Comparative transcriptome sequencing and de novo analysis of Vaccinium corymbosum during fruit and color development

Abstract

BackgroundBlueberry is an economically important fruit crop in Ericaceae family. The substantial quantities of flavonoids in blueberry have been implicated in a broad range of health benefits. However, the information regarding fruit development and flavonoid metabolites based on the transcriptome level is still limited. In the present study, the transcriptome and gene expression profiling over berry development, especially during color development were initiated.ResultsA total of approximately 13.67 Gbp of data were obtained and assembled into 186,962 transcripts and 80,836 unigenes from three stages of blueberry fruit and color development. A large number of simple sequence repeats (SSRs) and candidate genes, which are potentially involved in plant development, metabolic and hormone pathways, were identified. A total of 6429 sequences containing 8796 SSRs were characterized from 15,457 unigenes and 1763 unigenes contained more than one SSR. The expression profiles of key genes involved in anthocyanin biosynthesis were also studied. In addition, a comparison between our dataset and other published results was carried out.ConclusionsOur high quality reads produced in this study are an important advancement and provide a new resource for the interpretation of high-throughput data for blueberry species whether regarding sequencing data depth or species extension. The use of this transcriptome data will serve as a valuable public information database for the studies of blueberry genome and would greatly boost the research of fruit and color development, flavonoid metabolisms and regulation and breeding of more healthful blueberries.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0866-5) contains supplementary material, which is available to authorized users.

Diversity in Metabolites and Fruit Quality Traits in Blueberry Enables Ploidy and Species Differentiation and Establishes a Strategy for Future Genetic Studies

“…As demonstrated by cluster analysis (Supplementary Figure S3), glycosylation and acylation, two enzymatic reactions that contribute to anthocyanin diversification in plants (Jaakola et al, 2002;Noguchi et al, 2009;Zifkin et al, 2012;Cheng et al, 2014;Le Roy et al, 2016) can explain the diversity observed within the tetraploid accessions. Previous studies described genes involved in flavonoid and more specifically anthocyanin biosynthesis in blueberry (Jaakola et al, 2002;Kurilich et al, 2005;Charron et al, 2009;Zifkin et al, 2012;Jaakola, 2013;Li et al, 2016;Lin et al, 2018;Colle et al, 2019). Here based on data from multiple studies (Jaakola et al, 2002;Zifkin et al, 2012;Jaakola, 2013;Colle et al, 2019), we reconstructed a scheme of the flavonoid pathway in blueberry (Figure 9) that includes early and late biosynthetic genes (EBGs and LBGs, respectively).…”

“…Here based on data from multiple studies (Jaakola et al, 2002;Zifkin et al, 2012;Jaakola, 2013;Colle et al, 2019), we reconstructed a scheme of the flavonoid pathway in blueberry (Figure 9) that includes early and late biosynthetic genes (EBGs and LBGs, respectively). The early anthocyanin genes (EBGs) are highly conserved across the plant kingdom including Vaccinium species (Jaakola et al, 2002;Zifkin et al, 2012;Jaakola, 2013;Li et al, 2016;Lin et al, 2018;Colle et al, 2019). However, the late anthocyanins biosynthesis genes (LBGs) have not fully explored in Vaccinium.…”

Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

“…Using the MISA software (http://pgrc.ipk-gatersleben.de/misa/misa.html), 145,640 scaffolds of Acer truncatum were used for genomic SSR marker detection. The following search parameters were set for identification: Di-, Tri-, Tetra-, Penta-and Hexa-nucleotide motifs with a minimum of 6, 5, 4, 4 and 4 repeats, respectively, as previously described [29,30]. The primers for SSR markers were designed by Premier 5.0 (Premier Biosoft International, Palo Alto, CA, USA).…”

The first transcriptome sequencing and analysis of the endangered plant species Picea neoveitchii Mast. and potential EST-SSR markers development

“…The quality of the library was assessed by the Agilent Bioanalyzer 2100 system. The fragments (300 bp ± 25 bp) were purified and amplified as previously reported in detail [5], and then the library was sequenced using the Illumina HiSeq platform.…”

“…Recent studies have shown that RNA-Seq is a very effective and powerful technique for gathering extensive transcriptome information in many plants [5][6][7][8]. When compared with other hardwood species [9][10][11][12][13][14][15], conifers tend to have larger and highly repetitive genomes [16][17][18][19][20][21].…”