Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (<i>Physeter macrocephalus</i>)
Cetaceans are a group of secondary aquatic mammals whose ancestors returned to the ocean from land, and during evolution, their immune systems adapted to the aquatic environment. Their skin, as the primary barrier to environmental pathogens, supposedly evolved to adapt to a new living environment. H...
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MDPI AG
2021-02-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/2/233 |
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| author | Daling Wang Ying Li Reyilamu Aierken Qi Kang Xianyan Wang Qianhui Zeng Zhichang Fan Yu Zhen Liyuan Zhao |
| author_facet | Daling Wang Ying Li Reyilamu Aierken Qi Kang Xianyan Wang Qianhui Zeng Zhichang Fan Yu Zhen Liyuan Zhao |
| author_sort | Daling Wang |
| collection | DOAJ |
| description | Cetaceans are a group of secondary aquatic mammals whose ancestors returned to the ocean from land, and during evolution, their immune systems adapted to the aquatic environment. Their skin, as the primary barrier to environmental pathogens, supposedly evolved to adapt to a new living environment. However, the immune system in the skin of cetaceans and the associated molecular mechanisms are still largely unknown. To better understand the immune system, we extracted RNA from the sperm whale’s (<i>Physeter macrocephalus</i>) skin and performed PacBio full-length sequencing and RNA-seq sequencing. We obtained a total of 96,350 full-length transcripts with an average length of 1705 bp and detected 5150 genes that were associated with 21 immune-related pathways by gene annotation enrichment analysis. Moreover, we found 89 encoding genes corresponding to 33 proteins were annotated in the NOD-like receptor (NLR)-signaling pathway, including <i>NOD1</i>, <i>NOD2</i>, <i>RIP2</i>, and <i>NF-κB</i> genes, which were discussed in detail and predicted to play essential roles in the immune system of the sperm whale. Furthermore, <i>NOD1</i> was highly conservative during evolution by the sequence comparison and phylogenetic tree. These results provide new information about the immune system in the skin of cetaceans, as well as the evolution of immune-related genes. |
| first_indexed | 2024-03-09T05:32:37Z |
| format | Article |
| id | doaj.art-c57fe8c6c9ad45a9a99678b2fd389cfc |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T05:32:37Z |
| publishDate | 2021-02-01 |
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| record_format | Article |
| series | Genes |
| spelling | doaj.art-c57fe8c6c9ad45a9a99678b2fd389cfc2023-12-03T12:31:28ZengMDPI AGGenes2073-44252021-02-0112223310.3390/genes12020233Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (<i>Physeter macrocephalus</i>)Daling Wang0Ying Li1Reyilamu Aierken2Qi Kang3Xianyan Wang4Qianhui Zeng5Zhichang Fan6Yu Zhen7Liyuan Zhao8College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, ChinaCollege of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, ChinaLaboratory of Marine Biology and Ecology, Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, ChinaState Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, ChinaLaboratory of Marine Biology and Ecology, Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, ChinaLaboratory of Marine Biology and Ecology, Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, ChinaSchool of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, ChinaCollege of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, ChinaLaboratory of Marine Biology and Ecology, Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, ChinaCetaceans are a group of secondary aquatic mammals whose ancestors returned to the ocean from land, and during evolution, their immune systems adapted to the aquatic environment. Their skin, as the primary barrier to environmental pathogens, supposedly evolved to adapt to a new living environment. However, the immune system in the skin of cetaceans and the associated molecular mechanisms are still largely unknown. To better understand the immune system, we extracted RNA from the sperm whale’s (<i>Physeter macrocephalus</i>) skin and performed PacBio full-length sequencing and RNA-seq sequencing. We obtained a total of 96,350 full-length transcripts with an average length of 1705 bp and detected 5150 genes that were associated with 21 immune-related pathways by gene annotation enrichment analysis. Moreover, we found 89 encoding genes corresponding to 33 proteins were annotated in the NOD-like receptor (NLR)-signaling pathway, including <i>NOD1</i>, <i>NOD2</i>, <i>RIP2</i>, and <i>NF-κB</i> genes, which were discussed in detail and predicted to play essential roles in the immune system of the sperm whale. Furthermore, <i>NOD1</i> was highly conservative during evolution by the sequence comparison and phylogenetic tree. These results provide new information about the immune system in the skin of cetaceans, as well as the evolution of immune-related genes.https://www.mdpi.com/2073-4425/12/2/233NOD-like receptor (NLR)-signaling pathwayNOD1sperm whaletranscriptome |
| spellingShingle | Daling Wang Ying Li Reyilamu Aierken Qi Kang Xianyan Wang Qianhui Zeng Zhichang Fan Yu Zhen Liyuan Zhao Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (<i>Physeter macrocephalus</i>) Genes NOD-like receptor (NLR)-signaling pathway NOD1 sperm whale transcriptome |
| title | Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (<i>Physeter macrocephalus</i>) |
| title_full | Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (<i>Physeter macrocephalus</i>) |
| title_fullStr | Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (<i>Physeter macrocephalus</i>) |
| title_full_unstemmed | Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (<i>Physeter macrocephalus</i>) |
| title_short | Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (<i>Physeter macrocephalus</i>) |
| title_sort | integrated full length transcriptome and rna seq to identify immune system genes from the skin of sperm whale i physeter macrocephalus i |
| topic | NOD-like receptor (NLR)-signaling pathway NOD1 sperm whale transcriptome |
| url | https://www.mdpi.com/2073-4425/12/2/233 |
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