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Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes.

Alkio M, Jonas U, Declercq M, Van Nocker S, Knoche M - Hortic Res (2014)

Bottom Line: Coregulated genes were detected using partitional clustering of expression patterns.The results are discussed with emphasis on genes putatively involved in cuticle deposition, cell wall metabolism and sugar transport.The high temporal resolution of the expression patterns presented here reveals finely tuned developmental specialization of individual members of gene families.

View Article: PubMed Central - PubMed

Affiliation: Institute of Horticultural Production Systems, Leibniz Universität Hannover , D-30419 Hannover, Germany.

ABSTRACT
The exocarp, or skin, of fleshy fruit is a specialized tissue that protects the fruit, attracts seed dispersing fruit eaters, and has large economical relevance for fruit quality. Development of the exocarp involves regulated activities of many genes. This research analyzed global gene expression in the exocarp of developing sweet cherry (Prunus avium L., 'Regina'), a fruit crop species with little public genomic resources. A catalog of transcript models (contigs) representing expressed genes was constructed from de novo assembled short complementary DNA (cDNA) sequences generated from developing fruit between flowering and maturity at 14 time points. Expression levels in each sample were estimated for 34 695 contigs from numbers of reads mapping to each contig. Contigs were annotated functionally based on BLAST, gene ontology and InterProScan analyses. Coregulated genes were detected using partitional clustering of expression patterns. The results are discussed with emphasis on genes putatively involved in cuticle deposition, cell wall metabolism and sugar transport. The high temporal resolution of the expression patterns presented here reveals finely tuned developmental specialization of individual members of gene families. Moreover, the de novo assembled sweet cherry fruit transcriptome with 7760 full-length protein coding sequences and over 20 000 other, annotated cDNA sequences together with their developmental expression patterns is expected to accelerate molecular research on this important tree fruit crop.

No MeSH data available.


Growth and development of the sweet cherry ‘Regina’ fruit analyzed in this study. (a) Fruit mass and surface area from flowering to maturity. Stage I, cell division and expansion; Stage II (gray shading), seed development and pit hardening; Stage III, cell expansion. Color change from green to red occurred between 59 and 66 DAFB (arrow). (b) Mass of CM per fruit and calculated rate of CM deposition. Data points in a and b show the average of 30 measurements; error bars represent s.e. (not visible if smaller than symbols). Time is given in DAFB. (c) Representative photos of the analyzed fruit and sample codes identifying the RNA-seq samples. The numbers in images indicate the developmental age of the fruit in DAFB. Sample codes contain information on fruit age in DAFB (3–94), tissue type (G, whole ovaries after removal of other floral organs; E, exocarp-enriched tissue; M, mesocarp only) and replicate number (1 or 2) if applicable. Photos not to scale.
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fig1: Growth and development of the sweet cherry ‘Regina’ fruit analyzed in this study. (a) Fruit mass and surface area from flowering to maturity. Stage I, cell division and expansion; Stage II (gray shading), seed development and pit hardening; Stage III, cell expansion. Color change from green to red occurred between 59 and 66 DAFB (arrow). (b) Mass of CM per fruit and calculated rate of CM deposition. Data points in a and b show the average of 30 measurements; error bars represent s.e. (not visible if smaller than symbols). Time is given in DAFB. (c) Representative photos of the analyzed fruit and sample codes identifying the RNA-seq samples. The numbers in images indicate the developmental age of the fruit in DAFB. Sample codes contain information on fruit age in DAFB (3–94), tissue type (G, whole ovaries after removal of other floral organs; E, exocarp-enriched tissue; M, mesocarp only) and replicate number (1 or 2) if applicable. Photos not to scale.

Mentions: A total of 24 RNA samples isolated from following sweet cherry fruit tissues were used for transcriptome sequencing in one or two biological replicates as indicated in Figure 1c: whole ovaries (other floral organs removed) 3 DAFB; exocarp-enriched tissue (0.5–2 mm thin slices from the outermost pericarp) 10, 17, 24, 31, 38, 45, 52, 59, 66, 73, 80, 87 and 94 DAFB; mesocarp tissue 24 and 80 DAFB. The mesocarp samples served for detecting differential expression between exo- and mesocarp. Each biological replicate contained tissue from at least ten fruits collected from at least three trees.


Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes.

Alkio M, Jonas U, Declercq M, Van Nocker S, Knoche M - Hortic Res (2014)

Growth and development of the sweet cherry ‘Regina’ fruit analyzed in this study. (a) Fruit mass and surface area from flowering to maturity. Stage I, cell division and expansion; Stage II (gray shading), seed development and pit hardening; Stage III, cell expansion. Color change from green to red occurred between 59 and 66 DAFB (arrow). (b) Mass of CM per fruit and calculated rate of CM deposition. Data points in a and b show the average of 30 measurements; error bars represent s.e. (not visible if smaller than symbols). Time is given in DAFB. (c) Representative photos of the analyzed fruit and sample codes identifying the RNA-seq samples. The numbers in images indicate the developmental age of the fruit in DAFB. Sample codes contain information on fruit age in DAFB (3–94), tissue type (G, whole ovaries after removal of other floral organs; E, exocarp-enriched tissue; M, mesocarp only) and replicate number (1 or 2) if applicable. Photos not to scale.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4591669&req=5

fig1: Growth and development of the sweet cherry ‘Regina’ fruit analyzed in this study. (a) Fruit mass and surface area from flowering to maturity. Stage I, cell division and expansion; Stage II (gray shading), seed development and pit hardening; Stage III, cell expansion. Color change from green to red occurred between 59 and 66 DAFB (arrow). (b) Mass of CM per fruit and calculated rate of CM deposition. Data points in a and b show the average of 30 measurements; error bars represent s.e. (not visible if smaller than symbols). Time is given in DAFB. (c) Representative photos of the analyzed fruit and sample codes identifying the RNA-seq samples. The numbers in images indicate the developmental age of the fruit in DAFB. Sample codes contain information on fruit age in DAFB (3–94), tissue type (G, whole ovaries after removal of other floral organs; E, exocarp-enriched tissue; M, mesocarp only) and replicate number (1 or 2) if applicable. Photos not to scale.
Mentions: A total of 24 RNA samples isolated from following sweet cherry fruit tissues were used for transcriptome sequencing in one or two biological replicates as indicated in Figure 1c: whole ovaries (other floral organs removed) 3 DAFB; exocarp-enriched tissue (0.5–2 mm thin slices from the outermost pericarp) 10, 17, 24, 31, 38, 45, 52, 59, 66, 73, 80, 87 and 94 DAFB; mesocarp tissue 24 and 80 DAFB. The mesocarp samples served for detecting differential expression between exo- and mesocarp. Each biological replicate contained tissue from at least ten fruits collected from at least three trees.

Bottom Line: Coregulated genes were detected using partitional clustering of expression patterns.The results are discussed with emphasis on genes putatively involved in cuticle deposition, cell wall metabolism and sugar transport.The high temporal resolution of the expression patterns presented here reveals finely tuned developmental specialization of individual members of gene families.

View Article: PubMed Central - PubMed

Affiliation: Institute of Horticultural Production Systems, Leibniz Universität Hannover , D-30419 Hannover, Germany.

ABSTRACT
The exocarp, or skin, of fleshy fruit is a specialized tissue that protects the fruit, attracts seed dispersing fruit eaters, and has large economical relevance for fruit quality. Development of the exocarp involves regulated activities of many genes. This research analyzed global gene expression in the exocarp of developing sweet cherry (Prunus avium L., 'Regina'), a fruit crop species with little public genomic resources. A catalog of transcript models (contigs) representing expressed genes was constructed from de novo assembled short complementary DNA (cDNA) sequences generated from developing fruit between flowering and maturity at 14 time points. Expression levels in each sample were estimated for 34 695 contigs from numbers of reads mapping to each contig. Contigs were annotated functionally based on BLAST, gene ontology and InterProScan analyses. Coregulated genes were detected using partitional clustering of expression patterns. The results are discussed with emphasis on genes putatively involved in cuticle deposition, cell wall metabolism and sugar transport. The high temporal resolution of the expression patterns presented here reveals finely tuned developmental specialization of individual members of gene families. Moreover, the de novo assembled sweet cherry fruit transcriptome with 7760 full-length protein coding sequences and over 20 000 other, annotated cDNA sequences together with their developmental expression patterns is expected to accelerate molecular research on this important tree fruit crop.

No MeSH data available.