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Li X, Zhu M. Genome-wide identification of the Hsp70 gene family in Penaeus chinensis and their response to environmental stress. Anim Biotechnol 2024; 35:2344205. [PMID: 38651890 DOI: 10.1080/10495398.2024.2344205] [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] [Indexed: 04/25/2024]
Abstract
The heat shock protein 70 (HSP70) gene family plays a crucial role in the response of organisms to environmental stress. However, it has not been systematically characterized in shrimp. In this study, we identified 25 PcHsp70 genes in the Penaeus chinensis genome. The encoded proteins were categorized into six subgroups based on phylogenetic relationships. Tandem duplication was the main driver of amplification in the PcHsp70 family, and the genes have experienced strong purifying selection during evolution. Transcriptome data analysis revealed that the 25 PcHsp70 members have different expression patterns in shrimp under conditions of low temperature, low salinity, and white spot syndrome virus infection. Among them, PcHsp70.11 was significantly induced under all three stress conditions, suggesting that this gene plays an important role in response to environmental stress in P. chinensis. To the best of our knowledge, this is the first study to systematically analyze the Hsp70 gene family in shrimp. The results provide important information on shrimp Hsp70s, contributing to a better understanding of the role of these genes in environmental stress and providing a basis for further functional studies.
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Affiliation(s)
- Xinran Li
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, China
| | - Miao Zhu
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, China
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2
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Garcia BF, Mastrochirico-Filho VA, Gallardo-Hidalgo J, Campos-Montes GR, Medrano-Mendoza T, Rivero-Martínez PV, Caballero-Zamora A, Hashimoto DT, Yáñez JM. A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2024; 25:565. [PMID: 38840101 PMCID: PMC11155064 DOI: 10.1186/s12864-024-10431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei), such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools in order to improve economically relevant traits. Sexual dimorphism exists in Pacific white shrimp, and the mapping of the sex-determination region in this species may help in future reproductive applications. We have constructed male, female, and sex-averaged high-density genetic maps using a 50 K single-nucleotide polymorphism (SNP) array, followed by a genome-wide association study (GWAS) to identify genomic regions associated with sex in white shrimp. RESULTS The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The lengths of the male, female, and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. LG18 was found to be the largest for both sexes, whereas LG44 was the shortest for males and LG31 for females. A sex-determining region was found in LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and was able to identify 99% of the males and 88% of the females. Although other significant markers had a lower ability to determine sex, putative genes were intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidates with possible participation in important processes of sexual differentiation in shrimp. CONCLUSIONS Our results provide novel genomic resources for shrimp, including a high-density linkage map and new insights into the sex-determining region in L. vannamei, which may be usefulfor future genetics and reproduction applications.
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Affiliation(s)
- Baltasar F Garcia
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile
| | - Vito A Mastrochirico-Filho
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile
| | | | - Gabriel R Campos-Montes
- Departamento de El Hombre y su Ambiente, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Thania Medrano-Mendoza
- Doctorado en Ciencias Agropecuarias, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Psique Victoria Rivero-Martínez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Alejandra Caballero-Zamora
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Diogo T Hashimoto
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile.
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3
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Perez-Enriquez R, Juárez OE, Galindo-Torres P, Vargas-Aguilar AL, Llera-Herrera R. Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases. J Hered 2024; 115:302-310. [PMID: 38451162 DOI: 10.1093/jhered/esae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
The Pacific whiteleg shrimp Penaeus (Litopenaeus) vannamei is a highly relevant species for the world's aquaculture development, for which an incomplete genome is available in public databases. In this work, PacBio long-reads from 14 publicly available genomic libraries (131.2 Gb) were mined to improve the reference genome assembly. The libraries were assembled, polished using Illumina short-reads, and scaffolded with P. vannamei, Feneropenaeus chinensis, and Penaeus monodon genomes. The reference-guided assembly, organized into 44 pseudo-chromosomes and 15,682 scaffolds, showed an improvement from previous reference genomes with a genome size of 2.055 Gb, N50 of 40.14 Mb, L50 of 21, and the longest scaffold of 65.79 Mb. Most orthologous genes (92.6%) of the Arthropoda_odb10 database were detected as "complete," and BRAKER predicted 21,816 gene models; from these, we detected 1,814 single-copy orthologues conserved across the genomic references for Marsupenaeus japonicus, F. chinensis, and P. monodon. Transcriptomic-assembly data aligned in more than 99% to the new reference-guided assembly. The collinearity analysis of the assembled pseudo-chromosomes against the P. vannamei and P. monodon reference genomes showed high conservation in different sets of pseudo-chromosomes. In addition, more than 21,000 publicly available genetic marker sequences were mapped to single-site positions. This new assembly represents a step forward to previously reported P. vannamei assemblies. It will be helpful as a reference genome for future studies on the evolutionary history of the species, the genetic architecture of physiological and sex-determination traits, and the analysis of the changes in genetic diversity and composition of cultivated stocks.
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Affiliation(s)
- Ricardo Perez-Enriquez
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
| | - Oscar E Juárez
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
- Dirección de Investigación en Acuacultura, Programa de Recursos Genéticos, Instituto Mexicano de Investigación en Pesca y Acuacultura Sustentables, Coyoacán, Ciudad de México, Mexico
| | - Pavel Galindo-Torres
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
| | - Ana Luisa Vargas-Aguilar
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados, Unidad Mérida, Mérida, Yucatán, Mexico
| | - Raúl Llera-Herrera
- Functional Genomics Laboratory, Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán, Sinaloa, Mexico
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4
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Kawato S, Nozaki R, Kondo H, Hirono I. Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans. Microbiol Spectr 2024; 12:e0055923. [PMID: 38063384 PMCID: PMC10871703 DOI: 10.1128/spectrum.00559-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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5
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Zhang X, Xiang J, Yuan J, Li F. Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era. Genes (Basel) 2023; 14:2050. [PMID: 38002993 PMCID: PMC10671375 DOI: 10.3390/genes14112050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Chromosome studies provide the foundation for comprehending inheritance, variation, systematics, and evolution. Penaeid shrimps are a group of crustaceans with great economic importance. Basic cytogenetic information obtained from these shrimps can be used to study their genome structure, chromosome relationships, chromosome variation, polyploidy manipulation, and breeding. The study of shrimp chromosomes experienced significant growth in the 1990s and has been closely linked to the progress of genome research since the application of next-generation sequencing technology. To date, the genome sequences of five penaeid shrimp species have been published. The availability of these genomes has ushered the study of shrimp chromosomes into the post-genomic era. Currently, research on shrimp cytogenetics not only involves chromosome counting and karyotyping, but also extends to investigating submicroscopic changes; exploring genome structure and regulation during various cell divisions; and contributing to the understanding of mechanisms related to growth, sexual control, stress resistance, and genome evolution. In this article, we provide an overview of the progress made in chromosome research on penaeid shrimp. We emphasize the mutual promotion between studies on chromosome structure and genome research and highlight the impact of chromosome-level assembly on studies of genome structure and function. Additionally, we summarize the emerging trends in post-genomic-era shrimp chromosome research.
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Affiliation(s)
- Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Rutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, Theissinger K, Lecompte O. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes (Basel) 2023; 14:1627. [PMID: 37628678 PMCID: PMC10454600 DOI: 10.3390/genes14081627] [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: 07/07/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.
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Affiliation(s)
- Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Lena Bonassin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Ljudevit Luka Boštjančić
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Dorine Merlat
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
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7
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Xu M, Liu P, Huang Q, Xu S, Dumont HJ, Han BP. High-quality genome of Diaphanosoma dubium provides insights into molecular basis of its broad ecological adaptation. iScience 2023; 26:106006. [PMID: 36798432 PMCID: PMC9926121 DOI: 10.1016/j.isci.2023.106006] [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: 07/14/2022] [Revised: 07/20/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Diaphanosoma dubium Manuilova, 1964, is a widespread planktonic water flea in Asian freshwater. Although sharing similar ecological roles with species of Daphnia, studies on D. dubium and its congeners are still few and lacking a genome for the further studies. Here, we assembled a high quality and chromosome level genome of D. dubium by combining long reads sequencing and Hi-C technologies. The total length of assembled genome was 101.8 Mb, with 98.92 Mb (97.2%) anchored into 22 chromosomes. Through comparative genomic analysis, we found the genes, involved in anti-ROS, detoxification, protein digestion, germ cells regulation and protection, underwent expansion in D. dubium. These genes and their expansion helpfully explain its widespread geographical distribution and dominance in eutrophic waters. This study provides insight into the adaptive evolution of D. dubium at genomic perspectives, and the present high quality genomic resource will be a footstone for future omics studies of the species and its congeners.
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Affiliation(s)
- Meng Xu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Ping Liu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China,College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China
| | - Qi Huang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Shaolin Xu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Henri J. Dumont
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China,Ghent University, Department of Biology, Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China,Corresponding author
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8
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Assessing penaeid shrimp diversity in the northwest of Peninsular Malaysia: an integrated framework in taxonomy and phylogeny. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01283-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Down-Regulation of Lipid Metabolism in the Hepatopancreas of Shrimp Litopenaeus vannamei upon Light and Heavy Infection of Enterocytozoon hepatopenaei: A Comparative Proteomic Study. Int J Mol Sci 2022; 23:ijms231911574. [PMID: 36232879 PMCID: PMC9570011 DOI: 10.3390/ijms231911574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
Enterocytozoon hepatopenaei (EHP) is the pathogen of hepatopancreatic microsporidiosis (HPM) in shrimp. The diseased shrimp Litopenaeus vannamei exhibits a slow growth syndrome, which causes severe economic losses. Herein, 4D label-free quantitative proteomics was employed to analyze the hepatopancreas of L. vannamei with a light (EHPptp2 < 103 copies/50 ng hpDNA, L group) and heavy (EHPptp2 > 104 copies/50 ng hpDNA, H group) load of EHP to better understand the pathogenesis of HPM. Exactly 786 (L group) and 1056 (H group) differentially expressed proteins (DEPs) versus the EHP-free (C group) control were mainly clustered to lipid metabolism, amino acid metabolism, and energy production processing. Compared with the L group, the H group exhibited down-regulation significantly in lipid metabolism, especially in the elongation and degradation of fatty acid, biosynthesis of unsaturated fatty acid, metabolism of α-linolenic acid, sphingolipid, and glycerolipid, as well as juvenile hormone (JH) degradation. Expression pattern analysis showed that the degree of infection was positively correlated with metabolic change. About 479 EHP proteins were detected in infected shrimps, including 95 predicted transporters. These findings suggest that EHP infection induced the consumption of storage lipids and the entire down-regulation of lipid metabolism and the coupling energy production, in addition to the hormone metabolism disorder. These were ultimately responsible for the stunted growth.
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10
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Huerlimann R, Cowley JA, Wade NM, Wang Y, Kasinadhuni N, Chan CKK, Jabbari JS, Siemering K, Gordon L, Tinning M, Montenegro JD, Maes GE, Sellars MJ, Coman GJ, McWilliam S, Zenger KR, Khatkar MS, Raadsma HW, Donovan D, Krishna G, Jerry DR. Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence. G3 (BETHESDA, MD.) 2022; 12:6526390. [PMID: 35143647 PMCID: PMC8982415 DOI: 10.1093/g3journal/jkac034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/02/2022] [Indexed: 01/08/2023]
Abstract
Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.
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Affiliation(s)
- Roger Huerlimann
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Jeff A Cowley
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Nicholas M Wade
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Yinan Wang
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Naga Kasinadhuni
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Chon-Kit Kenneth Chan
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Jafar S Jabbari
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Kirby Siemering
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Lavinia Gordon
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Matthew Tinning
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Juan D Montenegro
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia.,Laboratory of Biodiversity and Evolutionary Genomics, Biogenomics-consultancy, KU Leuven, Leuven 3000, Belgium.,Center for Human Genetics, UZ Leuven- Genomics Core, KU Leuven, Leuven 3000, Belgium
| | | | - Greg J Coman
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,CSIRO Agriculture and Food, Bribie Island Research Centre, Woorim, QLD 4507, Australia
| | - Sean McWilliam
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Kyall R Zenger
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Mehar S Khatkar
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Herman W Raadsma
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Dallas Donovan
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Seafarms Group Ltd, Darwin, NT 0800, Australia
| | - Gopala Krishna
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Seafarms Group Ltd, Darwin, NT 0800, Australia
| | - Dean R Jerry
- ARC Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4811, Australia
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