Dataset Information

De novo sequencing and analysis of the transcriptome of two highbush blueberry (V. corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

ABSTRACT: This study describes the gene expression analysis of two commercial blueberry cultivars ‘Legacy’ and ‘Bluecrop’ at harvest and postharvest after cold storage. RNA was sequenced from berries in triplicate and separate transcriptomes were assemblied and used for differential gene expression analysis comparing treatment per cultivar as well as between cultivars.

PROVIDER: PRJEB45778 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6318200_1.fastq.gz	Fastqsanger.gz
	ERR6318200_2.fastq.gz	Fastqsanger.gz
	ERR6318210_1.fastq.gz	Fastqsanger.gz
	ERR6318210_2.fastq.gz	Fastqsanger.gz
	ERR6318201_1.fastq.gz	Fastqsanger.gz

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Project description:Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, 'Bluecrop' and 'Legacy', at harvest, three weeks storage in a non-modified environment at 4 °C and after three weeks storage at 4 °C followed by three days at 21 °C, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality. De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for 'Bluecrop' and 'Legacy' respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 290 unigenes were up-regulated in 'Legacy' only, 685 were up-regulated in 'Bluecrop', 252 were up-regulated in both cultivars and 948 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes. In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.

Project description:Plants are inhabited by millions of parasitic, commensal, and mutualistic microorganisms that coexist in complex ecological communities, and profoundly affect the plant's productivity, health, and capacity to cope with environmental stress. Therefore, a better understanding of the rhizosphere microbiome may open a yet untapped avenue for the rational exploitation of beneficial plant-microbe interactions in modern agriculture. Blueberries encompass several wild and cultivated species of shrubs of the genus Vaccinium that are native to North America. They are grown commercially for the production of fruits, which are considered a health food due to the rich content of minerals, trace elements, and phenolic compounds with antioxidant, antitumor, and anti-inflammatory properties. Despite a long history of breeding and extensive commercial use, remarkably little is known about the composition and function of the blueberry root microbiome. To address this gap, we employed molecular approaches to characterize and compare microbial communities inhabiting the roots of rabbiteye blueberry (Vaccinium virgatum), Darrow's blueberry (Vaccinium darrowii), and southern highbush blueberry (SHB; an interspecific hybrid of Vaccinium corymbosum and V. darrowii). Our results revealed that these plant species share a common core rhizobiome, but at the same time differ significantly in the diversity, relative abundance, richness, and evenness of multiple groups of prokaryotic and eukaryotic microorganisms. Although the host signature effects were especially pronounced at the plant species level, we also observed genotype-level variations in the distribution of specific microbial taxa, which suggests that the assembly of the blueberry microbiome is shaped by the plant genotype and modifications associated with the domestication and breeding of members of the Vaccinium genus. We also demonstrated that the studied Vaccinium species differ in the abundance of beneficial rhizobacteria and ericoid mycorrhizal fungi, which play a vital role in their adaptation to soils with low pH and slow turnover of organic matter.

Project description:BackgroundPropagation of cuttings is frequently used in various plant species, including blueberry, which shows special root characteristics that may hinder adventitious root (AR) formation. AR formation is influenced by various factors, and auxin is considered to play a central role; however, little is known of the related regulatory mechanisms. In this study, a comparative transcriptome analysis of green cuttings treated with or without indole-butyric acid (IBA) was performed via RNA_seq to identify candidate genes associated with IBA-induced AR formation.ResultsRooting phenotypes, especially the rooting rate, were significantly promoted by exogenous auxin in the IBA application. Blueberry AR formation was an auxin-induced process, during which adventitious root primordium initiation (rpi) began at 14 days after cutting (DAC), root primordium (rp) was developed at 21 DAC, mature AR was observed at 28 DAC and finally outgrowth from the stem occurred at 35 DAC. Higher IAA levels and lower ABA and zeatin contents might facilitate AR formation and development. A time series transcriptome analysis identified 14,970 differentially expressed genes (DEGs) during AR formation, of which there were 7467 upregulated and 7503 downregulated genes. Of these, approximately 35 candidate DEGs involved in the auxin-induced pathway and AR formation were further identified, including 10 auxin respective genes (ARFs and SAURs), 13 transcription factors (LOB domain-containing protein (LBDs)), 6 auxin transporters (AUX22, LAX3/5 and PIN-like 6 (PIL6s)) and 6 rooting-associated genes (root meristem growth factor 9 (RGF9), lateral root primordium 1 (LRP1s), and dormancy-associated protein homologue 3 (DRMH3)). All these identified DEGs were highly upregulated in certain stages during AR formation, indicating their potential roles in blueberry AR formation.ConclusionsThe transcriptome profiling results indicated candidate genes or major regulatory factors that influence adventitious root formation in blueberry and provided a comprehensive understanding of the rooting mechanism underlying the auxin-induced AR formation from blueberry green cuttings.

Dataset Information

De novo sequencing and analysis of the transcriptome of two highbush blueberry (V. corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

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