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Huang G, Hu Y, Li F, Zuo X, Wang X, Li F, Li R. Genome-wide characterization of heavy metal-associated isoprenylated plant protein gene family from Citrus sinensis in response to huanglongbing. FRONTIERS IN PLANT SCIENCE 2024; 15:1369883. [PMID: 38601304 PMCID: PMC11004388 DOI: 10.3389/fpls.2024.1369883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024]
Abstract
Introduction Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in maintaining heavy metal balance and responding to both biotic and abiotic stresses in vascular plants. However, the role of HIPPs in the response to Huanglongbing (HLB), a harmful disease of citrus caused by the phloem-colonizing bacterium Candidatus Liberibacter asiaticus (CLas), has not been examined. Methods and results In this study, a total of 26 HIPP genes were identified in Citrus sinensis, and they were grouped into 5 clades. The CsHIPP genes are distributed on 8 chromosomes and exhibited considerable synteny with HIPPs found in Arabidopsis thaliana. Additionally, we analyzed the gene structure, conserved motifs and domains of the CsHIPPs. Various cis-acting elements related to plant hormones and stress responses were identified in the promoters of CsHIPPs. Public transcriptome data and RT-qPCR analysis showed that the expression level of CsHIPP03 was significantly reduced in samples infected by CLas and Xanthomonas citri ssp. citri (Xcc). Furthermore, silencing the homologous gene of CsHIPP03 in Nicotiana benthamiana increased the disease resistance of plants to bacteria. Discussion Our results provide a basis for functional studies of HIPP gene family in C. sinensis, highlighting their functions in bacterial resistance, and improve our understanding to the susceptibility mechanism of HLB.
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Affiliation(s)
- Guiyan Huang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yanan Hu
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fuxuan Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xiru Zuo
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xinyou Wang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fengyao Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Ruimin Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
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Luo W, Chi S, Wang J, Yu X, Tong J. Comparative transcriptomic analyses of brain-liver-muscle in channel catfish (Ictalurus punctatus) with differential growth rate. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101178. [PMID: 38128380 DOI: 10.1016/j.cbd.2023.101178] [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: 07/13/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
Growth is an important economically trait for aquatic animals. The popularity of farmed channel catfish (Ictalurus punctatus) in China has recently surged, prompting a need for research into the genetic mechanisms that drive growth and development to expedite the selection of fast-growing variants. In this study, the brain, liver and muscle transcriptomes of channel catfish between fast-growing and slow-growing groups were analyzed using RNA-Seq. Totally, 63, 110 and 86 differentially expressed genes (DEGs) were from brain, liver and muscle tissues. DEGs are primarily involved in growth, development, metabolism and immunity, which are related to the growth regulation of channel catfish, such as growth hormone receptor b (ghrb), fibroblast growth factor receptor 4 (fgfr4), bone morphogenetic protein 1a (bmp1a), insulin-like growth factor 2a (igf2a), collagen, type I, alpha 1a (col1a1a), acyl-CoA synthetase long chain family member 2 (acsl2) and caveolin 1 (cav1). This study advances our knowledge of the genetic mechanisms accounting for differences in growth rate and offers crucial gene resources for future growth-related molecular breeding programs in channel catfish.
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Affiliation(s)
- Weiwei Luo
- Jiangsu Union Technical Institute, Yancheng Bioengineering Branch, Yancheng Aquatic Science Research Institute, Yancheng 224001, China
| | - Shuang Chi
- Jiangsu Union Technical Institute, Yancheng Bioengineering Branch, Yancheng Aquatic Science Research Institute, Yancheng 224001, China
| | - Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Yang J, Lu B, Yu Z, Zhang L, Chen Y, Chen Z, Han C, Shu H. Multiple Tissues Transcriptome of Zig-Zag Eel ( Mastacembelus armatus) with Different Growth Rates. Animals (Basel) 2024; 14:248. [PMID: 38254417 PMCID: PMC10812625 DOI: 10.3390/ani14020248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
In order to explore the main regulatory genes and related pathways of growth traits, transcriptome sequencing was first performed on the brain, liver, and muscle tissues of 3-month-old M. armatus with different growth rates. By comparative transcriptome analysis of fast-growing and slow-growing groups of M. armatus, a total of 2887 DEGs were screened, of which 59 up-regulated genes and 105 down-regulated genes were detected in the brain, 146 up-regulated genes and 202 down-regulated genes were detected in the liver, and 529 up-regulated genes and 1846 down-regulated genes were detected in muscle, including insulin-like growth factor binding protein 1a (IGFBP1A), insulin-like growth factor binding protein 1b (IGFBP1B), myosin, light chain 1 (MYL1), and myoglobin (MB). Through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we identified a total of 288 significantly enriched GO entries and 68 significantly enriched KEGG pathways related to growth, such as skeletal muscle tissue development, insulin-like growth factor binding, and the mitotic cell cycle. These key genes and signaling pathways may play a key role in regulating the growth of M. armatus. Digging into the regulatory mechanisms of these key genes will provide a theoretical basis for further exploration of the molecular mechanisms related to the growth and development of M. armatus, and help to breed new varieties of M. armatus with rapid growth.
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Affiliation(s)
| | | | | | | | | | | | - Chong Han
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (J.Y.); (B.L.); (Z.Y.); (L.Z.); (Y.C.); (Z.C.)
| | - Hu Shu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (J.Y.); (B.L.); (Z.Y.); (L.Z.); (Y.C.); (Z.C.)
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Yin Y, Zhang Y, Hua Z, Wu A, Pan X, Yang J, Wang X. Muscle transcriptome analysis provides new insights into the growth gap between fast- and slow-growing Sinocyclocheilus grahami. Front Genet 2023; 14:1217952. [PMID: 37538358 PMCID: PMC10394708 DOI: 10.3389/fgene.2023.1217952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Sinocyclocheilus grahami is an economically valuable and famous fish in Yunnan Province, China. However, given its slow growth (40 g/2 years) and large growth differences among individuals, its growth performance needs to be improved for sustainable future use, in which molecular breeding technology can play an important role. In the current study, we conducted muscle transcriptomic analysis to investigate the growth gaps among individuals and the mechanism underlying growth within 14 fast- and 14 slow-growth S. grahami. In total, 1,647 differentially expressed genes (DEGs) were obtained, including 947 up-regulated and 700 down-regulated DEGs in fast-growth group. Most DEGs were significantly enriched in ECM-receptor interaction, starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, amino acids biosynthesis and metabolism, peroxisome, and PPAR signaling pathway. Some genes related to glycogen degradation, glucose transport, and glycolysis (e.g., adipoq, prkag1, slc2a1, agl, pygm, pgm1, pfkm, gapdh, aldoa, pgk1, pgam2, bpgm, and eno3) were up-regulated, while some genes related to fatty acid degradation and transport (e.g., acox1, acaa1, fabp1b.1, slc27a1, and slc27a2) and amino acid metabolism (e.g., agxt, shmt1, glula, and cth) were down-regulated in the fast-growth group. Weighted gene co-expression network analysis identified col1a1, col1a2, col5a1, col6a2, col10a1, col26a1, bglap, and krt15 as crucial genes for S. grahami growth. Several genes related to bone and muscle growth (e.g., bmp2, bmp3, tgfb1, tgfb2, gdf10, and myog) were also up-regulated in the fast-growth group. These results suggest that fast-growth fish may uptake adequate energy (e.g., glucose, fatty acid, and amino acids) from fodder, with excess energy substances used to synthesize collagen to accelerate bone and muscle growth after normal life activities are maintained. Moreover, energy uptake may be the root cause, while collagen synthesis may be the direct reason for the growth gap between fast- and slow-growth fish. Hence, improving food intake and collagen synthesis may be crucial for accelerating S. grahami growth, and further research is required to fully understand and confirm these associations.
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Affiliation(s)
- Yanhui Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zexiang Hua
- Fishery Technology Extension Station of Yunnan, Kunming, Yunnan, China
| | - Anli Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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Li J, Gao X, Chen X, Fan Z, Zhang Y, Wang Z, Shi J, Wang C, Zhang H, Wang L, Zhao Q. Comparative transcriptome responses of leaf and root tissues to salt stress in wheat strains with different salinity tolerances. Front Genet 2023; 14:1015599. [PMID: 36911411 PMCID: PMC9996022 DOI: 10.3389/fgene.2023.1015599] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
Background: Salinity stress is a major adverse environmental factor that can limit crop yield and restrict normal land use. The selection of salt-tolerant strains and elucidation of the underlying mechanisms by plant breeding scientists are urgently needed to increase agricultural production in arid and semi-arid regions. Results: In this study, we selected the salt-tolerant wheat (Triticum aestivum) strain ST9644 as a model to study differences in expression patterns between salt-tolerant and salt-sensitive strains. High-throughput RNA sequencing resulted in more than 359.10 Gb of clean data from 54 samples, with an average of 6.65 Gb per sample. Compared to the IWGSC reference annotation, we identified 50,096 new genes, 32,923 of which have functional annotations. Comparisons of abundances between salt-tolerant and salt-sensitive strains revealed 3,755, 5,504, and 4,344 genes that were differentially expressed at 0, 6, and 24 h, respectively, in root tissue under salt stress. KEGG pathway analysis of these genes showed that they were enriched for phenylpropanoid biosynthesis (ko00940), cysteine and methionine metabolism (ko00270), and glutathione metabolism (ko00480). We also applied weighted gene co-expression network analysis (WGCNA) analysis to determine the time course of root tissue response to salt stress and found that the acute response lasts >6 h and ends before 12 h. We also identified key alternative splicing factors showing different splicing patterns in salt-sensitive and salt-tolerant strains; however, only few of them were differentially expressed in the two groups. Conclusion: Our results offer a better understanding of wheat salt tolerance and improve wheat breeding.
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Affiliation(s)
- Jianfeng Li
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Xin Gao
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Xunji Chen
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Zheru Fan
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Yueqiang Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Zhong Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Jia Shi
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Chunsheng Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Hongzhi Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Lihong Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Qi Zhao
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
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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.
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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
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Sun Y, Wei H, Chen J, Li P, Yang Q, Wang G, Li Q. Tissue-Specific Expression Pattern in Ancherythroculter nigrocauda, a Sexually Size Dimorphic Fish. Front Genet 2021; 12:777581. [PMID: 34956327 PMCID: PMC8694267 DOI: 10.3389/fgene.2021.777581] [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: 09/15/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022] Open
Abstract
Certain members of the Actinopterygii class are known to exhibit sexual dimorphism (SD) that results in major phenotypic differences between male and female fishes of a species. One of the most common differences between the two sexes is in body weight, a factor with a high economic value in aquaculture. In this study, we used RNA sequencing (RNA-seq) to study the liver and brain transcriptomes of Ancherythroculter nigrocauda, a fish exhibiting SD. Females attain about fourfold body weight of males at sexual maturity. Sample clustering showed that both sexes were grouped well with their sex phenotypes. In addition, 2,395 and 457 differentially expressed genes (DEGs) were identified in the liver and brain tissues, respectively. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses predicted the association of PPAR signaling, cytochrome P450, and steroid hormone biosynthesis to the differences in sexual size. In addition, weighted gene co-expression network analyses (WGCNA) were conducted, and the green module was identified to be significantly correlated with sexual size dimorphism (SSD). Altogether, these results improve our understanding of the molecular mechanism underlying SSD in A. nigrocauda.
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Affiliation(s)
- Yanhong Sun
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.,Wuhan Xianfeng Aquaculture Technology Co., Ltd., Wuhan, China
| | - Huijie Wei
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Jian Chen
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.,Wuhan Xianfeng Aquaculture Technology Co., Ltd., Wuhan, China
| | - Pei Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.,Wuhan Xianfeng Aquaculture Technology Co., Ltd., Wuhan, China
| | - Qing Yang
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, China
| | - Guiying Wang
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.,Wuhan Xianfeng Aquaculture Technology Co., Ltd., Wuhan, China
| | - Qing Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China.,Wuhan Xianfeng Aquaculture Technology Co., Ltd., Wuhan, China
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Liu M, Liu Y, Wang X, Wang H. Brain morphological adaptations of
Gambusia affinis
along climatic gradients in China. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Mengyu Liu
- College of Animal Science and Technology Northwest A&F University Yangling China
| | - Yanqiu Liu
- College of Animal Science and Technology Northwest A&F University Yangling China
| | - Xiaoqin Wang
- College of Animal Science and Technology Northwest A&F University Yangling China
| | - He Wang
- College of Animal Science and Technology Northwest A&F University Yangling China
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Fu B, Zhou Y, Liu H, Yu X, Tong J. Updated Genome Assembly of Bighead Carp ( Hypophthalmichthys nobilis) and Its Differences Between Male and Female on Genomic, Transcriptomic, and Methylation Level. Front Genet 2021; 12:728177. [PMID: 34552623 PMCID: PMC8452039 DOI: 10.3389/fgene.2021.728177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022] Open
Abstract
Cyprinidae is one of the largest family in freshwater fishes, and it is most intensively cultured fish taxon of the world. However, studies about sex determination in this large family is still rear, and one of the reasons is lack of high quality and complete genome. Here, we used nanopore to sequence the genome of a male bighead carp, obtaining contig N50 = 24.25 Mb, which is one of the best assemblies in Cyprinidae. Five males and five females were re-sequenced, and a male-specific region on LG19 was confirmed. We find this region holds many male-specific markers in other Cyprinidae fishes, such as grass carp and silver carp. Transcriptome analyses of hypothalamus and pituitary tissues showed that several sex-specific differentially expressed genes were associated with steroid biosynthesis. The UCH64E gene, located in the male-specific region on LG19, showed higher expression levels in male than female tissues of bighead carp. The methyl-RAD of hypothalamus tissues between males and females indicated that the sexual methylation differences are significant in bighead carp. We also compared the methylation sites recognized using methyl-RAD and nanopore raw reads and found that approximately 73% of the methylation sites identified using methyl-RAD were within nanopore CpG sites.
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Affiliation(s)
- Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
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10
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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.
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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.)
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Si Y, He F, Wen H, Li S, He H. Effects of low salinity on epigenetic changes of growth hormone and growth hormone receptor in half smooth tongue sole (Cynoglossus semilaevis). REPRODUCTION AND BREEDING 2021. [DOI: 10.1016/j.repbre.2021.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Luo W, Zhou Y, Wang J, Yu X, Tong J. Identifying Candidate Genes Involved in the Regulation of Early Growth Using Full-Length Transcriptome and RNA-Seq Analyses of Frontal and Parietal Bones and Vertebral Bones in Bighead Carp ( Hypophthalmichthys nobilis). Front Genet 2021; 11:603454. [PMID: 33519908 PMCID: PMC7844397 DOI: 10.3389/fgene.2020.603454] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022] Open
Abstract
Growth, one of the most important traits monitored in domestic animals, is essentially associated with bone development. To date, no large-scale transcriptome studies investigating bone development in bighead carp have been reported. In this study, we applied Isoform-sequencing technology to uncover the entire transcriptomic landscape of the bighead carp (Hypophthalmichthys nobilis) in early growth stage, and obtained 63,873 non-redundant transcripts, 20,907 long non-coding RNAs, and 1,579 transcription factors. A total of 381 alternative splicing events were seen in the frontal and parietal bones with another 784 events simultaneously observed in the vertebral bones. Coupling this to RNA sequencing (RNA-seq) data, we identified 27 differentially expressed unigenes (DEGs) in the frontal and parietal bones and 45 DEGs in the vertebral bones in the fast-growing group of fish, when compared to the slow-growing group of fish. Finally, 15 key pathways and 20 key DEGs were identified and found to be involved in regulation of early growth such as energy metabolism, immune function, and cytoskeleton function and important cellular pathways such as the arginine and proline metabolic pathway (p4ha1), FoxO signaling pathway (sgk1), cell adhesion molecules (b2m, ptprc, and mhcII), and peroxisome proliferator-activated receptor signaling pathway (scd). We established a novel full-length transcriptome resource and combined it with RNA-seq to elucidate the mechanism of genetic regulation of differential growth in bighead carp. The key DEGs identified in this study could fuel further studies investigating associations between growth and bone development and serve as a source of potential candidate genes for marker-assisted breeding programs.
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Affiliation(s)
- Weiwei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
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Luo W, Wang J, Yu X, Zhou Y, Tong J. Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100752. [PMID: 33126027 DOI: 10.1016/j.cbd.2020.100752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 10/23/2022]
Abstract
Body deformity occurs both in wild and farmed fishes, which is one of the most challenging problems for aquaculture industry. In most cases, such body deformities are linked to skeletal deformities. Currently, very limited information is available on skeletal deformities of farmed fish species which may be caused by genetic factor. In this study, we performed muscle and vertebra transcriptome analyses in body deformity and normality of bighead carp Hypophthalmichthys nobilis (from one meiotic gynogenesis family) using RNA-Seq. A total of 43,923 and 44,416 unigenes were predicted in muscles and vertebrae, respectively. Based on these data, we further explored the gene expression profiles in gynogenetic normal and abnormal bighead carp. No differentially expressed gene (DEG) was found in transcriptome data of muscles. Totally, 20 key DEGs were identified in transcriptome data of vertebrae, such as low density lipoprotein-related protein 2 (lrp2), bone morphogenetic protein 2B (bmp2b) and collagen alpha-1(IV) (col4a1). 12 potential pathways were also identified in vertebra transcriptome data, which were mainly involved in development, growth, cytoskeleton and energy metabolism, such as MAPK signaling pathway, regulation of actin cytoskeleton and TGF-beta signaling pathway. Results of this study will be informative for the understanding of genetic mechanisms for body shape formation and also provide potential candidate genes for selection program involved in body shape and skeletal development in H. nobilis.
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Affiliation(s)
- Weiwei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China.
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China.
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