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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ftmdpi:oai:mdpi.com:/2079-7737/10/12/1274/ 2023-08-20T04:09:01+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 agris 2021-12-05 application/pdf https://doi.org/10.3390/biology10121274 EN eng Multidisciplinary Digital Publishing Institute Bioinformatics https://dx.doi.org/10.3390/biology10121274 https://creativecommons.org/licenses/by/4.0/ Biology; Volume 10; Issue 12; Pages: 1274 Scleractinia zooxanthellae holobiont symbiosis PacBio transcriptomics Text 2021 ftmdpi https://doi.org/10.3390/biology10121274 2023-08-01T03:27:53Z 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. Text Ocean acidification MDPI Open Access Publishing Biology 10 12 1274 |
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English |
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Scleractinia zooxanthellae holobiont symbiosis PacBio transcriptomics |
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Scleractinia zooxanthellae holobiont symbiosis PacBio transcriptomics 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 |
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 |
Text |
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 |
Multidisciplinary Digital Publishing Institute |
publishDate |
2021 |
url |
https://doi.org/10.3390/biology10121274 |
op_coverage |
agris |
genre |
Ocean acidification |
genre_facet |
Ocean acidification |
op_source |
Biology; Volume 10; Issue 12; Pages: 1274 |
op_relation |
Bioinformatics https://dx.doi.org/10.3390/biology10121274 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/biology10121274 |
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Biology |
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10 |
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12 |
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1274 |
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