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

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 developmenta...

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Autores principales: Pervaiz, Tariq, Haifeng, Jia, Salman Haider, Muhammad, Cheng, Zhang, Cui, Mengjie, Wang, Mengqi, Cui, Liwen, Wang, Xicheng, Fang, Jinggui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732810/
https://www.ncbi.nlm.nih.gov/pubmed/26824474
http://dx.doi.org/10.1371/journal.pone.0147369
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author Pervaiz, Tariq
Haifeng, Jia
Salman Haider, Muhammad
Cheng, Zhang
Cui, Mengjie
Wang, Mengqi
Cui, Liwen
Wang, Xicheng
Fang, Jinggui
author_facet Pervaiz, Tariq
Haifeng, Jia
Salman Haider, Muhammad
Cheng, Zhang
Cui, Mengjie
Wang, Mengqi
Cui, Liwen
Wang, Xicheng
Fang, Jinggui
author_sort Pervaiz, Tariq
collection PubMed
description 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.
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spelling pubmed-47328102016-02-04 Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform Pervaiz, Tariq Haifeng, Jia Salman Haider, Muhammad Cheng, Zhang Cui, Mengjie Wang, Mengqi Cui, Liwen Wang, Xicheng Fang, Jinggui PLoS One Research Article 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. Public Library of Science 2016-01-29 /pmc/articles/PMC4732810/ /pubmed/26824474 http://dx.doi.org/10.1371/journal.pone.0147369 Text en © 2016 Pervaiz et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Pervaiz, Tariq
Haifeng, Jia
Salman Haider, Muhammad
Cheng, Zhang
Cui, Mengjie
Wang, Mengqi
Cui, Liwen
Wang, Xicheng
Fang, Jinggui
Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform
title Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform
title_full Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform
title_fullStr Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform
title_full_unstemmed Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform
title_short Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform
title_sort transcriptomic analysis of grapevine (cv. summer black) leaf, using the illumina platform
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732810/
https://www.ncbi.nlm.nih.gov/pubmed/26824474
http://dx.doi.org/10.1371/journal.pone.0147369
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