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Dorant Y, Quillien V, Le Luyer J, Ky CL. Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera. BMC Genomics 2024; 25:717. [PMID: 39049022 PMCID: PMC11270918 DOI: 10.1186/s12864-024-10636-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes. RESULTS We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene. CONCLUSIONS Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.
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Affiliation(s)
- Y Dorant
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France.
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France.
| | - V Quillien
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - J Le Luyer
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - C L Ky
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France
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Zhang E, Li Z, Dong L, Feng Y, Sun G, Xu X, Wang Z, Cui C, Wang W, Yang J. Exploration of Molecular Mechanisms of Immunity in the Pacific Oyster ( Crassostrea gigas) in Response to Vibrio alginolyticus Invasion. Animals (Basel) 2024; 14:1707. [PMID: 38891754 PMCID: PMC11171025 DOI: 10.3390/ani14111707] [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: 04/26/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Over the years, oysters have faced recurring mass mortality issues during the summer breeding season, with Vibrio infection emerging as a significant contributing factor. Tubules of gill filaments were confirmed to be in the hematopoietic position in Crassostrea gigas, which produce hemocytes with immune defense capabilities. Additionally, the epithelial cells of oyster gills produce immune effectors to defend against pathogens. In light of this, we performed a transcriptome analysis of gill tissues obtained from C. gigas infected with Vibrio alginolyticus for 12 h and 48 h. Through this analysis, we identified 1024 differentially expressed genes (DEGs) at 12 h post-injection and 1079 DEGs at 48 h post-injection. Enrichment analysis of these DEGs revealed a significant association with immune-related Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. To further investigate the immune response, we constructed a protein-protein interaction (PPI) network using the DEGs enriched in immune-associated KEGG pathways. This network provided insights into the interactions and relationships among these genes, shedding light on the underlying mechanisms of the innate immune defense mechanism in oyster gills. To ensure the accuracy of our findings, we validated 16 key genes using quantitative RT-PCR. Overall, this study represents the first exploration of the innate immune defense mechanism in oyster gills using a PPI network approach. The findings provide valuable insights for future research on oyster pathogen control and the development of oysters with enhanced antimicrobial resistance.
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Affiliation(s)
- Enshuo Zhang
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
| | - Zan Li
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
| | - Luyao Dong
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
| | - Zhongping Wang
- Yantai Kongtong Island Industrial Co., Ltd., Yantai 264000, China
| | - Cuiju Cui
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
- Yantai Kongtong Island Industrial Co., Ltd., Yantai 264000, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai 264025, China (Z.L.); (X.X.); (C.C.)
- Yantai Haiyu Marine Technology Co., Ltd., Yantai 264000, China
- Yantai Kongtong Island Industrial Co., Ltd., Yantai 264000, China
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Song X, Zhang M, Shahzad K, Zhang X, Guo L, Qi T, Tang H, Wang H, Qiao X, Feng J, Han Y, Xing C, Wu J. Comparative Transcriptome Profiling of CMS-D2 and CMS-D8 Systems Characterizes Fertility Restoration Genes Network in Upland Cotton. Int J Mol Sci 2023; 24:10759. [PMID: 37445936 DOI: 10.3390/ijms241310759] [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: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Resolving the genetic basis of fertility restoration for cytoplasmic male sterility (CMS) can improve the efficiency of three-line hybrid breeding. However, the genetic determinants of male fertility restoration in cotton are still largely unknown. This study comprehensively compared the full-length transcripts of CMS-D2 and CMS-D8 systems to identify potential genes linked with fertility restorer genes Rf1 or Rf2. Target comparative analysis revealed a higher percentage of differential genes in each restorer line as compared to their corresponding sterile and maintainer lines. An array of genes with specific expression in the restorer line of CMS-D2 had functional annotations related to floral development and pathway enrichments in various secondary metabolites, while specifically expressed genes in the CMS-D8 restorer line showed functional annotations related to anther development and pathway enrichment in the biosynthesis of secondary metabolites. Further analysis identified potentially key genes located in the target region of fertility restorer genes Rf1 or Rf2. In particular, Ghir_D05G032450 can be the candidate gene related to restorer gene Rf1, and Ghir_D05G035690 can be the candidate gene associated with restorer gene Rf2. Further gene expression validation with qRT-PCR confirmed the accuracy of our results. Our findings provide useful insights into decoding the potential regulatory network that retrieves pollen fertility in cotton and will help to further reveal the differences in the genetic basis of fertility restoration for two CMS systems.
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Affiliation(s)
- Xiatong Song
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Kashif Shahzad
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xuexian Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liping Guo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Tingxiang Qi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Huini Tang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hailin Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiuqin Qiao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Juanjuan Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yang Han
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chaozhu Xing
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jianyong Wu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
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Zhang E, Li Z, Lv T, Fu J, Dong L, Feng Y, Sun G, Xu X, Cui C, Wang W, Yang J. Transcriptome profiling explores the immune defence mechanism of triploid Pacific oyster (Crassostrea gigas) blood against Vibrio alginolyticus based on protein interaction networks. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 143:104677. [PMID: 36870582 DOI: 10.1016/j.dci.2023.104677] [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: 12/20/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Triploid oysters have provided the oyster industry with many benefits, such as fast growth rates, meat quality improvement, and increased oyster production and economic benefits, since the first report on triploid oysters was published. The development of polyploid technology has remarkably increased the output of triploid oysters to meet the increasing demand of consumers for Crassostrea gigas in the past decades. At present, research on triploid oyster has mainly focused on breeding and growth, but studies on the immunity of triploid oysters are limited. According to recent reports, Vibrio alginolyticus is a highly virulent strain that can cause disease and death in shellfish, shrimp, as well as serious economic losses. V. alginolyticus may be a reason why oysters die during summer. Therefore, using V. alginolyticus to explore the resistance and immune defense mechanisms of triploid oysters against pathogens presents practical significance. Transcriptome analysis of gene expression was performed in triploid C. gigas at 12 and 48 h after infection with V. alginolyticus, and the respective 2257 and 191 differentially expressed genes (DEGs) were identified. The results of GO and KEGG enrichment analyses showed that multiple significantly enriched GO terms and KEGG signaling pathways are associated with immunity. A protein-protein interaction network was constructed to investigate the interaction relationship of immune-related genes. Finally, we verified the expression situation of 16 key genes using quantitative RT-PCR. This study is the first to use the PPI network in exploring the immune defense mechanism of triploid C. gigas blood to fill the gap in the immune mechanism of triploid oysters and other mollusks, and provide valuable reference for future triploid farming and pathogen prevention and control.
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Affiliation(s)
- Enshuo Zhang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Tingjin Lv
- Yantai Institute of Marine Economy, Yantai, 264003, China
| | - Jingjing Fu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Luyao Dong
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Cuiju Cui
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China
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Zeng D, Guo X. Mantle Transcriptome Provides Insights into Biomineralization and Growth Regulation in the Eastern Oyster (Crassostrea virginica). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:82-96. [PMID: 34989931 DOI: 10.1007/s10126-021-10088-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Growth of the eastern oyster Crassostrea virginica, a major aquaculture species in the USA, is highly variable and not well understood at molecular levels. As growth of mollusks is confined in shells constructed by the mantle, mantle transcriptomes of large (fast-growing) and small (slow-growing) eastern oysters were sequenced and compared in this study. Transcription was observed for 31,186 genes, among which 104 genes were differentially expressed between the large and small oysters, including 48 upregulated and 56 downregulated in large oysters. Differentially expressed genes (DEGs) included genes from diverse pathways highlighting the complexity of shell formation and growth regulations. Seventeen of the 48 upregulated DEGs were related to shell matrix formation, most of which were upregulated in large oysters, indicating that large oysters are more active in biomineralization and shell formation. Genomic and transcriptomic analyses identified 22 genes encoding novel polyalanine containing proteins (Pacps) with characteristic motifs for matrix function that are tandemly duplicated on one chromosome, all specifically expressed in mantle and at higher levels in large oysters, suggesting that these expanded Pacps play important roles in shell formation and growth. Analysis of sequence variation identified 244,964 SNPs with 328 associated with growth. This study provides novel candidate genes and markers for shell formation and growth, and suggests that genes related to shell formation are important for the complex regulation of growth in the eastern oyster and possibly other bivalve mollusks. Results of this study show that both transcriptional modulation and functional polymorphism are important in determining growth.
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Affiliation(s)
- Dan Zeng
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, New Jersey, 08349, USA
- College of Life and Environmental Science, Hunan University of Arts and Science, 3150 Dongting Road, Wuling District, Changde, Hunan, 415000, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, New Jersey, 08349, USA.
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Transcriptomic analysis provides insights into candidate genes and molecular pathways involved in growth of Manila clam Ruditapes philippinarum. Funct Integr Genomics 2021; 21:341-353. [PMID: 33660117 DOI: 10.1007/s10142-021-00780-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 10/22/2022]
Abstract
Growth is one of the most important traits of aquaculture breeding programs. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Ruditapes philippinarum is an economically important marine bivalve. In order to gain insights into the molecular mechanisms to growth variability in marine shellfish, we conducted the transcriptome sequencing and examined the expression differences in growth-related gene and molecular pathways involved in growth trait of R. philippinarum. In this study, we investigated the molecular and gene expression differences in fast-growing and slow-growing Manila clam and focused on the analysis of the differential expression patterns of specific genes associated with growth by RNA-seq and qPCR analysis. A total of 61 differentially expressed genes (DEGs) were captured significantly differentially expressed, and were categorized into Ras signaling pathway, hedgehog signaling pathway, AMPK signaling pathway, p53 signaling pathway, regulation of actin cytoskeleton, focal adhesion, mTOR signaling pathway, VEGF signaling pathway, and TGF-beta signaling pathway. A total of 34 growth-related genes were validated significantly and up/downregulated at fast growing and slow growing of R. philippinarum. Functional enrichment analysis revealed the insulin signaling pathway, PI3K-Akt signaling pathway, and mTOR signaling pathway play pivotal roles in molecular function and regulation of growth trait in R. philippinarum. The growth-related genes and pathways obtained here provide important insights into the molecular basis of physiological acclimation, metabolic activity, and growth variability in marine bivalves.
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Zhang H, Xu H, Liu H, Pan X, Xu M, Zhang G, He M. PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome. BMC Genomics 2020; 21:481. [PMID: 32660426 PMCID: PMC7359550 DOI: 10.1186/s12864-020-06894-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/07/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The pearl oyster Pinctada fucata martensii is an economically valuable shellfish for seawater pearl production, and production of pearls depends on its growth. To date, the molecular mechanisms of the growth of this species remain poorly understood. The transcriptome sequencing has been considered to understanding of the complexity of mechanisms of the growth of P. f. martensii. The recently released genome sequences of P. f. martensii, as well as emerging Pacific Bioscience (PacBio) single-molecular sequencing technologies, provide an opportunity to thoroughly investigate these molecular mechanisms. RESULTS Herein, the full-length transcriptome was analysed by combining PacBio single-molecule long-read sequencing (PacBio sequencing) and Illumina sequencing. A total of 20.65 Gb of clean data were generated, including 574,561 circular consensus reads, among which 443,944 full-length non-chimeric (FLNC) sequences were identified. Through transcript clustering analysis of FLNC reads, 32,755 consensus isoforms were identified, including 32,095 high-quality consensus sequences. After removing redundant reads, 16,388 transcripts were obtained, and 641 fusion transcripts were derived by performing fusion transcript prediction of consensus sequences. Alternative splicing analysis of the 16,388 transcripts was performed after accounting for redundancy, and 9097 gene loci were detected, including 1607 new gene loci and 14,946 newly discovered transcripts. The original boundary of 11,235 genes on the chromosomes was corrected, 12,025 complete open reading frame sequences and 635 long non-coding RNAs (LncRNAs) were predicted, and functional annotation of 13,482 new transcripts was achieved. Two thousand three hundred eighteen alternative splicing events were detected. A total of 228 differentially expressed transcripts (DETs) were identified between the largest (L) and smallest (S) pearl oysters. Compared with the S, the L showed 99 and 129 significantly up-and down-regulated DETs, respectively. Six of these DETs were further confirmed by quantitative real-time RT-PCR (RT-qPCR) in independent experiment. CONCLUSIONS Our results significantly improve existing gene models and genome annotations, optimise the genome structure, and in-depth understanding of the complexity and diversity of the differential growth patterns of P. f. martensii.
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Affiliation(s)
- Hua Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hanzhi Xu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huiru Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaolan Pan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Xu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gege Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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Yamano-Adachi N, Ogata N, Tanaka S, Onitsuka M, Omasa T. Characterization of Chinese hamster ovary cells with disparate chromosome numbers: Reduction of the amount of mRNA relative to total protein. J Biosci Bioeng 2019; 129:121-128. [PMID: 31303495 DOI: 10.1016/j.jbiosc.2019.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/06/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
Chromosomes in Chinese hamster ovary (CHO) cells are labile. We have shown that high-chromosome-number CHO cells have greater potential to become robust producers of recombinant proteins. One explanation being the increase in transgene integration sites. However, high-chromosome-number cell clones produce more IgG3 following culture of single-cell clones, even under conditions that yield the same number of integrations as cells with normal chromosome numbers. Here, we characterized high-chromosome-number cells by transcriptome analysis. RNA standards were used to normalize transcriptomes of cells that had different chromosome numbers. Our results demonstrate that the mRNA ratio of β-actin and many other genes in high-chromosome-number cells to that in normal-chromosome-number cells per cell (normalized to RNA standards) was smaller than the equivalent genomic size and cell volume ratios. Many genes encoding membrane proteins are more highly expressed in high-chromosome-number cells, probably due to differences in cell size caused by the increase in chromosomes. In addition, genes related to histone modification and lipid metabolism are differentially expressed. The reduced transcript level required per protein produced in total and the different intracellular signal transductions might be key factors for antibody production.
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Affiliation(s)
- Noriko Yamano-Adachi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Norichika Ogata
- Nihon BioData Corporation, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan.
| | - Sho Tanaka
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, Tokushima 770-8506, Japan.
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Zhang F, Hu B, Fu H, Jiao Z, Li Q, Liu S. Comparative Transcriptome Analysis Reveals Molecular Basis Underlying Fast Growth of the Selectively Bred Pacific Oyster, Crassostrea gigas. Front Genet 2019; 10:610. [PMID: 31316550 PMCID: PMC6611504 DOI: 10.3389/fgene.2019.00610] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Fast growth is one of the most desired traits for all food animals, which affects the profitability of animal production. The Pacific oyster, Crassostrea gigas, is an important aquaculture shellfish around the world with the largest annual production. Growth of the Pacific oyster has been greatly improved by artificial selection breeding, but molecular mechanisms underlying growth remains poorly understood, which limited the molecular integrative breeding of fast growth with other superior traits. In this study, comparative transcriptome analyses between the fast-growing selectively bred Pacific oyster and unselected wild Pacific oysters were conducted by RNA-Seq. A total of 1,303 protein-coding genes differentially expressed between fast-growing oysters and wild controls were identified, of which 888 genes were expressed at higher levels in the fast-growing oysters. Functional analysis of the differentially expressed genes (DEGs) indicated that genes involved in microtubule motor activity and biosynthesis of nucleotides and proteins are potentially important for growth in the oyster. Positive selection analysis of genes at the transcriptome level showed that a significant number of ribosomal protein genes had undergone positive selection during the artificial selection breeding process. These results also indicated the importance of protein biosynthesis and metabolism for the growth of oysters. The alternative splicing (AS) of genes was also compared between the two groups of oysters. A total of 3,230 differential alternative splicing events (DAS) were identified, involved in 1,818 genes. These DAS genes were associated with specific functional pathways related to growth, such as “long-term potentiation,” “salivary secretion,” and “phosphatidylinositol signaling system.” The findings of this study will be valuable resources for future investigation to unravel molecular mechanisms underlying growth regulation in the oyster and other marine invertebrates and to provide solid support for breeding application to integrate fast growth with other superior traits in the Pacific oyster.
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Affiliation(s)
- Fuqiang Zhang
- Key Laboratory of Mariculture, Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China
| | - Boyang Hu
- Key Laboratory of Mariculture, Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China
| | - Huiru Fu
- Key Laboratory of Mariculture, Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China
| | - Zexin Jiao
- Key Laboratory of Mariculture, Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Wang W, Lei Q, Liang H, He J. Towards a better understanding of allograft-induced stress response in the pearl oyster Pinctada fucata martensii: Insights from iTRAQ-based comparative proteomic analysis. FISH & SHELLFISH IMMUNOLOGY 2019; 86:186-195. [PMID: 30458307 DOI: 10.1016/j.fsi.2018.11.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/10/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
Implantation of a spherical nucleus into a recipient oyster is a critical step in artificial pearl production. The implanted nucleus is known to trigger cellular stress responses at several levels, yet the molecular mechanism underpinning physiological adaptation of the pearl oysters to nucleus implantation is still poorly understood. In this study, we took advantage of the iTRAQ-based proteomics and LC-MS/MS approach to look into allograft induced gene regulation at the protein expression level in the pearl oyster Pinctada fucata martensii, across a period of 30 days following nucleus implantation. A wide variety of proteins, including a group of immune-related proteins such as E3 ubiquitin-ligase and heat shock proteins, exhibited differential expression in response to the surgical operation. Further comparisons between different sampling points revealed that GO terms including "translation" and "oxidation-reduction process" and KEGG pathways including "glycolysis/gluconeogenesis" and "pyruvate metabolism" were significantly enriched at several time points, indicating the important roles of these molecular events in the stress response of pearl oysters to nucleus implantation. In addition, considerable discrepancy between protein expression level and gene transcript abundancy was identified, as only a few genes showed at least 2-fold expression changes at both proteomic and transcriptomic levels. The result implies that post-transcriptional gene regulation for the key proteins may represent an important aspect of allograft-induced stress response in the pearl oysters. Taken together, the data obtained would contribute to a deeper understanding of the molecular mechanisms enabling stress adaptation of the pearl oysters in response to nucleus implantation.
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Affiliation(s)
- Wei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, PR China
| | - Qiannan Lei
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, PR China
| | - Haiying Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, PR China.
| | - Junjun He
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, PR China
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Isolation and characterization of three skeletal troponin genes and association with growth-related traits in Exopalaemon carinicauda. Mol Biol Rep 2018; 46:705-718. [DOI: 10.1007/s11033-018-4526-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/23/2018] [Indexed: 12/15/2022]
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