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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.


Selected expression patterns within the sweet cherry ‘Regina’ fruit skin transcriptome. (a) All 29 955 contigs in Group 1F (G1F) were first clustered in five clusters applying the NG algorithm on the normalized expression patterns. Clusters NG1, NG3 and NG4 are shown. (b) Each NG cluster was reclustered applying the QT clustering algorithm (cluster diameters adapted to data, minimum cluster size 20 contigs). Numbers in parentheses indicate the number of contigs in each cluster. Selected clusters are shown. Sample codes as in Figure 1. The complete set of cluster plots available as Supplementary Fig. S3.
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fig6: Selected expression patterns within the sweet cherry ‘Regina’ fruit skin transcriptome. (a) All 29 955 contigs in Group 1F (G1F) were first clustered in five clusters applying the NG algorithm on the normalized expression patterns. Clusters NG1, NG3 and NG4 are shown. (b) Each NG cluster was reclustered applying the QT clustering algorithm (cluster diameters adapted to data, minimum cluster size 20 contigs). Numbers in parentheses indicate the number of contigs in each cluster. Selected clusters are shown. Sample codes as in Figure 1. The complete set of cluster plots available as Supplementary Fig. S3.

Mentions: We identified expression patterns or clusters on the whole transcriptome scale and focused on the exocarp-specific genes within selected clusters. Two partitional clustering algorithms implemented in the Mayday workbench52 were used: The neural gas (NG) algorithm was applied to separate Group 1F contigs in five large clusters, followed by quality threshold (QT) clustering for more detailed expression patterns (see the section on ‘Materials and methods’). Neural gas clusters NG1 to NG5 contained 3053 to 8881 contigs each (Supplementary Fig. S3a). Each NG cluster had a characteristic average or centroid expression pattern: elevated expression during Stages I and II (NG1), in the ovary shortly after flowering (0–10 DAFB; NG2), during Stage II and early Stage III (NG3), from mid-Stage II to maturity (NG4) and mainly in the mesocarp (NG5) (Supplementary Fig. S3a and Fig. 6a). Several over-represented GO terms were detected in each NG cluster (Supplementary Table S8). For instance, in cluster NG2, the most specific, over-represented GO terms were related to translation, transcription and cell division. These functions are consistent with the high RNA levels in the tissue collected 3 and 10 DAFB (data not shown), reflecting the high cell division activity characteristic for this early stage of fruit development. Based on the GO analysis and the expression patterns, we expected to find the most exocarp-relevant contigs in clusters NG1, NG3 and NG4. Therefore, the following analyses concentrated on these three NG clusters. Only the GO terms in the category biological process will be considered below; the complete results are available in Supplementary Table S8.


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)

Selected expression patterns within the sweet cherry ‘Regina’ fruit skin transcriptome. (a) All 29 955 contigs in Group 1F (G1F) were first clustered in five clusters applying the NG algorithm on the normalized expression patterns. Clusters NG1, NG3 and NG4 are shown. (b) Each NG cluster was reclustered applying the QT clustering algorithm (cluster diameters adapted to data, minimum cluster size 20 contigs). Numbers in parentheses indicate the number of contigs in each cluster. Selected clusters are shown. Sample codes as in Figure 1. The complete set of cluster plots available as Supplementary Fig. S3.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig6: Selected expression patterns within the sweet cherry ‘Regina’ fruit skin transcriptome. (a) All 29 955 contigs in Group 1F (G1F) were first clustered in five clusters applying the NG algorithm on the normalized expression patterns. Clusters NG1, NG3 and NG4 are shown. (b) Each NG cluster was reclustered applying the QT clustering algorithm (cluster diameters adapted to data, minimum cluster size 20 contigs). Numbers in parentheses indicate the number of contigs in each cluster. Selected clusters are shown. Sample codes as in Figure 1. The complete set of cluster plots available as Supplementary Fig. S3.
Mentions: We identified expression patterns or clusters on the whole transcriptome scale and focused on the exocarp-specific genes within selected clusters. Two partitional clustering algorithms implemented in the Mayday workbench52 were used: The neural gas (NG) algorithm was applied to separate Group 1F contigs in five large clusters, followed by quality threshold (QT) clustering for more detailed expression patterns (see the section on ‘Materials and methods’). Neural gas clusters NG1 to NG5 contained 3053 to 8881 contigs each (Supplementary Fig. S3a). Each NG cluster had a characteristic average or centroid expression pattern: elevated expression during Stages I and II (NG1), in the ovary shortly after flowering (0–10 DAFB; NG2), during Stage II and early Stage III (NG3), from mid-Stage II to maturity (NG4) and mainly in the mesocarp (NG5) (Supplementary Fig. S3a and Fig. 6a). Several over-represented GO terms were detected in each NG cluster (Supplementary Table S8). For instance, in cluster NG2, the most specific, over-represented GO terms were related to translation, transcription and cell division. These functions are consistent with the high RNA levels in the tissue collected 3 and 10 DAFB (data not shown), reflecting the high cell division activity characteristic for this early stage of fruit development. Based on the GO analysis and the expression patterns, we expected to find the most exocarp-relevant contigs in clusters NG1, NG3 and NG4. Therefore, the following analyses concentrated on these three NG clusters. Only the GO terms in the category biological process will be considered below; the complete results are available in Supplementary Table S8.

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.