpropanoids. These results show that CmKFB functions as a posttranscriptional regulator that diverts flavonoid metabolic flux.

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Use of Non‐Normalized, Non‐Amplified cDNA for 454‐Based RNA Sequencing of Fleshy Melon Fruit

Cited by 29 publications

References 72 publications

Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation

Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation

Genome-Wide Identification and Phylogenetic Analysis of the ERF Gene Family in Melon

A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in Cucumis melo L.

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