Limits...
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.


Summary of the RNA-seq experiment, pre-processing of raw reads and de novo assembly of the sequence data. Details are given in section on ‘Material and methods’, Supplementary Method S1 and Supplementary Table S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Summary of the RNA-seq experiment, pre-processing of raw reads and de novo assembly of the sequence data. Details are given in section on ‘Material and methods’, Supplementary Method S1 and Supplementary Table S2.

Mentions: Tissue samples for RNA-seq analyses were collected in one or two biological replicates as indicated in Figure 1c. In total, cDNA generated from 24 individual samples representing 14 developmental time points was sequenced. The procedure and outcome of the sequencing, pre-processing, and assembly are outlined in Figure 2. Details on the pre-processing and assembly protocols, and the raw read and pre-processing results per sample are available as Supplementary Method S1, Supplementary Table S2 and Supplementary Fig. S1. Directional sequencing of 24 indexed samples in pools of four yielded a total of 665 million raw reads of 100 bp length each. After pre-processing and de novo assembly we obtained a final set of 68 101 assembled contigs of 107–14 149 bp length.


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)

Summary of the RNA-seq experiment, pre-processing of raw reads and de novo assembly of the sequence data. Details are given in section on ‘Material and methods’, Supplementary Method S1 and Supplementary Table S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Summary of the RNA-seq experiment, pre-processing of raw reads and de novo assembly of the sequence data. Details are given in section on ‘Material and methods’, Supplementary Method S1 and Supplementary Table S2.
Mentions: Tissue samples for RNA-seq analyses were collected in one or two biological replicates as indicated in Figure 1c. In total, cDNA generated from 24 individual samples representing 14 developmental time points was sequenced. The procedure and outcome of the sequencing, pre-processing, and assembly are outlined in Figure 2. Details on the pre-processing and assembly protocols, and the raw read and pre-processing results per sample are available as Supplementary Method S1, Supplementary Table S2 and Supplementary Fig. S1. Directional sequencing of 24 indexed samples in pools of four yielded a total of 665 million raw reads of 100 bp length each. After pre-processing and de novo assembly we obtained a final set of 68 101 assembled contigs of 107–14 149 bp length.

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.