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Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings
Citrus species are among the most economically important fruit crops. Physiological characteristics and molecular mechanisms associated with de-etiolation have been partially revealed. However, little is known about the mechanisms controlling the expression and function of genes associated with phot...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821843/ https://www.ncbi.nlm.nih.gov/pubmed/31666652 http://dx.doi.org/10.1038/s41598-019-52276-5 |
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author | Xiong, Bo Qiu, Xia Huang, Shengjia Wang, Xiaojia Zhang, Xu Dong, Tiantian Wang, Tie Li, Sichen Sun, Guochao Zhu, Jin Wang, Zhihui |
author_facet | Xiong, Bo Qiu, Xia Huang, Shengjia Wang, Xiaojia Zhang, Xu Dong, Tiantian Wang, Tie Li, Sichen Sun, Guochao Zhu, Jin Wang, Zhihui |
author_sort | Xiong, Bo |
collection | PubMed |
description | Citrus species are among the most economically important fruit crops. Physiological characteristics and molecular mechanisms associated with de-etiolation have been partially revealed. However, little is known about the mechanisms controlling the expression and function of genes associated with photosynthesis and chlorophyll biosynthesis in variegated citrus seedlings. The lower biomass, chlorophyll contents, and photosynthetic parameter values recorded for the variegated seedlings suggested that chlorophyll biosynthesis was partially inhibited. Additionally, roots of the variegated seedlings were longer than the roots of green seedlings. We obtained 567.07 million clean reads and 85.05 Gb of RNA-sequencing data, with more than 94.19% of the reads having a quality score of Q30 (sequencing error rate = 0.1%). Furthermore, we detected 4,786 and 7,007 differentially expressed genes (DEGs) between variegated and green Shiranuhi and Huangguogan seedlings. Thirty common pathways were differentially regulated, including pathways related to photosynthesis (GO: 0015979) and the chloroplast (GO: 0009507). Photosynthesis (44 and 63 DEGs), photosynthesis-antenna proteins (14 and 29 DEGs), and flavonoid biosynthesis (16 and 29 DEGs) pathways were the most common KEGG pathways detected in two analyzed libraries. Differences in the expression patterns of PsbQ, PetF, PetB, PsaA, PsaN, PsbP, PsaF, Cluster-2274.8338 (ZIP1), Cluster-2274.38688 (PTC52), and Cluster-2274.78784 might be responsible for the variegation in citrus seedlings. We completed a physiological- and transcriptome-level comparison of the Shiranuhi and Huangguogan cultivars that differ in terms of seedling variegation. We performed mRNA-seq analyses of variegated and green Shiranuhi and Huangguogan seedlings to explore the genes and regulatory pathways involved in the inhibition of chlorophyll biosynthesis and decreases in Chl a and Chl b contents. The candidate genes described herein should be investigated in greater detail to further characterize variegated citrus seedlings. |
format | Online Article Text |
id | pubmed-6821843 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-68218432019-11-05 Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings Xiong, Bo Qiu, Xia Huang, Shengjia Wang, Xiaojia Zhang, Xu Dong, Tiantian Wang, Tie Li, Sichen Sun, Guochao Zhu, Jin Wang, Zhihui Sci Rep Article Citrus species are among the most economically important fruit crops. Physiological characteristics and molecular mechanisms associated with de-etiolation have been partially revealed. However, little is known about the mechanisms controlling the expression and function of genes associated with photosynthesis and chlorophyll biosynthesis in variegated citrus seedlings. The lower biomass, chlorophyll contents, and photosynthetic parameter values recorded for the variegated seedlings suggested that chlorophyll biosynthesis was partially inhibited. Additionally, roots of the variegated seedlings were longer than the roots of green seedlings. We obtained 567.07 million clean reads and 85.05 Gb of RNA-sequencing data, with more than 94.19% of the reads having a quality score of Q30 (sequencing error rate = 0.1%). Furthermore, we detected 4,786 and 7,007 differentially expressed genes (DEGs) between variegated and green Shiranuhi and Huangguogan seedlings. Thirty common pathways were differentially regulated, including pathways related to photosynthesis (GO: 0015979) and the chloroplast (GO: 0009507). Photosynthesis (44 and 63 DEGs), photosynthesis-antenna proteins (14 and 29 DEGs), and flavonoid biosynthesis (16 and 29 DEGs) pathways were the most common KEGG pathways detected in two analyzed libraries. Differences in the expression patterns of PsbQ, PetF, PetB, PsaA, PsaN, PsbP, PsaF, Cluster-2274.8338 (ZIP1), Cluster-2274.38688 (PTC52), and Cluster-2274.78784 might be responsible for the variegation in citrus seedlings. We completed a physiological- and transcriptome-level comparison of the Shiranuhi and Huangguogan cultivars that differ in terms of seedling variegation. We performed mRNA-seq analyses of variegated and green Shiranuhi and Huangguogan seedlings to explore the genes and regulatory pathways involved in the inhibition of chlorophyll biosynthesis and decreases in Chl a and Chl b contents. The candidate genes described herein should be investigated in greater detail to further characterize variegated citrus seedlings. Nature Publishing Group UK 2019-10-30 /pmc/articles/PMC6821843/ /pubmed/31666652 http://dx.doi.org/10.1038/s41598-019-52276-5 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Xiong, Bo Qiu, Xia Huang, Shengjia Wang, Xiaojia Zhang, Xu Dong, Tiantian Wang, Tie Li, Sichen Sun, Guochao Zhu, Jin Wang, Zhihui Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings |
title | Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings |
title_full | Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings |
title_fullStr | Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings |
title_full_unstemmed | Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings |
title_short | Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings |
title_sort | physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated citrus (shiranuhi and huangguogan) seedlings |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821843/ https://www.ncbi.nlm.nih.gov/pubmed/31666652 http://dx.doi.org/10.1038/s41598-019-52276-5 |
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