Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform

• Published in: PloS one Vol. 11; no. 1; p. e0147369
• Main Authors: Pervaiz, Tariq, Haifeng, Jia, Salman Haider, Muhammad, Cheng, Zhang, Cui, Mengjie, Wang, Mengqi, Cui, Liwen, Wang, Xicheng, Fang, Jinggui
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 29.01.2016; Public Library of Science (PLoS)
• Subjects: Annotations; Anthocyanins; Arabidopsis; Biological activity; Biology and Life Sciences; Biosynthesis; Cell division; Developmental stages; DNA sequencing; Flavonoids; Flowers & plants; Flowers - genetics; Flowers - growth & development; Fruit - genetics; Fruit - growth & development; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene Ontology; Gene sequencing; Genes; Genetic aspects; Genome, Plant; Genomics; Grapes; Growth stage; High-Throughput Nucleotide Sequencing; Horticulture; Kinases; Laboratories; Leaves; Leucine; Metabolic Networks and Pathways - genetics; Metabolic pathways; Metabolism; Methods; Molecular Sequence Annotation; Nucleotide sequence; Nucleotides; Pathways; Photosystem II; Physical Sciences; Physiology; Plant Leaves - genetics; Plant Leaves - growth & development; Plant sciences; Protein C; Protein kinase; Proteins; Pyridine nucleotide reductase; Research and analysis methods; Ribonucleic acid; RNA; RNA, Messenger - genetics; Summer; Transcription; Transcription (Genetics); Transcriptome; Vitis - genetics; Vitis - growth & development; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0147369

Proceeding to illumina sequencing, determining RNA integrity numbers for poly RNA were separated from each of the four developmental stages of cv. Summer Black leaves by using Illumina HiSeq™ 2000. The sums of 272,941,656 reads were generated from vitis vinifera leaf at four different developmental stages, with more than 27 billion nucleotides of the sequence data. At each growth stage, RNA samples were indexed through unique nucleic acid identifiers and sequenced. KEGG annotation results depicted that the highest number of transcripts in 2,963 (2Avs4A) followed by 1Avs4A (2,920), and 3Avs4A (2,294) out of 15,614 (71%) transcripts were recorded. In comparison, a total of 1,532 transcripts were annotated in GOs, including Cellular component, with the highest number in "Cell part" 251 out of 353 transcripts (71.1%), followed by intracellular organelle 163 out of 353 transcripts (46.2%), while in molecular function and metabolic process 375 out of 525 (71.4%) transcripts, multicellular organism process 40 out of 525 (7.6%) transcripts in biological process were most common in 1Avs2A. While in case of 1Avs3A, cell part 476 out of 662 transcripts (71.9%), and membrane-bounded organelle 263 out of 662 transcripts (39.7%) were recorded in Cellular component. In the grapevine transcriptome, during the initial stages of leaf development 1Avs2A showed single transcript was down-regulated and none of them were up-regulated. While in comparison of 1A to 3A showed one up-regulated (photosystem II reaction center protein C) and one down regulated (conserved gene of unknown function) transcripts, during the hormone regulating pathway namely SAUR-like auxin-responsive protein family having 2 up-regulated and 7 down-regulated transcripts, phytochrome-associated protein showed 1 up-regulated and 9 down-regulated transcripts, whereas genes associated with the Leucine-rich repeat protein kinase family protein showed 7 up-regulated and 1 down-regulated transcript, meanwhile Auxin Resistant 2 has single up-regulated transcript in second developmental stage, although 3 were down-regulated at lateral growth stages (3A and 4A). In the present study, 489 secondary metabolic pathways related genes were identified during leaf growth, which mainly includes alkaloid (40), anthocyanins (21), Diterpenoid (144), Monoterpenoid (90) and Flavonoids (93). Quantitative real-time PCR was applied to validate 10 differentially expressed transcripts patterns from flower, leaf and fruit metabolic pathways at different growth stages.