1
|
Valenza‐Troubat N, Davy M, Storey R, Wylie MJ, Hilario E, Ritchie P, Wellenreuther M. Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally ( Pseudocaranx georgianus). Evol Appl 2022; 15:237-248. [PMID: 35233245 PMCID: PMC8867707 DOI: 10.1111/eva.13332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/01/2022] Open
Abstract
Ectotherm species, such as marine fishes, depend on environmental temperature to regulate their vital functions. In finfish aquaculture production, being able to predict physiological responses in growth and other economic traits to temperature is crucial to address challenges inherent in the selection of grow-out locations. This will become an even more significant issue under the various predicted future climate change scenarios. In this study, we used the marine teleost silver trevally (Pseudocaranx georgianus), a species currently being explored as a candidate for aquaculture in New Zealand, as a model to study plasticity in gene expression patterns and growth in response to different temperatures. Using a captive study population, temperature conditions were experimentally manipulated for 1 month to mimic seasonal extremes. Phenotypic differences in growth were measured in 400 individuals, and gene expression patterns of pituitary gland and liver were determined in a subset of 100 individuals. Results showed that growth increased 50% in the warmer compared with the colder condition, suggesting that temperature has a large impact on metabolic activities associated with growth. A total of 265,116,678 single-end RNA sequence reads were aligned to the trevally genome, and 28,416 transcript models were developed (27,887 of these had GenBank accessions, and 17,980 unique gene symbols). Further filtering reduced this set to 8597 gene models. 39 and 238 differentially expressed genes (DEGs) were found in the pituitary gland and the liver, respectively (|log2FC| > 0.26, p-value < 0.05). Of these, 6 DEGs showed a common expression pattern between both tissues, all involved in housekeeping functions. Temperature-modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signalling, previously shown to be important for temperature tolerance in other fish species. An interesting finding of this study was that genes linked to the reproductive system were up-regulated in both tissues in the high treatment, indicating the onset of sexual maturation. Few studies have investigated the thermal plasticity of the gene expression in the main organs of the somatotropic axis simultaneously. Our findings indicate that trevally exhibit substantial growth differences and predictable plastic regulatory responses to different temperature conditions. We identified a set of genes that provide a list of candidates for further investigations for selective breeding objectives and how populations may adapt to increasing temperatures.
Collapse
Affiliation(s)
| | - Marcus Davy
- The New Zealand Institute for Plant and Food Research LimitedTe PukeNew Zealand
| | - Roy Storey
- The New Zealand Institute for Plant and Food Research LimitedTe PukeNew Zealand
| | - Matthew J. Wylie
- The New Zealand Institute for Plant and Food Research LimitedNelsonNew Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research LimitedTe PukeNew Zealand
| | - Peter Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research LimitedNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| |
Collapse
|
2
|
Ren X, Liu J, Ndandala CB, Li X, Guo Y, Li G, Chen H. Physiological Effects and Transcriptomic Analysis of sbGnRH on the Liver in Pompano ( Trachinotus ovatus). Front Endocrinol (Lausanne) 2022; 13:869021. [PMID: 35586618 PMCID: PMC9108241 DOI: 10.3389/fendo.2022.869021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Pompano (Trachinotus ovatus) is one of the important economic marine fishes in the south coast of China. At present, the research on the basic biology of pompano is relatively weak, which has seriously affected the development of this economic important fish. The liver is an important digestive and metabolic organ of fish which plays an important regulatory role in its growth and development. It is necessary to clarify the effects of sea bream gonadotropin releasing hormone (sbGnRH) on liver physiology and metabolic enzyme activity. The effects of sbGnRH peptides (10 ng/gbw) on the physiological and biochemical indices and metabolic enzyme activities of pompano liver were studied. It was found that after injection of 10 ng/gbw sbGnRH peptides, the contents of albumin, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, glucose, creatine kinase, iron, magnesium, aspartate aminotransferase, alanine aminotransferase and creatinine increased, while of cholesterol and calcium contents decreased. The activities of amylase, lipase, pyruvate kinase, acyl CoA oxidase, superoxide dismutase, phospholipid hydroperoxide glutathione peroxidase, catalase, glucose-6-phosphate dehydrogenase, fatty acid synthase and lipoprotein lipase increased, while the activities of malic enzyme, carnitine acyl, carnitine translocation, acetyl CoA carboxylase and malondialdehyde decreased. Three hours after the injection of different concentrations of sbGnRH peptides (0 and 10 ng/gbw), the transcriptome sequences of the two groups of livers were sequenced. After quality control and removal of some low-quality data, clean reads of 21,283,647、19,427,359、21,873,990、21,732,174、23,660,062 and 21,592,338 were obtained respectively. In this study, 99 genes were screened and identified as differentially expressed genes, including 77 up-regulated genes and 22 down-regulated genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analyses, these pathways and the typical genes involved can be divided into cellular processes, environmental information processing, genetic information processing, diseases, metabolism and organismal systems. The results from this study provide a the oretical basis for studying the effects of sbGnRH on the physiology, biochemistry and metabolic enzyme activities of liver in pompano.
Collapse
Affiliation(s)
- Xilin Ren
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding. Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
| | - Jinlei Liu
- Guangdong Havwii Agricultural Group Co., Ltd, Zhanjiang, China
| | - Charles Brighton Ndandala
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding. Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Xiaomeng Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding. Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yuwen Guo
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding. Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Guangli Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding. Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Huapu Chen
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding. Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
- *Correspondence: Huapu Chen,
| |
Collapse
|
3
|
Chen H, Jiang D, Li Z, Wang Y, Yang X, Li S, Li S, Yang W, Li G. Comparative Physiological and Transcriptomic Profiling Offers Insight into the Sexual Dimorphism of Hepatic Metabolism in Size-Dimorphic Spotted Scat ( Scatophagus argus). Life (Basel) 2021; 11:life11060589. [PMID: 34205643 PMCID: PMC8233746 DOI: 10.3390/life11060589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/13/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022] Open
Abstract
The spotted scat (Scatophagus argus) is an economically important cultured marine fish that exhibits a typical sexual size dimorphism (SSD). SSD has captivated considerable curiosity for farmed fish production; however, up till now the exact underlying mechanism remains largely unclear. As an important digestive and metabolic organ, the liver plays key roles in the regulation of fish growth. It is necessary to elucidate its significance as a downstream component of the hypothalamic-pituitary-liver axis in the formation of SSD. In this study, the liver physiological differences between the sexes were evaluated in S. argus, and the activity of several digestive and metabolic enzymes were affected by sex. Females had higher amylase, protease, and glucose-6-phosphate dehydrogenase activities, while males exhibited markedly higher hepatic lipase and antioxidant enzymes activities. A comparative transcriptomics was then performed to characterize the responsive genes. Illumina sequencing generated 272.6 million clean reads, which were assembled into 79,115 unigenes. A total of 259 differentially expressed genes were identified and a few growth-controlling genes such as igf1 and igfbp1 exhibited female-biased expression. Further analyses showed that several GO terms and pathways associated with metabolic process, particularly lipid and energy metabolisms, were significantly enriched. The male liver showed a more active mitochondrial energy metabolism, implicating an increased energy expenditure associated with reproduction. Collectively, the female-biased growth dimorphism of S. argus may be partially attributed to sexually dimorphic metabolism in the liver. These findings would facilitate further understanding of the nature of SSD in teleost fish.
Collapse
Affiliation(s)
- Huapu Chen
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
| | - Dongneng Jiang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
| | - Zhiyuan Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
| | - Yaorong Wang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
| | - Xuewei Yang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518052, China; (X.Y.); (S.L.)
| | - Shuangfei Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518052, China; (X.Y.); (S.L.)
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China;
- Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei Yang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
- Food and Environmental Engineering Department, Yangjiang Polytechnic, Yangjiang 529566, China
- Correspondence: (W.Y.); (G.L.); Tel.: +86-662-3362800 (W.Y.); +86-759-2383124 (G.L.); Fax: +86-662-3316729 (W.Y.); +86-759-2382459 (G.L.)
| | - Guangli Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
- Correspondence: (W.Y.); (G.L.); Tel.: +86-662-3362800 (W.Y.); +86-759-2383124 (G.L.); Fax: +86-662-3316729 (W.Y.); +86-759-2382459 (G.L.)
| |
Collapse
|
4
|
Hu B, Zhou J, Qiu H, Lai X, Li J, Wu D, Sheng J, Hong Y. Comparison of nutritional quality and volatile flavor compounds among bighead carp from three aquaculture systems. Saudi J Biol Sci 2021; 28:4291-4299. [PMID: 34354411 PMCID: PMC8325028 DOI: 10.1016/j.sjbs.2021.03.079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 11/11/2022] Open
Abstract
To explore the differences in the nutritional quality of the muscles of bighead carp from different environments and aquaculture systems, we investigated three types of water bodies typically used for aquaculture: A common culture pond (NC), a natural lake (PY), and a cold water reservoir (XHK). Parameters affecting quality were evaluated, including muscle microstructure, fatty acid profiles, amino acid profiles, and volatile compounds. Fish from the XHK reservoir had the smallest muscle fiber diameter and the highest muscle fiber density (25.3 fibers/0.01 mm2), while muscle fiber density was lowest in fish from the NC pond (9.7 fibers/0.01 mm2). The bighead carp from the XHK reservoir had a much wider variety of unsaturated fatty acids, as well as higher levels of total polyunsaturated fatty acids. Eicosapentaenoic acid (EPA), docosahexenoic acid (DHA), and arachidonic acid (AA) were all significantly more abundant in the XHK group, increases of 7.48%, 12.12%, and 17.49%, respectively (P < 0.05). The bighead carp from NC contained more “fishy” volatile flavor substances, as well as hydrocarbons with higher threshold values. Fish from XHK and NC had a greater umami intensity due to the presence of abundant volatiles with special aromas, including 1-Octene-3ol, DL-Menthol, and 2-ethyl-.
Collapse
Affiliation(s)
- Beijuan Hu
- School of Life Science, Nanchang University, Nanchang 330031, China.,Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang 330031, China
| | - Jie Zhou
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Huimin Qiu
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Xinxin Lai
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Jing Li
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Di Wu
- School of Life Science, Nanchang University, Nanchang 330031, China.,Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang 330031, China
| | - Junqing Sheng
- School of Life Science, Nanchang University, Nanchang 330031, China.,Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang 330031, China
| | - Yijiang Hong
- School of Life Science, Nanchang University, Nanchang 330031, China.,Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang 330031, China
| |
Collapse
|
5
|
Feng X, Jia Y, Zhu R, Li K, Guan Z, Chen Y. Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration. BMC Genomics 2020; 21:835. [PMID: 33246415 PMCID: PMC7694923 DOI: 10.1186/s12864-020-07247-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/18/2020] [Indexed: 11/30/2022] Open
Abstract
Background The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in plateau waters with the elevation above 2500 m, is nearly esquamate and only covered with shoulder scales and anal scales, making it a good model species to study the molecular mechanism of scale degeneration. Results The transcriptomes of shoulder scaled skins (SSS), anal scaled skins (ASS) and scaleless skins (NSS) were sequenced and analyzed in G. eckloni at the age of 1 year. Histological examination showed that shoulder scale had completed its differentiation and anal scale just initiated the differentiation. A total of 578,046 unigenes were obtained from the transcriptomes, with 407,799 unigenes annotated in public databases. A total of 428 and 142 differentially expressed unigenes (DEUs) were identified between SSS and NSS, and between ASS and NSS, respectively, with 45 DEUs that were overlapped. Annotation analysis indicated that these DEUs were mainly enriched in Gene Ontology (GO) terms and KEGG pathways associated with bone and muscle formation, such as myofibril, contractile fiber, cytoskeletal protein binding, muscle structure development, cardiac muscle contraction, hypertrophic cardiomyopathy (HCM) and calcium signaling pathway. Conclusions Our results would provide insights into the molecular mechanisms of scale degeneration in G. eckloni and other congeneric fishes. In addition, the transcriptome data provides candidate genes and markers for future studies.
Collapse
Affiliation(s)
- Xiu Feng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yintao Jia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ren Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kemao Li
- QingHai Provincial Fishery Environmental Monitoring Center, Xining, 810012, China
| | - Zhongzhi Guan
- QingHai Provincial Fishery Environmental Monitoring Center, Xining, 810012, China
| | - Yifeng Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| |
Collapse
|
6
|
Fu J, Zhu W, Wang L, Luo M, Song F, Dong Z. Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis). BMC Genomics 2019; 20:781. [PMID: 31660854 PMCID: PMC6819325 DOI: 10.1186/s12864-019-6181-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Early development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hypophthalmichthys nobilis). In the present study, we performed transcriptome analysis of six development stages in H. nobilis, aiming to understand the dynamic molecular regulation of early development in this fish. RESULTS A total of 76,573 unigenes were assembled from clean sequence reads, with an average length of 1768 base. Among which, 41,742 (54.54%) unigenes were annotated to public protein databases, and an additional 59,014 simple sequence repeat (SSR) loci were identified among the unigenes. Furthermore, 30,199 differentially expressed transcripts (DETs) (fold change > 4 or < 0.25, and the false discovery rate FDR < 0.01) were observed in comparisons between the adjacent developmental stages, and nine expression patterns (profiles) were simulated using series-cluster analysis across six developmental stages. The unigenes expression level markedly increased after the DS1 stage (early blastula), and the numbers of DETs gradually decreased during subsequent development. The largest transcriptomic change (up- or down-regulated) was detected during the period from DS1 to DS2 (6-somite stage), which was enriched for many biological processes and metabolic pathways related to maternal to zygotic transition (MZT). Distinctly protein-protein interaction (PPI) networks were plotted for DETs during the period from DS1 to DS2. The genes (or proteins) from the same pathways were integrated together, and showed with obvious co-regulation patterns. In the series-cluster analysis, a remarkable profile of gene expression (profile_48) was identified that is probably related to the hatching during H. nobilis development, and the strict co-expression of a hatching enzyme gene (hce1) with 33 other annotated genes was identified from this profile. CONCLUSIONS The results indicated that strict dynamic regulation occurs during the early development in H. nobilis, especially in embryogenesis before hatching. This study provides valuable new information and transcriptomic resources related to H. nobilis early development, and for certain events such as MZT and hatching.
Collapse
Affiliation(s)
- Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenbin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Lanmei Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Mingkun Luo
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Feibiao Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| |
Collapse
|
7
|
Fu B, Yu X, Tong J, Pang M, Zhou Y, Liu Q, Tao W. Comparative transcriptomic analysis of hypothalamus-pituitary-liver axis in bighead carp (Hypophthalmichthys nobilis) with differential growth rate. BMC Genomics 2019; 20:328. [PMID: 31039751 PMCID: PMC6492341 DOI: 10.1186/s12864-019-5691-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 04/12/2019] [Indexed: 12/27/2022] Open
Abstract
Background Growth rate is one of the most important features for aquaculture species and deciphering its regulation mechanism has great significance both in genetics and in economics. Hypothalamus-pituitary growth axis (HP growth axis) or neuro-endocrine axis plays a vital role in growth regulation in different aquaculture animals. Results In this study, the HP and liver transcriptomes of two female groups (H and L) with phenotypically extreme growth rate were sequenced using RNA-Seq. A total of 30,524 and 22,341 genes were found expressed in the two tissues, respectively. The average expression levels for the two tissues were almost the same, but the median differed significantly. A differential expression analysis between H and L groups identified 173 and 204 differentially expressed genes (DEGs) in HP and liver tissue, respectively. Pathway analysis revealed that DEGs in HP tissue were enriched in regulation of cell proliferation and angiogenesis while in liver tissue these genes were overrepresented in sterol biosynthesis and transportation. Genomic overlapping analyses found that 4 and 5 DEGs were within growth-related QTL in HP and liver tissue respectively. A deeper analysis of these 9 genes revealed 3 genes were functionally linked to the trait of interest. The expression of 2075 lncRNAs in HP tissue and 1490 in liver tissue were also detected, and some of lncRNAs were highly expressed in the two tissues. Conclusions Above all, the results of the present study greatly contributed to the knowledge of the regulation of growth and then assisted the design of new selection strategies for bighead carp with improved growth-related traits. Electronic supplementary material The online version of this article (10.1186/s12864-019-5691-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innnovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innnovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innnovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innnovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innnovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingshan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innnovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| |
Collapse
|
8
|
Zhang C, Su S, Li X, Li B, Yang B, Zhu J, Wang W. Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PLoS One 2018; 13:e0206615. [PMID: 30395585 PMCID: PMC6218049 DOI: 10.1371/journal.pone.0206615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/16/2018] [Indexed: 01/01/2023] Open
Abstract
We have created a new, fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. To better understand the impacts of gene regulation in intestinal tissue on growth and unsaturated fatty acid content, we conducted a comparative RNA-Seq transcriptome analysis between intestine samples of Selected and Control groups (and corroborated selected results by PCR). After eight weeks of cage culture, weight gain of the Selected group was 20.84% higher. In muscles of the control group, monounsaturated fatty acids (FAs) were more abundant, whereas polyunsaturated FAs were more abundant in muscles of the Selected group. In total, we found 106 differentially expressed genes (DEGs) between the two groups. Only the endocytosis pathway was significantly enriched in DEGs, with two upregulated genes: il2rb and ehd1. The latter is involved in the growth hormone/insulin-like growth factor (Gh/Igf) axis, which plays a key role in the regulation of growth in animals. tll2, which is known to be associated with intestinal regeneration, was extremely highly upregulated in both transcriptomic (infinite) and qPCR (610.70) analyses. Two of the upregulated genes are associated with the fatty acid metabolism, several genes are likely to be indicators of heightened transcription levels, several are associated with metabolic and developmental roles, several with neuronal functions (including two with vision), several with the immune system, and two downregulated genes with the development of vasculature. The higher growth rate of the Selected group is likely to be at least partially attributed to increased endocytosis efficiency and genetically-driven behavioural differences (higher aggression levels). There are some indications that this new strain might have slightly impaired immune responses, and a higher propensity for inherited diseases leading to sight impairment, as well for neurodegenerative diseases in general, but these indications still need to be confirmed.
Collapse
Affiliation(s)
- Chengfeng Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Shengyan Su
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, PR China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, PR China
| | - Bing Li
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Baojuan Yang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
- * E-mail: (JZ); (WW)
| | - Weimin Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- * E-mail: (JZ); (WW)
| |
Collapse
|