Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont
Coral–zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral–zooxanthellae. Although some Scleractin...
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ftdoajarticles:oai:doaj.org/article:622f3206164447cbbdc62406efc7bf6b 2023-10-01T03:58:38+02:00 Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont Yunqing Liu Xin Liao Tingyu Han Ao Su Zhuojun Guo Na Lu Chunpeng He Zuhong Lu 2021-12-01T00:00:00Z https://doi.org/10.3390/biology10121274 https://doaj.org/article/622f3206164447cbbdc62406efc7bf6b EN eng MDPI AG https://www.mdpi.com/2079-7737/10/12/1274 https://doaj.org/toc/2079-7737 doi:10.3390/biology10121274 2079-7737 https://doaj.org/article/622f3206164447cbbdc62406efc7bf6b Biology, Vol 10, Iss 1274, p 1274 (2021) Scleractinia zooxanthellae holobiont symbiosis PacBio transcriptomics Biology (General) QH301-705.5 article 2021 ftdoajarticles https://doi.org/10.3390/biology10121274 2023-09-03T00:46:11Z Coral–zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral–zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa . Our results provide better material for studying coral symbiosis. Article in Journal/Newspaper Ocean acidification Directory of Open Access Journals: DOAJ Articles Biology 10 12 1274 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
topic |
Scleractinia zooxanthellae holobiont symbiosis PacBio transcriptomics Biology (General) QH301-705.5 |
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Scleractinia zooxanthellae holobiont symbiosis PacBio transcriptomics Biology (General) QH301-705.5 Yunqing Liu Xin Liao Tingyu Han Ao Su Zhuojun Guo Na Lu Chunpeng He Zuhong Lu Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont |
topic_facet |
Scleractinia zooxanthellae holobiont symbiosis PacBio transcriptomics Biology (General) QH301-705.5 |
description |
Coral–zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral–zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa . Our results provide better material for studying coral symbiosis. |
format |
Article in Journal/Newspaper |
author |
Yunqing Liu Xin Liao Tingyu Han Ao Su Zhuojun Guo Na Lu Chunpeng He Zuhong Lu |
author_facet |
Yunqing Liu Xin Liao Tingyu Han Ao Su Zhuojun Guo Na Lu Chunpeng He Zuhong Lu |
author_sort |
Yunqing Liu |
title |
Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont |
title_short |
Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont |
title_full |
Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont |
title_fullStr |
Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont |
title_full_unstemmed |
Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral–Zooxanthellae Holobiont |
title_sort |
full-length transcriptome sequencing of the scleractinian coral montipora foliosa reveals the gene expression profile of coral–zooxanthellae holobiont |
publisher |
MDPI AG |
publishDate |
2021 |
url |
https://doi.org/10.3390/biology10121274 https://doaj.org/article/622f3206164447cbbdc62406efc7bf6b |
genre |
Ocean acidification |
genre_facet |
Ocean acidification |
op_source |
Biology, Vol 10, Iss 1274, p 1274 (2021) |
op_relation |
https://www.mdpi.com/2079-7737/10/12/1274 https://doaj.org/toc/2079-7737 doi:10.3390/biology10121274 2079-7737 https://doaj.org/article/622f3206164447cbbdc62406efc7bf6b |
op_doi |
https://doi.org/10.3390/biology10121274 |
container_title |
Biology |
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10 |
container_issue |
12 |
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1274 |
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1778531559575388160 |