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De novo assembly and characterization of narrow-ridged finless porpoise renal transcriptome and identification of candidate genes involved in osmoregulation.

Ruan R, Guo AH, Hao YJ, Zheng JS, Wang D - Int J Mol Sci (2015)

Bottom Line: Among these annotations, 22,231 (NAS) and 21,849 (NAA) unigenes were annotated against the NCBI nr protein database.The ion channel complex GO term and four pathways were detected as relevant to osmoregulation by GO and KEGG pathway classification of these annotated unigenes.Although the endangered status of the study species prevented analysis of biological replicates, we identified nine differentially expressed genes (DEGs) that may be vital in the osmoregulation of the narrow-ridged finless porpoise and worthwhile for future studies.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan 430072, China. ruan.rui@163.com.

ABSTRACT
During the evolutionary transition from land to water, cetaceans have undergone numerous critical challenges, with osmoregulation being the major one. Two subspecies of the narrow-ridged finless porpoise (Neophocaena asiaeorientalis), the freshwater Yangtze finless porpoise (N. a. asiaeorientalis, NAA) and the marine East Asian finless porpoise (N. a. sunameri, NAS), provide excellent subjects to understand the genetic basis of osmoregulatory divergence between freshwater and marine mammals. The kidney plays an important and well-established role in osmoregulation in marine mammals and thus, herein, we utilized RNA-seq to characterize the renal transcriptome and preliminarily analyze the divergence between the NAA and the NAS. Approximately 48.98 million clean reads from NAS and 49.40 million clean reads from NAA were obtained by RNA-Seq. And 73,449 (NAS) and 68,073 (NAA) unigenes were assembled. Among these annotations, 22,231 (NAS) and 21,849 (NAA) unigenes were annotated against the NCBI nr protein database. The ion channel complex GO term and four pathways were detected as relevant to osmoregulation by GO and KEGG pathway classification of these annotated unigenes. Although the endangered status of the study species prevented analysis of biological replicates, we identified nine differentially expressed genes (DEGs) that may be vital in the osmoregulation of the narrow-ridged finless porpoise and worthwhile for future studies. Of these DEGs, the differential expression and distribution of the aquaporin-2 (AQP2) in the collecting duct were verified using immunohistochemical experiments. Together, this work is the first report of renal transcriptome sequencing in cetaceans, and it will provide a valuable resource for future molecular genetics studies on cetacean osmoregulation.

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GO enrichment analysis of DEGs between NAS and NAA. GO: Gene Ontology; DEGs: differentially expressed genes; NAS: the East Asian finless porpoise; NAA: the Yangtze finless porpoise.
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ijms-16-02220-f003: GO enrichment analysis of DEGs between NAS and NAA. GO: Gene Ontology; DEGs: differentially expressed genes; NAS: the East Asian finless porpoise; NAA: the Yangtze finless porpoise.

Mentions: A total of 785 differentially expressed sequences were obtained using the DEGseq software, but only 656 DEGs (including 388 up-regulated DEGs and 268 down-regulated DEGs in NAS) were successfully annotated (Table S6). And the GO enrichment of these annotated DEGs was analyzed using GOseq software (Table S7). We found that the GO term integral to membrane showed the most significant enrichment and also presented the greatest number of DEGs among the enriched GO terms (Figure 3), with 163 DEGs being significantly enriched in this term.


De novo assembly and characterization of narrow-ridged finless porpoise renal transcriptome and identification of candidate genes involved in osmoregulation.

Ruan R, Guo AH, Hao YJ, Zheng JS, Wang D - Int J Mol Sci (2015)

GO enrichment analysis of DEGs between NAS and NAA. GO: Gene Ontology; DEGs: differentially expressed genes; NAS: the East Asian finless porpoise; NAA: the Yangtze finless porpoise.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4307359&req=5

ijms-16-02220-f003: GO enrichment analysis of DEGs between NAS and NAA. GO: Gene Ontology; DEGs: differentially expressed genes; NAS: the East Asian finless porpoise; NAA: the Yangtze finless porpoise.
Mentions: A total of 785 differentially expressed sequences were obtained using the DEGseq software, but only 656 DEGs (including 388 up-regulated DEGs and 268 down-regulated DEGs in NAS) were successfully annotated (Table S6). And the GO enrichment of these annotated DEGs was analyzed using GOseq software (Table S7). We found that the GO term integral to membrane showed the most significant enrichment and also presented the greatest number of DEGs among the enriched GO terms (Figure 3), with 163 DEGs being significantly enriched in this term.

Bottom Line: Among these annotations, 22,231 (NAS) and 21,849 (NAA) unigenes were annotated against the NCBI nr protein database.The ion channel complex GO term and four pathways were detected as relevant to osmoregulation by GO and KEGG pathway classification of these annotated unigenes.Although the endangered status of the study species prevented analysis of biological replicates, we identified nine differentially expressed genes (DEGs) that may be vital in the osmoregulation of the narrow-ridged finless porpoise and worthwhile for future studies.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan 430072, China. ruan.rui@163.com.

ABSTRACT
During the evolutionary transition from land to water, cetaceans have undergone numerous critical challenges, with osmoregulation being the major one. Two subspecies of the narrow-ridged finless porpoise (Neophocaena asiaeorientalis), the freshwater Yangtze finless porpoise (N. a. asiaeorientalis, NAA) and the marine East Asian finless porpoise (N. a. sunameri, NAS), provide excellent subjects to understand the genetic basis of osmoregulatory divergence between freshwater and marine mammals. The kidney plays an important and well-established role in osmoregulation in marine mammals and thus, herein, we utilized RNA-seq to characterize the renal transcriptome and preliminarily analyze the divergence between the NAA and the NAS. Approximately 48.98 million clean reads from NAS and 49.40 million clean reads from NAA were obtained by RNA-Seq. And 73,449 (NAS) and 68,073 (NAA) unigenes were assembled. Among these annotations, 22,231 (NAS) and 21,849 (NAA) unigenes were annotated against the NCBI nr protein database. The ion channel complex GO term and four pathways were detected as relevant to osmoregulation by GO and KEGG pathway classification of these annotated unigenes. Although the endangered status of the study species prevented analysis of biological replicates, we identified nine differentially expressed genes (DEGs) that may be vital in the osmoregulation of the narrow-ridged finless porpoise and worthwhile for future studies. Of these DEGs, the differential expression and distribution of the aquaporin-2 (AQP2) in the collecting duct were verified using immunohistochemical experiments. Together, this work is the first report of renal transcriptome sequencing in cetaceans, and it will provide a valuable resource for future molecular genetics studies on cetacean osmoregulation.

Show MeSH