Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed Bangiales
As an important seedling source, monospores closely associate with yields in nori farming. However, the molecular mechanism underlying differences in monospore production for different strains remains unknown. Comparative transcriptome analysis was performed to examine gene expression differences be...
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KeAi Communications Co., Ltd.
2023-03-01
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| Series: | Aquaculture and Fisheries |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468550X2100112X |
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| author | Qingjie Zhang Shanshan Song Dahai Gao Xinghong Yan |
| author_facet | Qingjie Zhang Shanshan Song Dahai Gao Xinghong Yan |
| author_sort | Qingjie Zhang |
| collection | DOAJ |
| description | As an important seedling source, monospores closely associate with yields in nori farming. However, the molecular mechanism underlying differences in monospore production for different strains remains unknown. Comparative transcriptome analysis was performed to examine gene expression differences between the spore abundant wild-type strain (WT) and spore deficient mutant (Y1) of Pyropia chauhanii. The WT strain that produces monospores in abundance exhibited more differentially expressed genes (DEGs) in both number and higher fold-changes than the Y1 strain incapable of producing monospores, indicating that the specific regulation of genes is involved in monospore production. Three lists of DEGs were obtained between the two strains using intersection and displayed in Venn diagram: one expressed only in WT strain, another expressed only in Y1 strain, and the third shared in both strains. DEGs annotated as homologous genes of Arabidopsis thaliana in these 3 lists were curated for online functional enrichment analysis on Metascape website. Gene regulatory networks of WT were functionally enriched in the processing, proteolysis, and transport of proteins, especially within the small GTPase protein family, which might be account for the monospore production ability, whereas Y1 were functionally enriched in the metabolism of essential substance and utilization of indispensable energy, which might be account for the rapid growth of blades. We found the differentially enriched gene regulatory networks between strains might be the intrinsic mechanisms of the different monospore production traits. These findings provide novel insights into the genes and regulatory networks associated with monospore production abilities, which are essential for developing accurate breeding technologies for optimal release of monospores and increase of total nori production. |
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| spelling | doaj.art-ffa44c1b79034ba7bb4ca4eade348a952024-04-16T20:02:37ZengKeAi Communications Co., Ltd.Aquaculture and Fisheries2468-550X2023-03-0182124134Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed BangialesQingjie Zhang0Shanshan Song1Dahai Gao2Xinghong Yan3Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, ChinaKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, ChinaKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, ChinaKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China; Corresponding author. Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China.As an important seedling source, monospores closely associate with yields in nori farming. However, the molecular mechanism underlying differences in monospore production for different strains remains unknown. Comparative transcriptome analysis was performed to examine gene expression differences between the spore abundant wild-type strain (WT) and spore deficient mutant (Y1) of Pyropia chauhanii. The WT strain that produces monospores in abundance exhibited more differentially expressed genes (DEGs) in both number and higher fold-changes than the Y1 strain incapable of producing monospores, indicating that the specific regulation of genes is involved in monospore production. Three lists of DEGs were obtained between the two strains using intersection and displayed in Venn diagram: one expressed only in WT strain, another expressed only in Y1 strain, and the third shared in both strains. DEGs annotated as homologous genes of Arabidopsis thaliana in these 3 lists were curated for online functional enrichment analysis on Metascape website. Gene regulatory networks of WT were functionally enriched in the processing, proteolysis, and transport of proteins, especially within the small GTPase protein family, which might be account for the monospore production ability, whereas Y1 were functionally enriched in the metabolism of essential substance and utilization of indispensable energy, which might be account for the rapid growth of blades. We found the differentially enriched gene regulatory networks between strains might be the intrinsic mechanisms of the different monospore production traits. These findings provide novel insights into the genes and regulatory networks associated with monospore production abilities, which are essential for developing accurate breeding technologies for optimal release of monospores and increase of total nori production.http://www.sciencedirect.com/science/article/pii/S2468550X2100112XPyropia chauhaniiMonosporeArcheosporeComparative transcriptomeGene regulatory network |
| spellingShingle | Qingjie Zhang Shanshan Song Dahai Gao Xinghong Yan Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed Bangiales Aquaculture and Fisheries Pyropia chauhanii Monospore Archeospore Comparative transcriptome Gene regulatory network |
| title | Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed Bangiales |
| title_full | Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed Bangiales |
| title_fullStr | Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed Bangiales |
| title_full_unstemmed | Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed Bangiales |
| title_short | Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed Bangiales |
| title_sort | comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed bangiales |
| topic | Pyropia chauhanii Monospore Archeospore Comparative transcriptome Gene regulatory network |
| url | http://www.sciencedirect.com/science/article/pii/S2468550X2100112X |
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