Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (<i>Neophocaena asiaeorientalis</i>)
The Yangtze finless porpoise (<i>Neophocaena asiaeorientalis</i>) is the sole freshwater subspecies of <i>Neophocaena</i><i>phocaenoides</i>, and there is a lack of data on its transcriptome. In this study, we applied RNA-seq technology to assemble, de novo, a tra...
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MDPI AG
2022-03-01
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| Series: | Fishes |
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| Online Access: | https://www.mdpi.com/2410-3888/7/2/61 |
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| author | Di-An Fang Kai Liu Dong-Po Xu Yin-Ping Wang Pao Xu |
| author_facet | Di-An Fang Kai Liu Dong-Po Xu Yin-Ping Wang Pao Xu |
| author_sort | Di-An Fang |
| collection | DOAJ |
| description | The Yangtze finless porpoise (<i>Neophocaena asiaeorientalis</i>) is the sole freshwater subspecies of <i>Neophocaena</i><i>phocaenoides</i>, and there is a lack of data on its transcriptome. In this study, we applied RNA-seq technology to assemble, de novo, a transcriptome and analyzed differential expressed genes (DEGs). About 6 Gb of clean data was generated for the Yangtze finless porpoise blood (<i>n</i> = 6) through de novo sequencing. In total, 151,211 unigenes were generated and a total of 119,039 of these unigenes (78.72%) were functionally annotated when searched for within the NCBI Nr, SwissProt, GO, COG, and KEGG databases. Diverse and extensive expressed gene catalogs were sampled for the Yangtze finless porpoise. DESeq2 was used to analyze the differential expression genes (DEGs) obtained from the assembled transcriptome. The results indicated that DEGs have close relationships with the Yangtze finless porpoise’s development, evolution and adaptation. Further, we found that genes involved in cetacean TAG synthesis might directly explain the molecular basis of cetacean blubber thickening. These transcriptome data will assist in understanding molecular mechanisms of Yangtze finless porpoise adaptation. |
| first_indexed | 2024-03-09T10:37:45Z |
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| institution | Directory Open Access Journal |
| issn | 2410-3888 |
| language | English |
| last_indexed | 2024-03-09T10:37:45Z |
| publishDate | 2022-03-01 |
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| spelling | doaj.art-6a134f3c807344e9a2394a5d86c6b8692023-12-01T20:52:44ZengMDPI AGFishes2410-38882022-03-01726110.3390/fishes7020061Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (<i>Neophocaena asiaeorientalis</i>)Di-An Fang0Kai Liu1Dong-Po Xu2Yin-Ping Wang3Pao Xu4Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Wuxi 214081, ChinaScientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Wuxi 214081, ChinaScientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Wuxi 214081, ChinaScientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Wuxi 214081, ChinaScientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, CAFS, Wuxi 214081, ChinaThe Yangtze finless porpoise (<i>Neophocaena asiaeorientalis</i>) is the sole freshwater subspecies of <i>Neophocaena</i><i>phocaenoides</i>, and there is a lack of data on its transcriptome. In this study, we applied RNA-seq technology to assemble, de novo, a transcriptome and analyzed differential expressed genes (DEGs). About 6 Gb of clean data was generated for the Yangtze finless porpoise blood (<i>n</i> = 6) through de novo sequencing. In total, 151,211 unigenes were generated and a total of 119,039 of these unigenes (78.72%) were functionally annotated when searched for within the NCBI Nr, SwissProt, GO, COG, and KEGG databases. Diverse and extensive expressed gene catalogs were sampled for the Yangtze finless porpoise. DESeq2 was used to analyze the differential expression genes (DEGs) obtained from the assembled transcriptome. The results indicated that DEGs have close relationships with the Yangtze finless porpoise’s development, evolution and adaptation. Further, we found that genes involved in cetacean TAG synthesis might directly explain the molecular basis of cetacean blubber thickening. These transcriptome data will assist in understanding molecular mechanisms of Yangtze finless porpoise adaptation.https://www.mdpi.com/2410-3888/7/2/61transcriptomethe Yangtze finless porpoisepopulation decliningadaptive biology |
| spellingShingle | Di-An Fang Kai Liu Dong-Po Xu Yin-Ping Wang Pao Xu Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (<i>Neophocaena asiaeorientalis</i>) Fishes transcriptome the Yangtze finless porpoise population declining adaptive biology |
| title | Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (<i>Neophocaena asiaeorientalis</i>) |
| title_full | Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (<i>Neophocaena asiaeorientalis</i>) |
| title_fullStr | Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (<i>Neophocaena asiaeorientalis</i>) |
| title_full_unstemmed | Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (<i>Neophocaena asiaeorientalis</i>) |
| title_short | Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (<i>Neophocaena asiaeorientalis</i>) |
| title_sort | comparative analysis of blood transcriptome in the yangtze finless porpoise i neophocaena asiaeorientalis i |
| topic | transcriptome the Yangtze finless porpoise population declining adaptive biology |
| url | https://www.mdpi.com/2410-3888/7/2/61 |
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