RNA-Seq-based transcriptome analysis of dormant flower buds of Chinese cherry (Prunus pseudocerasus)

Zhu, Yanbing; Li, Yongqiang; Xin, Dedong; Chen, Wenrong; Xu, Shumin; Wang, Yue; Guo, Weidong

doi:10.1016/j.gene.2014.11.032

Cited by 88 publications

(61 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…MADS-box (DAM) genes associated with dormancy-have been isolated to investigate their expression pattern in some fruit plants during dormancy [12, 13]. For example, DAM1 through DAM6 have been identified in peach and Japanese apricot [14, 15], while MADS13-1 , MADS13-2, MADS13-3 , PpMADS1 and PpMADS2 were found in Japanese pear and Chinese white pear (Suli) [16, 17].…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, several other genes are involved in the complex molecular network regulating dormancy in deciduous plants. Therefore, segregating single gene is not sufficient for illuminating underlying molecular processed associated with bud dormancy [13]. …”

Section: Introductionmentioning

confidence: 99%

“…Moreover, in another study the transcriptomic analysis revealed the dormancy-related regulatory pathways involving photoperiod, hormones and circadian clocks [20–22]. Although previous studies have investigated the physiological as well as the molecular mechanism of bud dormancy using the transcriptomic approach in deciduous fruits as well as other crops [13, 16, 23], no attempt has yet been made to study grape bud dormancy at the transcriptomic level.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

et al. 2017

View full text Add to dashboard Cite

BackgroundBud dormancy is an important biological phenomenon of perennial plants that enables them to survive under harsh environmental circumstances. Grape (Vitis vinifera) is one of the most grown fruit crop worldwide; however, underlying mechanisms involved in grape bud dormancy are not yet clear. This work was aimed to explore the underlying molecular mechanism regulating bud dormancy in grape.ResultsWe have performed transcriptome and differential transcript expression analyses of “Shine Muscat” grape buds using the Illumina RNA-seq system. Comparisons of transcript expression levels among three stages of dormancy, paradormancy (PD) vs endodormancy (ED), summer buds (SB) vs ED and SB vs PD, resulted in the detection of 8949, 9780 and 3938 differentially expressed transcripts, respectively. Out of approximately 78 million high-quality generated reads, 6096 transcripts were differentially expressed (log2 ratio ≥ 1, FDR ≤ 0.001). Grape reference genome was used for alignment of sequence reads and to measure the expression level of transcripts. Furthermore, findings obtained were then compared using two different databases; Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), to annotate the transcript descriptions and to assign a pathway to each transcript. KEGG analysis revealed that secondary metabolites biosynthesis and plant hormone signaling was found most enriched out of the 127 total pathways. In the comparisons of the PD vs ED and SB vs ED stages of grape buds, the gibberellin (GA) and abscisic acid (ABA) pathways were found to be the most enriched. The ABA and GA pathways were further analyzed to observe the expression pattern of differentially expressed transcripts. Transcripts related to the PP2C family (ABA pathway) were found to be up-regulated in the PD vs ED comparison and down-regulated in the SB vs ED and SB vs PD comparisons. GID1 family transcripts (GA pathway) were up-regulated while DELLA family transcripts were down-regulated during the three dormancy stages. Differentially expressed transcripts (DEGs) related to redox activity were abundant in the GO biological process category. RT-qPCR assay results for 12 selected transcripts validated the data obtained by RNA-seq.ConclusionAt this stage, taking into account the results obtained so far, it is possible to put forward a hypothesis for the molecular mechanism underlying grape bud dormancy, which may pave the way for ultimate improvements in the grape industry.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0960-8) contains supplementary material, which is available to authorized users.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Transcriptome assembly has been successfully applied to many fruit trees, such as pear, melon, litchi, and Chinese cherry (Bai et al, 2013; Corbacho et al, 2013; Lu et al, 2014; Zhu et al, 2015). In our study, we have constructed independent cDNA libraries of four different flower stages in A. squamosa for Illumina RNA-seq.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

et al. 2016

View full text Add to dashboard Cite

Sugar apple (Annona squamosa L.) is a semi-deciduous subtropical tree that progressively sheds its leaves in the spring. However, little information is available on the mechanism involved in flower developmental pattern. To gain a global perspective on the floral transition and flower development of sugar apple, cDNA libraries were prepared independently from inflorescent meristem and three flowering stages. Illumina sequencing generated 107,197,488 high quality reads that were assembled into 71,948 unigenes, with an average sequence length of 825.40 bp. Among the unigenes, various transcription factor families involved in floral transition and flower development were elucidated. Furthermore, a Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that unigenes exhibiting differential expressions were involved in various phytohormone signal transduction events and circadian rhythms. In addition, 147 unigenes exhibiting sequence similarities to known flowering-related genes from other plants were differentially expressed during flower development. The expression patterns of 20 selected genes were validated using quantitative-PCR. The expression data presented in our study is the most comprehensive dataset available for sugar apple so far and will serve as a resource for investigating the genetics of the flowering process in sugar apple and other Annona species.

show abstract

“…Zhu et al (2015) performed the de novo transcriptome assembly and expression profiling of flower buds from Chinese cherry ( Prunus pseudocerasus ). Results identified dormancy-associated MADS-box, AGAMOUS -like, and APETALA3 -like as genes related to bud dormancy release.…”

Section: Deep Sequencing Of Transcriptomes: Rna-seqmentioning

confidence: 99%

Application of Genomic Technologies to the Breeding of Trees

et al. 2016

View full text Add to dashboard Cite

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.

show abstract

RNA-Seq-based transcriptome analysis of dormant flower buds of Chinese cherry (Prunus pseudocerasus)

Cited by 88 publications

References 61 publications

Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

Application of Genomic Technologies to the Breeding of Trees

Contact Info

Product

Resources

About