Dataset Information

Molecular analysis of the processes of surface brown spot (SBS) formation in pear fruit (Pyrus bretschneideri Rehd. cv. Dangshansuli) by de novo transcriptome assembly.

ABSTRACT: Browning disorder, which usually occurs post-harvest in pears subjected to long-term storage, can cause browning of the pear flesh and/or core. In 2011, investigators in China found a novel type of brown spot (designated as surface brown spot, SBS) in pre-harvest 'Dangshansuli' pears (Pyrus bretschneideri Rehd.). SBS has a large impact on the exterior quality of the pears. Interestingly, the brown coloration was only found on the peel and not the flesh or the core. In this paper, de novo transcriptome analysis of the exocarp of pears with SBS using Illumina sequencing showed that SBS up-regulated the expression of genes related to oxidative phosphorylation, phenolic compound synthesis and polyphenoloxidase (PPO), and SBS was associated with inhibition of primary and secondary metabolism genes. Ca(2+)-sensor proteins might be involved in the signal transduction that occurs during the process of SBS formation, and this signaling is likely to be regulated by H2O2, abscisic acid (ABA) and gibberellic acid (GA3). Phytohormone and mineral element analyses confirmed that GA3, ABA, H2O2 and Ca(2+) contribute to SBS formation. In addition to the seasonal characteristics, low levels of O2 and Ca(2+) in the fruit are potential causes of the browning response due to exposure to oxidative stress, oxidative-reductive imbalance and the accumulation of reactive oxygen species (ROS), which affected the membrane integrity. Disruption of the membranes allows for PPO and phenolic compounds to come into contact, and the phenolic compounds are oxidized to form the browning pigments.

SUBMITTER: Liu P

PROVIDER: S-EPMC3776823 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Molecular analysis of the processes of surface brown spot (SBS) formation in pear fruit (Pyrus bretschneideri Rehd. cv. Dangshansuli) by de novo transcriptome assembly.

Liu Pu P Xue Cheng C Wu Ting-ting TT Heng Wei W Jia Bing B Ye Zhenfeng Z Liu Li L Zhu Liwu L

PloS one 20130918 9

Browning disorder, which usually occurs post-harvest in pears subjected to long-term storage, can cause browning of the pear flesh and/or core. In 2011, investigators in China found a novel type of brown spot (designated as surface brown spot, SBS) in pre-harvest 'Dangshansuli' pears (Pyrus bretschneideri Rehd.). SBS has a large impact on the exterior quality of the pears. Interestingly, the brown coloration was only found on the peel and not the flesh or the core. In this paper, de novo transcr ...[more]

PMID: 24058529

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Project description:Although pear is an important edible fruit species, the current available genomic information is limited. Combining the Solexa/ Illumina RNA-seq high-throughput sequencing approach with Digital Gene Expression (DGE) analysis results in a powerful transcriptomic study. This publication reports the transcriptome profiling analysis of Pyrus bretschneideri Rehd. using RNA-seq and DGE in order to better understand the molecular mechanisms underlying biological aspects of pear, especially fruit development and maturation.Using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system, de novo transcriptome assembly and gene expression analysis of P. bretschneideri were performed at an unprecedented depth (5.47 gigabase pairs). Approximately 60.77 million reads were obtained, trimmed, and assembled into 90,227 unigenes. The unigenes comprised 17,619 contig clusters and 72,608 singletons and were an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found 61,636 unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms. 34.6% of the unigenes (31,215) were annotated against KEGG into 121 known metabolic or signaling pathways. DGE libraries of five different developmental fruit stages were constructed and analyzed, and the gene expression variations between two consecutive stages were compared. Thousands of genes showed significantly different expression levels based on the various comparisons. Extensive transcriptome and DGE profiling data have been obtained from the deep sequencing of the Chinese white pear, which can serve as an important public information platform for gene expression, genomic, and functional genomic studies in P. bretschneideri and which provides comprehensive gene expression information at the transcriptional level that could facilitate understanding of the molecular mechanisms in fruit development and maturation.

Project description:BackgroundPear (Pyrus spp) is an important fruit species worldwide; however, its genetics and genomic information is limited. Combining the Solexa/Illumina RNA-seq high-throughput sequencing approach (RNA-seq) with Digital Gene Expression (DGE) analysis would be a powerful tool for transcriptomic study. This paper reports the transcriptome profiling analysis of Chinese white pear (P. bretschneideri) using RNA-seq and DGE to better understand the molecular mechanisms in fruit development and maturation of Chinese white pear.ResultsDe novo transcriptome assembly and gene expression analysis of Chinese white pear were performed in an unprecedented depth (5.47 gigabase pairs) using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system. Approximately, 60.77 million reads were sequenced, trimmed, and assembled into 90,227 unigenes. These unigenes comprised 17,619 contigs and 72,608 singletons with an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR, and COGs at NCBI, Pfam, InterPro, and KEGG) found that 61,636 unigenes can be annotated with gene descriptions, conserved protein domains, or gene ontology terms. By BLASTing all 61,636 unigenes in KEGG, a total of 31,215 unigenes were annotated into 121 known metabolic or signaling pathways in which a few primary, intermediate, and secondary metabolic pathways are directly related to pear fruit quality. DGE libraries were constructed for each of the five fruit developmental stages. Variations in gene expression among all developmental stages of pear fruit were significantly different in a large amount of unigenes.ConclusionExtensive transcriptome and DGE profiling data at five fruit developmental stages of Chinese white pear have been obtained from a deep sequencing, which provides comprehensive gene expression information at the transcriptional level. This could facilitate understanding of the molecular mechanisms in fruit development and maturation. Such a database can also be used as a public information platform for research on molecular biology and functional genomics in pear and other related species.

Dataset Information

Molecular analysis of the processes of surface brown spot (SBS) formation in pear fruit (Pyrus bretschneideri Rehd. cv. Dangshansuli) by de novo transcriptome assembly.

Publications

Molecular analysis of the processes of surface brown spot (SBS) formation in pear fruit (Pyrus bretschneideri Rehd. cv. Dangshansuli) by de novo transcriptome assembly.

Similar Datasets

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