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Liu D, Li Q, Liu T, Zhang Y, Zheng R, Liu H, Yang Z, Yu Q, Lin C, Qiu Z, Wang D, Li Y. Decreased acetylation of HDGF improves oviduct production in Rana dybowskii, Rana amurensis, and Rana huanrenensis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101102. [PMID: 37384958 DOI: 10.1016/j.cbd.2023.101102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/01/2023]
Abstract
The oviduct of female Rana dybowskii is a functional food and can be used as a component of Traditional Chinese medicine. The differentially expressed genes enriched was screened in cell growth of three Rana species. We quantitatively analyzed 4549 proteins using proteomic techniques, enriching the differentially expressed proteins of Rana for growth and signal transduction. The results showed that log2 expression of hepatoma-derived growth factor (HDGF) was increased. We further verified 5 specific differential genes (EIF4a, EIF4g, HDGF1, HDGF2 and SF1) and found that HDGF expression was increased in Rana dybowskii. Through acetylation modification analysis, we identified 1534 acetylation modification sites in 603 proteins, including HDGF, and found that HDGF acetylation expression was significantly reduced in Rana dybowskii. Our results suggest that HDGF is involved in the development of oviductus ranae, which is regulated by acetylation modification.
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Affiliation(s)
- Da Liu
- Department of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Qirong Li
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Tianjia Liu
- The Third Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Yi Zhang
- Department of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ran Zheng
- Department of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Huimin Liu
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Jilin University, Changchun, China
| | - Zhijing Yang
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Jilin University, Changchun, China
| | - Qi Yu
- Department of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Chao Lin
- School of grain science and technology, Jilin Business and Technology College, Changchun, China
| | - Zhidong Qiu
- Department of Pharmacy, Changchun University of Chinese Medicine, Changchun, China.
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China.
| | - Yiping Li
- Department of Pharmacy, Changchun University of Chinese Medicine, Changchun, China.
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Li W, Lan Y, Wang L, He L, Tang R, Price M, Yue B, Fan Z. Comparative transcriptomes of nine tissues for the Heilongjiang brown frog (Rana amurensis). Sci Rep 2022; 12:20759. [PMID: 36456629 PMCID: PMC9715712 DOI: 10.1038/s41598-022-24631-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
The Heilongjiang brown frog (Rana amurensis) is widely used in traditional Chinese medicine. In particular, the oviduct and skin have been developed into various health products. However, limited numbers of complete genomes of amphibian species have been reported, excluding the Heilongjiang brown frog. Here, the transcriptomes of 45 samples from the liver, spleen, heart, ovaries, thigh muscles, skin, oviduct, stomach and intestine of five Heilongjiang brown frog were reassembled and analyzed. A total of 1,085,532 unigenes with an average length of 676.6 bp and N50 of 722 bp were obtained. Comparative transcriptomics of different tissues detected tissue-specific expression. There were 3248 differentially expressed genes (DEGs) in the ovary, and the number of unique DEGs between the ovary and spleen was the largest. The results of DEGs enrichment showed there were many pathways and items related to protein synthesis and metabolism in the oviduct. The DEGs of the skin were enriched with many bacterial defense items, indicating that there were a large number of antimicrobial peptides in the skin. Thus, these were suitable as biological sources for the development and extraction of antimicrobial peptides. Through the assembly of transcriptome sequencing data and functional annotation of the Heilongjiang brown frog genome, this study provides reference materials for further exploring and utilizing functional gene resources of frogs and lays a foundation for medical research and the development of new products.
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Affiliation(s)
- Wanyu Li
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Yue Lan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Lei Wang
- grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,Sichuan Engineering Research Center for Medicinal Animals, Xichang, 615000 Sichuan China
| | - Lewei He
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Ruixiang Tang
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Megan Price
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Bisong Yue
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,Sichuan Engineering Research Center for Medicinal Animals, Xichang, 615000 Sichuan China
| | - Zhenxin Fan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
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Wang X, Xie Y, Hu W, Wei Z, Wei X, Yuan H, Yao H, Dunxue C. Transcriptome characterization and SSR discovery in the giant spiny frog Quasipaa spinosa. Gene 2022; 842:146793. [PMID: 35952842 DOI: 10.1016/j.gene.2022.146793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/04/2022]
Abstract
The giant spiny frog Quasipaa spinosa (Amphibia: Ranidae) is a large unique frog species found mainly in southern China with a low amount of fat and high protein, and it has become one of the most important aquaculture animal species in China. To better understand its genetic background and screen potential molecular markers for artificial breeding and species conservation, we constructed an expression profile of Q. spinosa with high-throughput RNA sequencing and acquired potential SSR markers. Approximately 81.7 Gb of data and 93,887 unigenes were generated. The transcriptome contains 2085 (80.7 %) complete BUSCOs, suggesting that our assembly methods were effective and accurate.These unigenes were functionally classified using 7 functional databases, yielding 17,482 Pfam-, 12,752 Sting-, 17,526 KEGG-, 24,341 Swiss-Prot-, 28,604 Nr-, 16,287 GO- and 12,752 COG-annotated unigenes. Among several amphibian species, Q. spinosa unigenes had the highest number of hits to Xenopus tropicalis (35.25 %), followed by Xenopus laevis (12.68 %). 1417 unigenes were assigned to the immune system. In addition, a total of 33,019 candidate SSR markers were identified from the constructed library. Further tests with 20 loci and 118 large-scale breeding specimens gathered from four culture farms in China showed that 15 (75 %) loci were polymorphic, with the number of alleles per locus varying from 3 to 9 (mean of 4.3). The PIC values for the SSR markers ranged from 0.19 to 0.82, with an average value of 0.43, indicating moderate polymorphism in Q. spinosa. The transcriptomic profile and SSR repertoire obtained in the present study will facilitate population genetic studies and the selective breeding of amphibian species.
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Affiliation(s)
- Xiaodong Wang
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Yongguang Xie
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Wei Hu
- School of Animal Science, Yangtze University, Jingzhou 434020, China
| | - Zhaoyu Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Xiuying Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hong Yuan
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hongyan Yao
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Chen Dunxue
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China.
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Wang X, He Y, Zhang C, Tian YA, Lei X, Li D, Bai S, Deng X, Lin H. Physiological and transcriptional responses of Phalaris arundinacea under waterlogging conditions. JOURNAL OF PLANT PHYSIOLOGY 2021; 261:153428. [PMID: 33957505 DOI: 10.1016/j.jplph.2021.153428] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
As a high-yielding forage grass, Phalaris arundinacea widely distributed in the Qinghai-Tibet Plateau region of China. To explore physiological and molecular response mechanism of Phalaris arundinacea under waterlogging, we analyzed the biomass and physiological indexes of three locally grown strains under the submerged condition of 10 cm. The material Z0611 showed the strongest waterlogging resistance while the YS showed the weakest performance. Transcriptome sequencing analysis demonstrated that the YS and Z0611 had 17010 and 7566 differently expression genes (DEGs), respectively, which were mainly concentrated in the metabolic process, cell, ribosome, phenylpropanoid biosynthesis pathway in GO and KEGG databases. We also identified a large number of genes involved in carbohydrate metabolism, hormone signaling regulation, transcription factors, antioxidant system, and ethylene signaling. Our research may provide a scientific basis for the restoration of wetland environment on the Qinghai-Tibet Plateau, and lay a foundation for further exploration of the waterlogging resistance genes of Phalaris arundinacea and breeding of new strains resistant with waterlogging stress.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Ying He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Changbing Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China
| | - Yu-Ang Tian
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China.
| | - Xingguang Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China.
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China.
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Shu L, Qiu J, Räsänen K. De novo oviduct transcriptome of the moor frog Rana arvalis: a quest for maternal effect candidate genes. PeerJ 2018; 6:e5452. [PMID: 30128207 PMCID: PMC6098945 DOI: 10.7717/peerj.5452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/22/2018] [Indexed: 12/02/2022] Open
Abstract
Maternal effects can substantially affect ecological and evolutionary processes in natural populations. However, as they often are environmentally induced, establishing their genetic basis is challenging. One important, but largely neglected, source of maternal effects are egg coats (i.e., the maternally derived extracellular matrix that surrounds the embryo). In the moor frog, the gelatinous egg coats (i.e., egg jelly) are produced in the mother’s oviduct and consist primarily of highly glycosylated mucin type O-glycans. These O-glycans affect jelly water balance and, subsequently, contribute to adaptive divergence in embryonic acid tolerance. To identify candidate genes for maternal effects, we conducted RNAseq transcriptomics on oviduct samples from seven R. arvalis females, representing the full range of within and among population variation in embryonic acid stress tolerance across our study populations. De novo sequencing of these oviduct transcriptomes detected 124,071 unigenes and functional annotation analyses identified a total of 57,839 unigenes, of which several identified genes likely code for variation in egg jelly coats. These belonged to two main groups: mucin type core protein genes and five different types of glycosylation genes. We further predict 26,711 gene-linked microsatellite (simple sequence repeats) and 231,274 single nucleotide polymorphisms. Our study provides the first set of genomic resources for R. arvalis, an emerging model system for the study of ecology and evolution in natural populations, and gives insight into the genetic architecture of egg coat mediated maternal effects.
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Affiliation(s)
- Longfei Shu
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, Swiss Federal Institute of Technology in Zürich, Zürich, Switzerland
| | - Jie Qiu
- Institutue of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Katja Räsänen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, Swiss Federal Institute of Technology in Zürich, Zürich, Switzerland
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6
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Comparative Proteomic Analysis of Rana chensinensis Oviduct. Molecules 2018; 23:molecules23061384. [PMID: 29890619 PMCID: PMC6099995 DOI: 10.3390/molecules23061384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022] Open
Abstract
As one of most important traditional Chinese medicine resources, the oviduct of female Rana chensinensis (Chinese brown frog) was widely used in the treatment of asthenia after sickness or delivery, deficiency in vigor, palpitation, and insomnia. Unlike other vertebrates, the oviduct of Rana chensinensis oviduct significantly expands during prehibernation, in contrast to the breeding period. To explain this phenomenon at the molecular level, the protein expression profiles of Rana chensinensis oviduct during the breeding period and prehibernation were observed using isobaric tags for relative and absolute quantitation (iTRAQ) technique. Then, all identified proteins were used to obtain gene ontology (GO) annotation. Ultimately, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis was performed to predict the pathway on differentially expressed proteins (DEPs). A total of 4479 proteins were identified, and 312 of them presented different expression profiling between prehibernation and breeding period. Compared with prehibernation group, 86 proteins were upregulated, and 226 proteins were downregulated in breeding period. After KEGG enrichment analysis, 163 DEPs were involved in 6 pathways, which were lysosome, RNA transport, glycosaminoglycan degradation, extracellular matrix (ECM)–receptor interaction, metabolic pathways and focal adhesion. This is the first report on the protein profiling of Rana chensinensis oviduct during the breeding period and prehibernation. Results show that this distinctive physiological phenomenon of Rana chensinensis oviduct was mainly involved in ECM–receptor interaction, metabolic pathways, and focal adhesion.
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Ma Y, Li B, Ke Y, Zhang Y, Zhang Y. Transcriptome analysis of Rana chensinensis liver under trichlorfon stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:487-493. [PMID: 28910747 DOI: 10.1016/j.ecoenv.2017.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
Abstract
Trichlorfon is a selective organophosphate insecticide that is widely applied in aquaculture and agriculture for control of various parasites. However, repeated and excess applications of trichlorfon often lead to water pollution and threaten non-targeted species. Our previous studies showed that trichlorfon could cause oxidative stress, lipid peroxidation and hepatic lesions in the liver of Rana chensinensis, but the related molecular mechanisms remain unclear. To explore the interference of trichlorfon in gene transcription, the differentially expressed genes in the liver of R. chensinensis exposed to trichlorfon were characterized using the RNA-seq platform. A search of all unigenes against non-redundant protein sequence (Nr), non-redundant nucleotide (Nt), Swiss-Prot, Kyoto Encyclopaedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG) and Gene Ontology (GO) databases resulted in 22,888, 21,719, 20,934, 16,923, 7375 and 15,631 annotations, respectively, and provided a total of 27,781 annotated unigenes. Among the annotated unigenes, 16,923 were mapped to 257 signalling pathways. A set of 3329 differentially expressed unigenes was identified by comparison of the two groups in liver. Notably, relative expression of metabolism-related genes, including both up- and down-regulated genes, were also validated by qPCR. The present study depicts the high degree of transcriptional complexity in R. chensinensis under trichlorfon stress and provides new insights into the molecular mechanisms of organophosphate insecticide toxicology. Some of these metabolism-responsive genes could be useful for understanding the toxicological mechanism of trichlorfon on non-target aquatic organisms and will contribute to the conservation of aquatic life.
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Affiliation(s)
- Yu Ma
- College of Life Science, Shaanxi Normal University, Xi'an 710062, China; Shaanxi Microbiology Institute, Xi'an 710043, China
| | - Bo Li
- College of Life Science, Shaanxi Normal University, Xi'an 710062, China; Shaanxi Microbiology Institute, Xi'an 710043, China
| | - Yang Ke
- Shaanxi Microbiology Institute, Xi'an 710043, China
| | - Yongan Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuhui Zhang
- College of Life Science, Shaanxi Normal University, Xi'an 710062, China.
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Huang Y, Xiong JL, Gao XC, Sun XH. Transcriptome analysis of the Chinese giant salamander ( Andrias davidianus) using RNA-sequencing. GENOMICS DATA 2017; 14:126-131. [PMID: 29159068 PMCID: PMC5675895 DOI: 10.1016/j.gdata.2017.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/21/2017] [Accepted: 10/21/2017] [Indexed: 12/21/2022]
Abstract
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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RNA-Seq analysis and gene discovery of Andrias davidianus using Illumina short read sequencing. PLoS One 2015; 10:e0123730. [PMID: 25874626 PMCID: PMC4395309 DOI: 10.1371/journal.pone.0123730] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 03/05/2015] [Indexed: 11/19/2022] Open
Abstract
The Chinese giant salamander, Andrias davidianus, is an important species in the course of evolution; however, there is insufficient genomic data in public databases for understanding its immunologic mechanisms. High-throughput transcriptome sequencing is necessary to generate an enormous number of transcript sequences from A. davidianus for gene discovery. In this study, we generated more than 40 million reads from samples of spleen and skin tissue using the Illumina paired-end sequencing technology. De novo assembly yielded 87,297 transcripts with a mean length of 734 base pairs (bp). Based on the sequence similarities, searching with known proteins, 38,916 genes were identified. Gene enrichment analysis determined that 981 transcripts were assigned to the immune system. Tissue-specific expression analysis indicated that 443 of transcripts were specifically expressed in the spleen and skin. Among these transcripts, 147 transcripts were found to be involved in immune responses and inflammatory reactions, such as fucolectin, β-defensins and lymphotoxin beta. Eight tissue-specific genes were selected for validation using real time reverse transcription quantitative PCR (qRT-PCR). The results showed that these genes were significantly more expressed in spleen and skin than in other tissues, suggesting that these genes have vital roles in the immune response. This work provides a comprehensive genomic sequence resource for A. davidianus and lays the foundation for future research on the immunologic and disease resistance mechanisms of A. davidianus and other amphibians.
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Transcriptome characterization and SSR discovery in large-scale loach Paramisgurnus dabryanus (Cobitidae, Cypriniformes). Gene 2015; 557:201-8. [DOI: 10.1016/j.gene.2014.12.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/02/2014] [Accepted: 12/15/2014] [Indexed: 12/26/2022]
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Immunostimulatory activity of protein hydrolysate from oviductus ranae on macrophage in vitro. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:180234. [PMID: 25610475 PMCID: PMC4283414 DOI: 10.1155/2014/180234] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 01/21/2023]
Abstract
Oviductus Ranae is the dry oviduct of Rana chensinensis, which is also called R. chensinensis oil. Oviductus Ranae is a valuable Chinese crude drug and is recorded in the Pharmacopoeia of the People's Republic of China. The aim of this study was to investigate the immunostimulatory activity of protein hydrolysate of Oviductus Ranae (ORPH) and to assess its possible mechanism. Immunomodulatory activity of ORPH was examined in murine macrophage RAW 264.7 cells. The effect of ORPH on the phagocytic activity of macrophages was determined by the neutral red uptake assay. After treatment with ORPH, NO production levels in the culture supernatant were investigated by Griess assay. The mRNA and protein expressions of inducible nitric oxide synthase (iNOS) were detected by RT-PCR and Western blotting. The production of TNF-α, IL-1β, and IL-6 after treatment with ORPH was measured using ELISA assay. In addition, NF-κB levels were also investigated by Western blot. The results showed that ORPH enhanced the phagocytosis of macrophage, increased productions of TNF-α, IL-1β, IL-6, and NO in RAW 264.7 cells, and upregulated the mRNA and protein expression of iNOS. Besides, NF-κB, levels in RAW 264.7 cells were elevated after ORPH treatment. These findings suggested that ORPH might stimulate macrophage activities by activating the NF-κB pathway.
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Liu Y, Weng J, Huang S, Shen Y, Sheng X, Han Y, Xu M, Weng Q. Immunoreactivities of PPARγ2, leptin and leptin receptor in oviduct of Chinese brown frog during breeding period and pre-hibernation. Eur J Histochem 2014; 58:2422. [PMID: 25308849 PMCID: PMC4194397 DOI: 10.4081/ejh.2014.2422] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 12/14/2022] Open
Abstract
The Chinese brown frog (Rana dybowskii) is a special amphibian with one unique physiological phenomenon, which is that its oviduct expands prior to hibernation, instead of during the breeding period. In this study, we investigate the localization and expression level of PPARγ2, leptin and leptin receptor proteins in oviduct of Rana dybowskii during breeding period and pre-hibernation. There were significant variations in oviductal weight and size, with values much lower in the breeding period than in pre-hibernation. PPARγ2 was observed in stromal and epithelial cells in both periods. Leptin was immunolocalized in epithelial cells in both periods, whereas leptin receptor was detected only in stromal cells. Consistently, the protein levels of PPARγ2, leptin and leptin receptor were higher in pre-hibernation as compared to the breeding period. These results suggested that oviduct was the target organ of leptin, which may play an important paracrine role in regulating the oviductal hypertrophy during prehibernation.
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Affiliation(s)
- Y Liu
- Beijing Forestry University.
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Lamanna F, Kirschbaum F, Tiedemann R. De novo assembly and characterization of the skeletal muscle and electric organ transcriptomes of the African weakly electric fish Campylomormyrus compressirostris (Mormyridae, Teleostei). Mol Ecol Resour 2014; 14:1222-30. [PMID: 24690394 DOI: 10.1111/1755-0998.12260] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/18/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
African weakly electric fishes (Mormyridae) underwent an outstanding adaptive radiation (about 200 species), putatively owing to their ability to communicate through species-specific weak electric signals. The electric organ discharge (EOD) is produced by muscle-derived electrocytes organized in piles to form an electric organ. Despite the importance of this trait as a prezygotic isolation mechanism, genomic resources remained limited. We present here a first draft of the skeletal muscle and electric organ transcriptomes from the weakly electric fish species Campylomormyrus compressirostris, obtained using the Illumina HiSeq2000 sequencing technology. Approximately 6.8 Gbp of cDNA sequence data were produced from both tissues, resulting in 57,268,109 raw reads for the skeletal muscle and 46,934,923 for the electric organ, and assembled de novo into 46,143 and 89,270 contigs, respectively. About 50% of both transcriptomes were annotated after protein databases search. The two transcriptomes show similar profiles in terms of Gene Ontology categories composition. We identified several candidate genes which are likely to play a central role in the production and evolution of the electric signal. For most of these genes, and for many other housekeeping genes, we were able to obtain the complete or partial coding DNA sequences (CDS), which can be used for the development of primers to be utilized in qRT-PCR experiments. We present also the complete mitochondrial genome and compare it to those available from other weakly electric fish species. Additionally, we located 1671 SSR-containing regions with their flanking sites and designed the relative primers. This study establishes a first step in the development of genomic tools aimed at understanding the role of electric communication during speciation.
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Affiliation(s)
- Francesco Lamanna
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, Germany
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Chen H, Zha J, Liang X, Bu J, Wang M, Wang Z. Sequencing and de novo assembly of the Asian clam (Corbicula fluminea) transcriptome using the Illumina GAIIx method. PLoS One 2013; 8:e79516. [PMID: 24244519 PMCID: PMC3820681 DOI: 10.1371/journal.pone.0079516] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/28/2013] [Indexed: 11/19/2022] Open
Abstract
Background The Asian clam (Corbicula fluminea) is currently one of the most economically important aquatic species in China and has been used as a test organism in many environmental studies. However, the lack of genomic resources, such as sequenced genome, expressed sequence tags (ESTs) and transcriptome sequences has hindered the research on C. fluminea. Recent advances in large-scale RNA-Seq enable generation of genomic resources in a short time, and provide large expression datasets for functional genomic analysis. Methodology/Principal Findings We used a next-generation high-throughput DNA sequencing technique with an Illumina GAIIx method to analyze the transcriptome from the whole bodies of C. fluminea. More than 62,250,336 high-quality reads were generated based on the raw data, and 134,684 unigenes with a mean length of 791 bp were assembled using the Velvet and Oases software. All of the assembly unigenes were annotated by running BLASTx and BLASTn similarity searches on the Nt, Nr, Swiss-Prot, COG and KEGG databases. In addition, the Clusters of Orthologous Groups (COGs), Gene Ontology (GO) terms and Kyoto Encyclopedia of Gene and Genome (KEGG) annotations were also assigned to each unigene transcript. To provide a preliminary verification of the assembly and annotation results, and search for potential environmental pollution biomarkers, 15 functional genes (five antioxidase genes, two cytochrome P450 genes, three GABA receptor-related genes and five heat shock protein genes) were cloned and identified. Expressions of the 15 selected genes following fluoxetine exposure confirmed that the genes are indeed linked to environmental stress. Conclusions/Significance The C. fluminea transcriptome advances the underlying molecular understanding of this freshwater clam, provides a basis for further exploration of C. fluminea as an environmental test organism and promotes further studies on other bivalve organisms.
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Affiliation(s)
- Huihui Chen
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jinmiao Zha
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- * E-mail: (JZ); (ZW)
| | - Xuefang Liang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jihong Bu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Miao Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zijian Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- * E-mail: (JZ); (ZW)
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Qiao L, Yang W, Fu J, Song Z. Transcriptome profile of the green odorous frog (Odorrana margaretae). PLoS One 2013; 8:e75211. [PMID: 24073255 PMCID: PMC3779193 DOI: 10.1371/journal.pone.0075211] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/13/2013] [Indexed: 12/02/2022] Open
Abstract
Transcriptome profiles provide a practical and inexpensive alternative to explore genomic data in non-model organisms, particularly in amphibians where the genomes are very large and complex. The odorous frog Odorranamargaretae (Anura: Ranidae) is a dominant species in the mountain stream ecosystem of western China. Limited knowledge of its genetic background has hindered research on this species, despite its importance in the ecosystem and as biological resources. Here we report the transcriptome of O. margaretae in order to establish the foundation for genetic research. Using an Illumina sequencing platform, 62,321,166 raw reads were acquired. After a de novo assembly, 37,906 transcripts were obtained, and 18,933 transcripts were annotated to 14,628 genes. We functionally classified these transcripts by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 11,457 unique transcripts were assigned to 52 GO terms, and 1,438 transcripts were assigned to 128 KEGG pathways. Furthermore, we identified 27 potential antimicrobial peptides (AMPs), 50,351 single nucleotide polymorphism (SNP) sites, and 2,574 microsatellite DNA loci. The transcriptome profile of this species will shed more light on its genetic background and provide useful tools for future studies of this species, as well as other species in the genus Odorrana. It will also contribute to the accumulation of amphibian genomic data.
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Affiliation(s)
- Liang Qiao
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Weizhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail: (JF); (ZS)
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- * E-mail: (JF); (ZS)
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