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Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis

Conchosporangia maturation is crucial for the yield of Pyropia/Porphyra. However, the molecular mechanisms underlying this process are poorly understood. In this study, we selected two strains of Pyropia haitanensis that show significant differences in conchosporangia maturation as materials to prod...

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Autores principales: Lin, Yinghui, Xu, Kai, Xu, Yan, Ji, Dehua, Chen, Changsheng, Wang, Wenlei, Xie, Chaotian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8278576/
https://www.ncbi.nlm.nih.gov/pubmed/34276783
http://dx.doi.org/10.3389/fgene.2021.680120
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author Lin, Yinghui
Xu, Kai
Xu, Yan
Ji, Dehua
Chen, Changsheng
Wang, Wenlei
Xie, Chaotian
author_facet Lin, Yinghui
Xu, Kai
Xu, Yan
Ji, Dehua
Chen, Changsheng
Wang, Wenlei
Xie, Chaotian
author_sort Lin, Yinghui
collection PubMed
description Conchosporangia maturation is crucial for the yield of Pyropia/Porphyra. However, the molecular mechanisms underlying this process are poorly understood. In this study, we selected two strains of Pyropia haitanensis that show significant differences in conchosporangia maturation as materials to produce RNA-Seq libraries. Then, we identified key molecular pathways and genes involved in conchosporangia maturation by conducting a weighted gene co-expression network analysis. Two specific modules were identified, and included functions such as phosphorus metabolism, lipid metabolism, and the phosphatidylinositol signaling system. The hub genes that responded positively during conchosporangia maturation encoded diacylglycerol kinase (DGK) and phosphatidylinositol-3-phosphate-5-kinase, which are involved in the synthesis of phosphatidic acid, a key component of lipid metabolism. A full-length DGK sequence of P. haitanensis, designated as PhDGK1, was obtained by rapid-amplification of cDNA ends. Conserved motif and phylogenetic tree analyses showed that PhDGK1 belongs to DGK Cluster II. The transcript level of PhDGK1 increased during conchosporangia maturation in both strains, but increased earlier, and to higher levels, in the early-maturing strain than in the late-maturing strain. This pattern of gene expression was consistent with the patterns of maturity and changes in pigment contents. These results indicate that lipid metabolism plays a key role in regulating conchosporangia maturation in Pyropia spp., and that PhDGK1 might be a useful molecular marker for breeding new early-maturing strains.
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spelling pubmed-82785762021-07-15 Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis Lin, Yinghui Xu, Kai Xu, Yan Ji, Dehua Chen, Changsheng Wang, Wenlei Xie, Chaotian Front Genet Genetics Conchosporangia maturation is crucial for the yield of Pyropia/Porphyra. However, the molecular mechanisms underlying this process are poorly understood. In this study, we selected two strains of Pyropia haitanensis that show significant differences in conchosporangia maturation as materials to produce RNA-Seq libraries. Then, we identified key molecular pathways and genes involved in conchosporangia maturation by conducting a weighted gene co-expression network analysis. Two specific modules were identified, and included functions such as phosphorus metabolism, lipid metabolism, and the phosphatidylinositol signaling system. The hub genes that responded positively during conchosporangia maturation encoded diacylglycerol kinase (DGK) and phosphatidylinositol-3-phosphate-5-kinase, which are involved in the synthesis of phosphatidic acid, a key component of lipid metabolism. A full-length DGK sequence of P. haitanensis, designated as PhDGK1, was obtained by rapid-amplification of cDNA ends. Conserved motif and phylogenetic tree analyses showed that PhDGK1 belongs to DGK Cluster II. The transcript level of PhDGK1 increased during conchosporangia maturation in both strains, but increased earlier, and to higher levels, in the early-maturing strain than in the late-maturing strain. This pattern of gene expression was consistent with the patterns of maturity and changes in pigment contents. These results indicate that lipid metabolism plays a key role in regulating conchosporangia maturation in Pyropia spp., and that PhDGK1 might be a useful molecular marker for breeding new early-maturing strains. Frontiers Media S.A. 2021-06-30 /pmc/articles/PMC8278576/ /pubmed/34276783 http://dx.doi.org/10.3389/fgene.2021.680120 Text en Copyright © 2021 Lin, Xu, Xu, Ji, Chen, Wang and Xie. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Lin, Yinghui
Xu, Kai
Xu, Yan
Ji, Dehua
Chen, Changsheng
Wang, Wenlei
Xie, Chaotian
Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis
title Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis
title_full Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis
title_fullStr Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis
title_full_unstemmed Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis
title_short Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis
title_sort transcriptome co-expression network analysis identifies key genes regulating conchosporangia maturation of pyropia haitanensis
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8278576/
https://www.ncbi.nlm.nih.gov/pubmed/34276783
http://dx.doi.org/10.3389/fgene.2021.680120
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