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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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KEGG pathway classification of unigenes. (a) NAA; (b) NAS. The KEGG pathways were categorized into five groups, A: Cellular process, B: Environmental information processing, C: Genetic information processing, D: Metabolism and E: Organismal system. KEGG: Kyoto Encyclopedia of Genes and Genomes; NAS: the East Asian finless porpoise; NAA: the Yangtze finless porpoise.
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ijms-16-02220-f002: KEGG pathway classification of unigenes. (a) NAA; (b) NAS. The KEGG pathways were categorized into five groups, A: Cellular process, B: Environmental information processing, C: Genetic information processing, D: Metabolism and E: Organismal system. KEGG: Kyoto Encyclopedia of Genes and Genomes; NAS: the East Asian finless porpoise; NAA: the Yangtze finless porpoise.

Mentions: To identify the biological pathways that are active in the kidney of the narrow-ridge finless porpoise, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways classification was performed. Unigenes for NAA (11,165) were grouped into 241 pathways, and unigenes for NAS (11,163) were also grouped into 241 pathways (Table 2, Table S4). On the basis of the unigenes involved in the KEGG pathways, they were classified into five categories which included cellular processes, environmental information processing, genetic information processing, metabolism and organismal systems. The distributions of KEGG pathways for NAA and NAS were extremely similar (Figure 2a,b). As shown in Figure 2, the signal transduction pathway had the largest number of unigenes in NAA and NAS among the pathways. Clearly, however, the osmoregulatory process was mainly involved with two pathways: the endocrine system and the excretory system [3]. In NAA, the numbers of unigenes in the endocrine and excretory systems were 508 and 162, respectively; in NAS, there were 505 unigenes for the endocrine system and 164 unigenes for the excretory system (Figure 2a,b). In the endocrine system, the renin-angiotensin system was found which regulates blood pressure and water balance [16]. We found that aldosterone-regulated sodium reabsorption, proximal tubule bicarbonate reclamation and vasopressin-regulated water reabsorption were in the excretory system. In Table 3, the numbers of unigenes were listed, which were assigned to the renin-angiotensin system, the aldosterone-regulated sodium reabsorption, the proximal tubule bicarbonate reclamation and the vasopressin-regulated water reabsorption.


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)

KEGG pathway classification of unigenes. (a) NAA; (b) NAS. The KEGG pathways were categorized into five groups, A: Cellular process, B: Environmental information processing, C: Genetic information processing, D: Metabolism and E: Organismal system. KEGG: Kyoto Encyclopedia of Genes and Genomes; 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-f002: KEGG pathway classification of unigenes. (a) NAA; (b) NAS. The KEGG pathways were categorized into five groups, A: Cellular process, B: Environmental information processing, C: Genetic information processing, D: Metabolism and E: Organismal system. KEGG: Kyoto Encyclopedia of Genes and Genomes; NAS: the East Asian finless porpoise; NAA: the Yangtze finless porpoise.
Mentions: To identify the biological pathways that are active in the kidney of the narrow-ridge finless porpoise, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways classification was performed. Unigenes for NAA (11,165) were grouped into 241 pathways, and unigenes for NAS (11,163) were also grouped into 241 pathways (Table 2, Table S4). On the basis of the unigenes involved in the KEGG pathways, they were classified into five categories which included cellular processes, environmental information processing, genetic information processing, metabolism and organismal systems. The distributions of KEGG pathways for NAA and NAS were extremely similar (Figure 2a,b). As shown in Figure 2, the signal transduction pathway had the largest number of unigenes in NAA and NAS among the pathways. Clearly, however, the osmoregulatory process was mainly involved with two pathways: the endocrine system and the excretory system [3]. In NAA, the numbers of unigenes in the endocrine and excretory systems were 508 and 162, respectively; in NAS, there were 505 unigenes for the endocrine system and 164 unigenes for the excretory system (Figure 2a,b). In the endocrine system, the renin-angiotensin system was found which regulates blood pressure and water balance [16]. We found that aldosterone-regulated sodium reabsorption, proximal tubule bicarbonate reclamation and vasopressin-regulated water reabsorption were in the excretory system. In Table 3, the numbers of unigenes were listed, which were assigned to the renin-angiotensin system, the aldosterone-regulated sodium reabsorption, the proximal tubule bicarbonate reclamation and the vasopressin-regulated water reabsorption.

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