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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.


Length distribution of assembled sweet cherry ‘Regina’ contigs in Group 1 (‘high abundance’, 34695 contigs, length 200–12 485 bp) and Group 2 (‘low abundance’, 32 712 contigs, 107–1482 bp). Length distribution of predicted transcripts in the P. persica genome (v.1.0) (28 702 sequences, 96–15 738 bp) is shown for reference. The x-values give the center of each bin; bin width is 100 bp, except for the first bin which is from 1 to 98 bp. Note logarithmic scale of the y-axis; bins with 0 sequences not shown.
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fig3: Length distribution of assembled sweet cherry ‘Regina’ contigs in Group 1 (‘high abundance’, 34695 contigs, length 200–12 485 bp) and Group 2 (‘low abundance’, 32 712 contigs, 107–1482 bp). Length distribution of predicted transcripts in the P. persica genome (v.1.0) (28 702 sequences, 96–15 738 bp) is shown for reference. The x-values give the center of each bin; bin width is 100 bp, except for the first bin which is from 1 to 98 bp. Note logarithmic scale of the y-axis; bins with 0 sequences not shown.

Mentions: The length distribution of contigs in Group 1 was somewhat biased towards the contigs shorter than 600 bp, although a considerable number of the contigs were 2000 to 5000 bp long or longer (Figure 3 and Table 1). This length distribution is similar to that of the P. persica predicted transcripts (Figure 3). A total of 330 million reads (49.6% of all reads) mapped to Group 1 contigs, 99.8% of them being unique matches; 16.0% mapped to Group 3 and only 0.4% to Group 2 (Table 1 and Supplementary Table S3). Averaging over the 24 samples, 75% (s.d. 8%) of the mappable reads mapped to Group 1 contigs, 24% (s.d. 8%) to Group 3 and 0.5% (s.d. 0.1%) to Group 2 (Figure 4).


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)

Length distribution of assembled sweet cherry ‘Regina’ contigs in Group 1 (‘high abundance’, 34695 contigs, length 200–12 485 bp) and Group 2 (‘low abundance’, 32 712 contigs, 107–1482 bp). Length distribution of predicted transcripts in the P. persica genome (v.1.0) (28 702 sequences, 96–15 738 bp) is shown for reference. The x-values give the center of each bin; bin width is 100 bp, except for the first bin which is from 1 to 98 bp. Note logarithmic scale of the y-axis; bins with 0 sequences not shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Length distribution of assembled sweet cherry ‘Regina’ contigs in Group 1 (‘high abundance’, 34695 contigs, length 200–12 485 bp) and Group 2 (‘low abundance’, 32 712 contigs, 107–1482 bp). Length distribution of predicted transcripts in the P. persica genome (v.1.0) (28 702 sequences, 96–15 738 bp) is shown for reference. The x-values give the center of each bin; bin width is 100 bp, except for the first bin which is from 1 to 98 bp. Note logarithmic scale of the y-axis; bins with 0 sequences not shown.
Mentions: The length distribution of contigs in Group 1 was somewhat biased towards the contigs shorter than 600 bp, although a considerable number of the contigs were 2000 to 5000 bp long or longer (Figure 3 and Table 1). This length distribution is similar to that of the P. persica predicted transcripts (Figure 3). A total of 330 million reads (49.6% of all reads) mapped to Group 1 contigs, 99.8% of them being unique matches; 16.0% mapped to Group 3 and only 0.4% to Group 2 (Table 1 and Supplementary Table S3). Averaging over the 24 samples, 75% (s.d. 8%) of the mappable reads mapped to Group 1 contigs, 24% (s.d. 8%) to Group 3 and 0.5% (s.d. 0.1%) to Group 2 (Figure 4).

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.