Abstract
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.
Highlights
Vitaceae comprised of 14 genera and about 900 species which are distributed all over the globe in tropical regions of Australia, Asia, Africa and the Pacific Islands with a small number of genera in temperate areas [1]
Few organ-specific genes were shared among the different developmental stages; up to 16% of the organspecific genes expressed in the flower were common to the different floral organs
We studied the reference transcriptomes for RNA-Seq analysis, validate several transcriptional changes recorded with the help of quantitative real-time PCR and validated with the flower fruit and leaf growth stages, metabolic pathways described the biological processes that are supplemented in differentially regulated transcripts
Summary
Vitaceae comprised of 14 genera and about 900 species which are distributed all over the globe in tropical regions of Australia, Asia, Africa and the Pacific Islands with a small number of genera in temperate areas [1]. Leaf is the most important vegetative organ supplying the energy, nutrition and hormones for the fruit growth and development. Leaf growth and development in all vascular plants is begun with the growth of meristem tissues. Subsequent cell multiplication and elongation occurs primarily from a basal intercalary meristem producing a gradient of cells along the leaf, with the sequence of interconnected and overlapping phases: initiation, general cell division, transition, cell expansion and meristemoid division phases [3]. Consecutive transverse segments of leaf provide harmonized large number of cells at various developmental stages. Successive transverse sections of a leaf provides synchronized number of cells at different growth stages [4]. Few organ-specific genes were shared among the different developmental stages; up to 16% of the organspecific genes expressed in the flower were common to the different floral organs
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