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Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods
BACKGROUND: Camellia oleifera Abel. (C. oleifera) is an important traditional woody species in China that produces edible oil. However, the current literature lacks a proper understanding of C. oleifera’s ability to adapt to different photoperiods. RESULTS: Our results indicate that the photoperiod...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465947/ https://www.ncbi.nlm.nih.gov/pubmed/36089577 http://dx.doi.org/10.1186/s12870-022-03798-0 |
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author | Yan, Jindong He, Jiacheng Li, Jian’an Ren, Shuangshuang Wang, Ying Zhou, Junqin Tan, Xiaofeng |
author_facet | Yan, Jindong He, Jiacheng Li, Jian’an Ren, Shuangshuang Wang, Ying Zhou, Junqin Tan, Xiaofeng |
author_sort | Yan, Jindong |
collection | PubMed |
description | BACKGROUND: Camellia oleifera Abel. (C. oleifera) is an important traditional woody species in China that produces edible oil. However, the current literature lacks a proper understanding of C. oleifera’s ability to adapt to different photoperiods. RESULTS: Our results indicate that the photoperiod can significantly impact flowering time in C. oleifera. We grew a total of nine samples under the short day condition (SD), middle day condition (MD) and long day condition (LD). Transcriptome analysis yielded 66.94 Gb of high-quality clean reads, with an average of over 6.73 Gb of reads for per sample. Following assembly, a total of 120,080 transcripts were obtained and 94,979 unigenes annotated. A total of 3475 differentially expressed genes (DEGs) were identified between the SD_MD, SD_LD, and MD_LD gene sets. Moreover, WGCNA identified ten gene modules. Genes in pink module (92 genes) were positively correlated with SD, and negatively correlated with both MD and LD. Genes in the magenta module (42 genes) were positively correlated with MD and negatively correlated with both LD and SD. Finally, genes in the yellow module (1758 genes) were positively correlated with both SD and MD, but negatively correlated with LD. KEGG enrichment analysis revealed that genes in the pink, magenta, and yellow modules were involved in flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism and circadian rhythm pathways. Additionally, eight hub genes (GI, AP2, WRKY65, SCR, SHR, PHR1, ERF106, and SCL3) were obtained through network analysis. The hub genes had high connectivity with other photoperiod-sensitive DEGs. The expression levels of hub genes were verified by qRT-PCR analysis. CONCLUSION: An increase in light duration promotes earlier flowering of C. oleifera. Flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism, and circadian rhythm pathways may function in the photoperiodic flowering pathway of C. oleifera. We also identified eight hub genes that may play a role in this pathway. Ultimately, this work contributes to our understanding of the photoperiodic flowering pathway of C. oleifera and further informs molecular breeding programs on the plant’s photoperiodic sensitivity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03798-0. |
format | Online Article Text |
id | pubmed-9465947 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-94659472022-09-13 Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods Yan, Jindong He, Jiacheng Li, Jian’an Ren, Shuangshuang Wang, Ying Zhou, Junqin Tan, Xiaofeng BMC Plant Biol Research BACKGROUND: Camellia oleifera Abel. (C. oleifera) is an important traditional woody species in China that produces edible oil. However, the current literature lacks a proper understanding of C. oleifera’s ability to adapt to different photoperiods. RESULTS: Our results indicate that the photoperiod can significantly impact flowering time in C. oleifera. We grew a total of nine samples under the short day condition (SD), middle day condition (MD) and long day condition (LD). Transcriptome analysis yielded 66.94 Gb of high-quality clean reads, with an average of over 6.73 Gb of reads for per sample. Following assembly, a total of 120,080 transcripts were obtained and 94,979 unigenes annotated. A total of 3475 differentially expressed genes (DEGs) were identified between the SD_MD, SD_LD, and MD_LD gene sets. Moreover, WGCNA identified ten gene modules. Genes in pink module (92 genes) were positively correlated with SD, and negatively correlated with both MD and LD. Genes in the magenta module (42 genes) were positively correlated with MD and negatively correlated with both LD and SD. Finally, genes in the yellow module (1758 genes) were positively correlated with both SD and MD, but negatively correlated with LD. KEGG enrichment analysis revealed that genes in the pink, magenta, and yellow modules were involved in flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism and circadian rhythm pathways. Additionally, eight hub genes (GI, AP2, WRKY65, SCR, SHR, PHR1, ERF106, and SCL3) were obtained through network analysis. The hub genes had high connectivity with other photoperiod-sensitive DEGs. The expression levels of hub genes were verified by qRT-PCR analysis. CONCLUSION: An increase in light duration promotes earlier flowering of C. oleifera. Flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism, and circadian rhythm pathways may function in the photoperiodic flowering pathway of C. oleifera. We also identified eight hub genes that may play a role in this pathway. Ultimately, this work contributes to our understanding of the photoperiodic flowering pathway of C. oleifera and further informs molecular breeding programs on the plant’s photoperiodic sensitivity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03798-0. BioMed Central 2022-09-12 /pmc/articles/PMC9465947/ /pubmed/36089577 http://dx.doi.org/10.1186/s12870-022-03798-0 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Yan, Jindong He, Jiacheng Li, Jian’an Ren, Shuangshuang Wang, Ying Zhou, Junqin Tan, Xiaofeng Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods |
title | Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods |
title_full | Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods |
title_fullStr | Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods |
title_full_unstemmed | Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods |
title_short | Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods |
title_sort | analysis of camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465947/ https://www.ncbi.nlm.nih.gov/pubmed/36089577 http://dx.doi.org/10.1186/s12870-022-03798-0 |
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