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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.


GO terms of 7628 Group 1F contigs with predicted full-length open reading frames. GO terms in categories biological process, molecular function and cellular component were retrieved from combined graph analyses performed in Blast2GO platform (sequence filter 100, score alpha 0.6, node score filter 100). The GO terms are sorted in descending graph score order; numbers in parentheses indicate annotation levels.
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fig5: GO terms of 7628 Group 1F contigs with predicted full-length open reading frames. GO terms in categories biological process, molecular function and cellular component were retrieved from combined graph analyses performed in Blast2GO platform (sequence filter 100, score alpha 0.6, node score filter 100). The GO terms are sorted in descending graph score order; numbers in parentheses indicate annotation levels.

Mentions: To estimate how well the assembled contigs represent expression of real genes and not just random sequences, a brief summary is given on the Group 1F contigs containing full-length ORFs. A full-length ORF was identified in 7628 contigs (25% of all), when the presence of a full-length ORF was predicted based on the alignment of the contig to its most similar PAVE hit: complete coverage from start to stop codon indicated a full-length ORF. More contigs are likely to be predicted to include full-length ORFs, if a different ORF finding procedure is applied. Here, the contigs with predicted full-length ORFs in Group 1F were 247–12 130 bp long (median 1563 bp; Supplementary Table S4). Ninety-six percent of them had best hits against P. persica, 77% had SwissProt hits, 97% had InterProScan matches and 82% had GO terms assigned (Table 2 and Supplementary Table S4). The InterProScan matches and GO terms assigned were largely consistent with each other and with the functions suggested by the best hits (Supplementary Table S4).The assigned GO terms covered a wide range of processes, functions and cellular compartments from ‘cell division’ (171 contigs) and ‘chloroplast’ (1042 contigs) to ‘transcription factor activity’ (300 contigs) and ‘response to stimulus’ (2424 contigs) (Figure 5 and Supplementary Table S5).


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)

GO terms of 7628 Group 1F contigs with predicted full-length open reading frames. GO terms in categories biological process, molecular function and cellular component were retrieved from combined graph analyses performed in Blast2GO platform (sequence filter 100, score alpha 0.6, node score filter 100). The GO terms are sorted in descending graph score order; numbers in parentheses indicate annotation levels.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591669&req=5

fig5: GO terms of 7628 Group 1F contigs with predicted full-length open reading frames. GO terms in categories biological process, molecular function and cellular component were retrieved from combined graph analyses performed in Blast2GO platform (sequence filter 100, score alpha 0.6, node score filter 100). The GO terms are sorted in descending graph score order; numbers in parentheses indicate annotation levels.
Mentions: To estimate how well the assembled contigs represent expression of real genes and not just random sequences, a brief summary is given on the Group 1F contigs containing full-length ORFs. A full-length ORF was identified in 7628 contigs (25% of all), when the presence of a full-length ORF was predicted based on the alignment of the contig to its most similar PAVE hit: complete coverage from start to stop codon indicated a full-length ORF. More contigs are likely to be predicted to include full-length ORFs, if a different ORF finding procedure is applied. Here, the contigs with predicted full-length ORFs in Group 1F were 247–12 130 bp long (median 1563 bp; Supplementary Table S4). Ninety-six percent of them had best hits against P. persica, 77% had SwissProt hits, 97% had InterProScan matches and 82% had GO terms assigned (Table 2 and Supplementary Table S4). The InterProScan matches and GO terms assigned were largely consistent with each other and with the functions suggested by the best hits (Supplementary Table S4).The assigned GO terms covered a wide range of processes, functions and cellular compartments from ‘cell division’ (171 contigs) and ‘chloroplast’ (1042 contigs) to ‘transcription factor activity’ (300 contigs) and ‘response to stimulus’ (2424 contigs) (Figure 5 and Supplementary Table S5).

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.