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Xu P, Guo H, Wang H, Xie Y, Lee SC, Liu M, Zheng J, Mao X, Wang H, Liu F, Wan C, Qin S, Liu Y, Zhao M, Wang L. Identification and profiling of microRNAs responsive to cadmium toxicity in hepatopancreas of the freshwater crab Sinopotamon henanense. Hereditas 2019; 156:34. [PMID: 31708719 PMCID: PMC6829971 DOI: 10.1186/s41065-019-0110-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022] Open
Abstract
Background Cadmium (Cd) is a ubiquitous environmental toxicant for aquatic animals. The freshwater crab, Sinopotamon henanense (S. henanense), is a useful model for monitoring Cd exposure since it is widely distributed in sediments whereby it tends to accumulate several toxicants, including Cd. In the recent years, the toxic effects of Cd in the hepatopancreas of S. henanense have been demonstrated by a series of biochemical analysis and ultrastructural observations as well as the deep sequencing approaches and gene expression profile analysis. However, the post-transcriptional regulatory network underlying Cd toxicity in S.henanense is still largely unknown. Results The miRNA transcriptional profile of the hepatopancreas of S. henanense was used to investigate the expression levels of miRNAs in response to Cd toxicity. In total, 464 known miRNAs and 191 novel miRNAs were identified. Among these 656 miRNAs, 126 known miRNAs could be matched with the miRNAs of Portunus trituberculatus, Eriocheir sinensis and Scylla paramamosain. Furthermore, a total of 24 conserved miRNAs were detected in these four crab species. Fifty-one differentially expressed miRNAs were identified in the Cd-exposed group, with 31 up-regulated and 20 down-regulated. Eight of the differentially expressed miRNAs were randomly selected and verified by the quantitative real-time PCR (qRT-PCR), and there was a general consistency (87.25%) between the qRT-PCR and miRNA transcriptome data. A total of 5258 target genes were screened by bioinformatics prediction. GO term analysis showed that, 17 GO terms were significantly enriched, which were mainly related to the regulation of oxidoreductase activity. KEGG pathway analysis showed that 18 pathways were significantly enriched, which were mainly associated with the biosynthesis, modification and degradation of proteins. Conclusion In response to Cd toxicity, in the hepatopancreas of S. henanense, the expressions of significant amount of miRNAs were altered, which may be an adaptation to resist the oxidative stress induced by Cd. These results provide a basis for further studies of miRNA-mediated functional adaptation of the animal to combat Cd toxicity.
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Affiliation(s)
- Peng Xu
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China.,2Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Huiqin Guo
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Huihui Wang
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Yuxin Xie
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Shao Chin Lee
- 3School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 China.,1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Ming Liu
- 4State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,5University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jian Zheng
- Department of Cardiopulmonary Function Examination, Shanxi Provincial Cancer Hospital, Taiyuan, 030013 China
| | - Xiuli Mao
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Huan Wang
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
| | - Fatao Liu
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092 China
| | - Chunling Wan
- 2Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Shengying Qin
- 2Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Yun Liu
- 8Department of Oncology, Fudan University Pudong Medical Center, Shanghai, 201300 China
| | - Meirong Zhao
- 9Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Lan Wang
- 1School of Life Science, Shanxi University, 92 Wucheng Road, Xiaodian District, Taiyuan, 030006 People's Republic of China
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Núñez-Acuña G, Gallardo-Escárate C. Characterization of the salmon louse Lepeophtheirus salmonis miRNome: Sex-biased differences related to the coding and non-coding RNA interplay. Mar Genomics 2019; 45:38-47. [PMID: 30772247 DOI: 10.1016/j.margen.2019.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/12/2022]
Abstract
The salmon louse Lepeophtheirus salmonis is a marine ectoparasite that has a detrimental impact on salmon farms. Genomic knowledge of adult stages is critical to understand the reproductive success and lifecycle completion of this species. Here, we report a comprehensive characterization of the L. salmonis miRNome with emphasis on the sex-differences of the parasite. Small-RNA sequencing was conducted on males and females, and mRNA-sequencing was also conducted to identify miRNA-targets at these stages. Based on bioinformatics analyses, 3101 putative miRNAs were found in L. salmonis, including precursors and variants. The most abundant and over-expressed miRNAs belonged to the bantam, mir-100, mir-1, mir-263a and mir-276 families, while the most differentially expressed mRNAs corresponded to genes related to reproduction and other biological processes involved in cell-differentiation. Target analyses revealed that the most up-regulated miRNAs in males can act by inhibiting the expression of genes related to female differentiation such as vitellogenin genes. Target prediction and expression patterns suggested a pivotal role of miRNAs in the reproductive development of L. salmonis.
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Affiliation(s)
- Gustavo Núñez-Acuña
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
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Identification and characteristics of muscle growth-related microRNA in the Pacific abalone, Haliotis discus hannai. BMC Genomics 2018; 19:915. [PMID: 30545311 PMCID: PMC6293614 DOI: 10.1186/s12864-018-5347-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/03/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Pacific abalone, Haliotis discus hannai, is the most important cultivated abalone in China. Improving abalone muscle growth and increasing the rate of growth are important genetic improvement programs in this industry. MicroRNAs are important small noncoding RNA molecules that regulate post-transcription gene expression. However, no miRNAs have been reported to regulate muscle growth in H. discus hannai. RESULTS we profiled six small RNA libraries for three large abalone individuals (L_HD group) and three small individuals (S_HD group) using RNA sequencing technology. A total of 205 miRNAs, including 200 novel and 5 known miRNAs, were identified. In the L_HD group, 3 miRNAs were up-regulated and 7 were down-regulated compared to the S_HD specimens. Bioinformatics analysis of miRNA target genes revealed that miRNAs participated in the regulation of cellular metabolic processes, the regulation of biological processes, the Wnt signaling pathway, ECM-receptor interaction, and the MAPK signaling pathway, which are associated with regulating growth. Bone morphogenetic protein 7 (BMP7) was verified as a target gene of hdh-miR-1984 by a luciferase reporter assay and we examined the expression pattern in different developmental stages. CONCLUSION This is the first study to demonstrate that miRNAs are related to the muscle growth of H. discus hannai. This information could be used to study the mechanisms of abalone muscle growth. These DE-miRNAs may be useful as molecular markers for functional genomics and breeding research in abalone and closely related species.
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Chen X, Chen J, Shen Y, Bi Y, Hou W, Pan G, Wu X. Transcriptional responses to low-salinity stress in the gills of adult female Portunus trituberculatus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 29:86-94. [PMID: 30463042 DOI: 10.1016/j.cbd.2018.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 11/03/2018] [Indexed: 01/22/2023]
Abstract
The swimming crab (Portunus trituberculatus, Portunus) can tolerate low salinity, but the mechanism of its varied salinity adaptation at the molecular level remains unclear. In this study, we prepared four mRNA and microRNA (miRNA) libraries using the gills collected from four salinity groups and performed RNA-sequencing (RNA-Seq) to identify the genes related to the low salinity. We set 25 ppt as the control group. A total of 659 genes were differentially expressed in at least one of the six comparison groups (25 ppt vs. 20 ppt, 25 ppt vs. 15 ppt, 25 ppt vs. 10 ppt, 20 ppt vs. 15 ppt, 20 ppt vs. 10 ppt and 15 ppt vs. 10 ppt). A total of 15 and 9 unigenes were downregulated and upregulated under low salinity compared with that in 25 ppt, respectively. Six genes, namely, aminopeptidase, centromere protein, cytochrome b5 reductase, bone morphogenetic protein, and two carbonic anhydrases, were selected for verification through quantitative real-time PCR. The results were consistent with the RNA-Seq results. Furthermore, 95 conserved miRNAs and 16 novel miRNAs were differentially expressed in at least one of the six comparison groups. Analysis of the miRNA-mRNA interaction showed that miR-2 and miR-317 regulated >50 mRNA targets. In addition, let-7c was downregulated in all groups under low salinity compared with that in the control group. This study helped elucidate the adaptation mechanism of the swimming crab in low-saline environments.
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Affiliation(s)
- Xiaowu Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, No 999 Huchenghuan Road, Lingang New District, Shanghai 201306, China
| | - Jianpeng Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, No 999 Huchenghuan Road, Lingang New District, Shanghai 201306, China
| | - Yawei Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, No 999 Huchenghuan Road, Lingang New District, Shanghai 201306, China
| | - Yanhui Bi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, No 999 Huchenghuan Road, Lingang New District, Shanghai 201306, China
| | - Wenjie Hou
- Shanghai Fisheries Research Institute and Shanghai Fisheries Technical Extension Station, Shanghai 200433, China
| | - Guiping Pan
- Shanghai Fisheries Research Institute and Shanghai Fisheries Technical Extension Station, Shanghai 200433, China
| | - Xugan Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, No 999 Huchenghuan Road, Lingang New District, Shanghai 201306, China; National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.
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Tu J, Tian C, Zhao P, Sun J, Wang M, Fan Q, Yuan Y. Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi). BMC Genomics 2017; 18:489. [PMID: 28659132 PMCID: PMC5490230 DOI: 10.1186/s12864-017-3851-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 06/07/2017] [Indexed: 12/17/2022] Open
Abstract
Background MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of diverse biological processes in eukaryotes. Chinese perch (Siniperca chuatsi) is one of the most economically important fish species widely cultured in China. Growth is an extremely important characteristic in fish. Individual differences in body size are common in Siniperca chuatsi, which significantly influence the aquaculture production of Siniperca chuatsi. However, the underline growth-related regulatory factors, such as miRNAs, are still unknown. Results To investigate the growth-related miRNAs in Siniperca chuatsi, two RNA libraries from four growth-related tissues (brain, pituitary, liver, and muscle) of Siniperca chuatsi at 6-month stage with relatively high or low growth rates (big-size group or small-size group) were obtained and sequenced using Solexa sequencing. A total of 252 known miRNAs and 12 novel miRNAs were identified. The expression patterns of these miRNAs in big-size group and small-size group were compared, and the results showed that 31 known and 5 novel miRNAs were differently expressed (DE). Furthermore, to verify the Solexa sequencing, five DE miRNAs were randomly selected and quantified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that their expression patterns were consistent with those of Solexa sequencing. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes of DE miRNAs was performed. It showed that the target genes were involved in multiple biological processes including metabolic process, suggesting that metabolic process played an important role in growth of fish. Conclusions Siniperca chuatsi is a popular and economically important species in aquaculture. In this study, miRNAs in Siniperca chuatsi with different growth rates were identified, and their expression profiles were compared. The data provides the first large-scale miRNA profiles related to growth of Siniperca chuatsi, which is expected to contribute to a better understanding of the role of miRNAs in regulating the biological processes of growth and possibly useful for Siniperca chuatsi breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3851-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiagang Tu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Changxu Tian
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Peiqi Zhao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junxiao Sun
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qixue Fan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongchao Yuan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. .,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, Hubei, 430070, China.
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The Caligus rogercresseyi miRNome: Discovery and transcriptome profiling during the sea lice ontogeny. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Li Y, Lai S, Wang R, Zhao Y, Qin H, Jiang L, Li N, Fu Q, Li C. RNA-Seq Analysis of the Antioxidant Status and Immune Response of Portunus trituberculatus Following Aerial Exposure. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:89-101. [PMID: 28138936 DOI: 10.1007/s10126-017-9731-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Desiccation tolerance has been long considered as an important trait for the life survival under acute environmental stress. One of the biggest problems for modern commercial crab farming is desiccation during transportation; high mortality could occur following the aerial exposure. In this regard, here, we utilized RNA-seq-based transcriptome profiling to characterize the molecular responses of swimming crab in response to aerial exposure. In present study, following aerial exposure, the gill samples were sequenced at 0, 6, 12, and 18 h. And the sequenced reads were assembled into 274,594 contigs, with average length of 735.59 bp and N50 size of 1262 bp. After differential expression analysis, a total of 1572 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, chaperones/heat shock proteins, immune alteration, cell proliferation/apoptosis, and cytoskeletal. Our analysis revealed the dramatic tissue oxidant stress and the alteration of the tissue epithelial integrity, especially many genes that have not been reported in crab species. With the limited functional information in crab, further studies are needed and underway in our lab to further characterize the key cellular actors governing the crab tolerance to aerial exposure. Taken together, our results provide molecular resources for further identification of key genes for desiccation tolerance, and to facilitate the molecular selection and breeding of desiccation tolerant strain and family.
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Affiliation(s)
- Yuquan Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shoumin Lai
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Renjie Wang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuchao Zhao
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hao Qin
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lingxu Jiang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Na Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China.
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