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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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Mangabeira-Silva IS, Soares PET, Vieira da Silva YT, Rodrigues de Albuquerque BHD, Câmera de Oliveira MTF, Ferreira LAH, Bezerra de Souza MF, Vieira de Lucena D, Paiva Pereira JM, Pinheiro e Silva RP, Lanza DCF. Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome. PLoS One 2024; 19:e0289351. [PMID: 38696386 PMCID: PMC11065258 DOI: 10.1371/journal.pone.0289351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 07/18/2023] [Indexed: 05/04/2024] Open
Abstract
In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation. To validate the accuracy of the findings, a sample of nine markers was subjected to in vitro testing, which confirmed the presence of polymorphisms within the population. These results suggest the existence of different protein isoforms within the population, indicating the potential of these markers for application in both population and phenotype-genotype association studies. This innovative approach opens up new possibilities for investigating the impact of genomic plasticity in populations of P. vannamei.
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Affiliation(s)
- Iasmim Santos Mangabeira-Silva
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biotechnology, RENORBIO, Natal, RN, Brazil
| | - Paulo Eduardo Toscano Soares
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Yago Tomaz Vieira da Silva
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Beatriz Helena Dantas Rodrigues de Albuquerque
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Maryana Thalyta Ferreira Câmera de Oliveira
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Maria Fernanda Bezerra de Souza
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Danyllo Vieira de Lucena
- Postgraduate Program in Civil and Environmental Engineering, Federal University of Campina Grande, Campina Grande, PB, Brazil
| | | | | | - Daniel Carlos Ferreira Lanza
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biotechnology, RENORBIO, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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Chen X, Peng M, Yang C, Li Q, Feng P, Zhu W, Zhang Y, Zeng D, Zhao Y. Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2024; 25:414. [PMID: 38671371 PMCID: PMC11046935 DOI: 10.1186/s12864-024-10328-9] [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: 02/11/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Growth rate is a crucial economic trait for farmed animals, but the genetic regulation of this trait is largely unknown in non-model organisms such as shrimp. RESULTS In this study, we performed genome-wide phenotypic quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) mapping analyses to identify genes affecting the growth rate of Pacific white shrimp (Litopenaeus vannamei), which is the most commercially-farmed crustacean worldwide. We used RNA-sequencing of 268 individuals in a mapping population, and subsequently validated our findings through gene silencing and shrimp growth experiments. We constructed a high-density genetic linkage map comprising 5533 markers spanning 44 linkage groups, with a total distance of 6205.75 cM and an average marker interval of 1.12 cM. Our analyses identified 11 QTLs significantly correlated with growth rate, and 117,525 eQTLs. By integrating QTL and eQTL data, we identified a gene (metalloreductase STEAP4) highly associated with shrimp growth rate. RNA interference (RNAi) analysis and growth experiments confirmed that STEAP4 was significantly correlated with growth rate in L. vannamei. CONCLUSIONS Our results indicate that the comprehensive analysis of QTL and eQTL can effectively identify genes involved in complex animal traits. This is important for marker-assisted selection (MAS) of animals. Our work contributes to the development of shrimp breeding and available genetic resources.
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Affiliation(s)
- Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Pengfei Feng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Weilin Zhu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yongde Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
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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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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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Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp. Commun Biol 2021; 4:186. [PMID: 33574498 PMCID: PMC7878876 DOI: 10.1038/s42003-021-01716-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Simple sequence repeats (SSRs) are rare (approximately 1%) in most genomes and are generally considered to have no function. However, penaeid shrimp genomes have a high proportion of SSRs (>23%), raising the question of whether these SSRs play important functional and evolutionary roles in these SSR-rich species. Here, we show that SSRs drive genome plasticity and adaptive evolution in two penaeid shrimp species, Fenneropenaeus chinensis and Litopenaeus vannamei. Assembly and comparison of genomes of these two shrimp species at the chromosome-level revealed that transposable elements serve as carriers for SSR expansion, which is still occurring. The remarkable genome plasticity identified herein might have been shaped by significant SSR expansions. SSRs were also found to regulate gene expression by multi-omics analyses, and be responsible for driving adaptive evolution, such as the variable osmoregulatory capacities of these shrimp under low-salinity stress. These data provide strong evidence that SSRs are an important driver of the adaptive evolution in penaeid shrimp.
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Bao W, Tang KFJ, Alcivar-Warren A. The Complete Genome of an Endogenous Nimavirus ( Nimav-1_LVa) From the Pacific Whiteleg Shrimp Penaeus ( Litopenaeus) Vannamei. Genes (Basel) 2020; 11:E94. [PMID: 31947590 PMCID: PMC7016691 DOI: 10.3390/genes11010094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/09/2023] Open
Abstract
White spot syndrome virus (WSSV), the lone virus of the genus Whispovirus under the family Nimaviridae, is one of the most devastating viruses affecting the shrimp farming industry. Knowledge about this virus, in particular, its evolution history, has been limited, partly due to its large genome and the lack of other closely related free-living viruses for comparative studies. In this study, we reconstructed a full-length endogenous nimavirus consensus genome, Nimav-1_LVa (279,905 bp), in the genome sequence of Penaeus (Litopenaeus) vannamei breed Kehai No. 1 (ASM378908v1). This endogenous virus seemed to insert exclusively into the telomeric pentanucleotide microsatellite (TAACC/GGTTA)n. It encoded 117 putative genes, with some containing introns, such as g012 (inhibitor of apoptosis, IAP), g046 (crustacean hyperglycemic hormone, CHH), g155 (innexin), g158 (Bax inhibitor 1 like). More than a dozen Nimav-1_LVa genes are involved in the pathogen-host interactions. We hypothesized that g046, g155, g158, and g227 (semaphorin 1A like) were recruited host genes for their roles in immune regulation. Sequence analysis indicated that a total of 43 WSSV genes belonged to the ancestral/core nimavirus gene set, including four genes reported in this study: wsv112 (dUTPase), wsv206, wsv226, and wsv308 (nucleocapsid protein). The availability of the Nimav-1_LVa sequence would help understand the genetic diversity, epidemiology, evolution, and virulence of WSSV.
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Affiliation(s)
- Weidong Bao
- Genetic Information Research Institute, 20380 Town Center Lane, Suite 240, Cupertino, CA 95014, USA
| | - Kathy F. J. Tang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Acacia Alcivar-Warren
- Fundación para la Conservation de la Biodiversidad Acuática y Terrestre (FUCOBI), Quito EC1701, Ecuador
- Environmental Genomics Inc., ONE HEALTH Epigenomics Educational Initiative, P.O. Box 196, Southborough, MA 01772, USA
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Mondal D, Dutta S, Chakrabarty U, Mallik A, Mandal N. Development and characterization of white spot disease linked microsatellite DNA markers in Penaeus monodon, and their application to determine the population diversity, cluster and structure. J Invertebr Pathol 2019; 168:107275. [PMID: 31715182 DOI: 10.1016/j.jip.2019.107275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 11/03/2019] [Accepted: 11/07/2019] [Indexed: 11/15/2022]
Abstract
Pathogens that are introduced suddenly to natural populations can potentially cause quick changes to the genetics and diversity of the host. In the past three decades, white spot syndrome virus (WSSV) has caused damaging epizootics in Penaeus monodon populations. In this study, we developed WSSV resistance- or susceptibility-linked microsatellite DNA markers, and their effectiveness was validated experimentally. WSSV-resistant marker linked retroelements and genes that may have an important role in WSSV-resistance phenomena were partially identified. Allelic data of 1,694 samples from nine distinct geographic locations in India were revealed that populations from Digha and Kochi were highly dispersed, and also showed higher genetic diversity, higher population diversity, and lower prevalence of disease resistance. A very high level of gene flow was observed within all populations and a very high level of genetic variation was present within populations. Two genetically admixture population clusters were estimated in nature. WSSV-resistance has a significant link with genetic diversity, population cluster and population diversity. Microsatellite marker analysis characterized genetic divergence, diversity and structure among wild populations.
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Affiliation(s)
- Debabrata Mondal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India
| | - Sourav Dutta
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India
| | - Usri Chakrabarty
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India
| | - Ajoy Mallik
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India; Department of Zoology, Dinabandhu Mahavidyalaya, Bongaon, North 24 Parganas, West Bengal, India
| | - Nripendranath Mandal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India.
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Guppy JL, Jones DB, Jerry DR, Wade NM, Raadsma HW, Huerlimann R, Zenger KR. The State of " Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization. Front Genet 2018; 9:282. [PMID: 30123237 PMCID: PMC6085479 DOI: 10.3389/fgene.2018.00282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.
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Affiliation(s)
- Jarrod L. Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - David B. Jones
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Dean R. Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Nicholas M. Wade
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Aquaculture Program, CSIRO Agriculture & Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Herman W. Raadsma
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Roger Huerlimann
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Kyall R. Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
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Torrecilla Z, Martínez-Lage A, Perina A, González-Ortegón E, González-Tizón AM. Comparative cytogenetic analysis of marine Palaemon species reveals a X 1X 1X 2X 2/X 1X 2Y sex chromosome system in Palaemon elegans. Front Zool 2017; 14:47. [PMID: 29046707 PMCID: PMC5639736 DOI: 10.1186/s12983-017-0233-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/02/2017] [Indexed: 12/01/2022] Open
Abstract
Background The maintenance of species and the promotion of speciation are closely related to chromosomal rearrangements throughout evolution. Decapoda represents the most species-rich order among crustaceans and, despite its ecological and economic importance, little is known about decapod karyology. We aim at cytogenetically characterizing two sympatric prawn species. Results Analysis of mitotic metaphases and meiotic diakinesis of the common prawn Palaemon serratus and the rockpool prawn P. elegans, revealed considerable differences between their karyotypes including chromosome numbers and sex determination systems. The cytogenetic data for P. serratus showed a diploid number of 56 and the putative absence of heteromorphic sex chromosomes. However, the diploid chromosome number in P. elegans was 90 for females and 89 for males. The karyotype of the females consisted of the three largest acrocentric pairs and 42 submetacentric and metacentric pairs, while the karyotype of the males comprised a clearly identifiable large metacentric chromosome and two acrocentric pairs as well as the smaller 42 pairs. These results highlight the presence of the X1X1X2X2/X1X2Y multiple sex chromosome system in P. elegans, which constitute the only sexual system for Decapoda reported cytogenetically using modern techniques. The origin of this sex chromosome system is discussed. We hypothesize that the chromosome evolution within the genus could involve several fusion events giving rise to a reduction on the chromosome number in P. serratus. In both species, the major ribosomal genes were located in two chromosome pairs and hybridization signals of the telomeric sequences (TTAGGG)n were visualized at the telomeres of all chromosomes. C-banding revealed that, when present, constitutive heterochromatin had a predominantly telomeric distribution and no centromeric constitutive heterochromatin was observed. Conclusions Although more comparative cytogenetic analyses are needed to clarify our hypotheses, the findings of this work indicate that the prawns of the genus Palaemon represent a promising model among Decapoda representatives to investigate the karyotype evolution and the patterns of sex chromosome differentiation.
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Affiliation(s)
- Zeltia Torrecilla
- Grupo de Investigación en Biología Evolutiva (GIBE), Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira, 15071 A Coruña, Spain
| | - Andrés Martínez-Lage
- Grupo de Investigación en Biología Evolutiva (GIBE), Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira, 15071 A Coruña, Spain
| | - Alejandra Perina
- Grupo de Investigación en Biología Evolutiva (GIBE), Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira, 15071 A Coruña, Spain
| | - Enrique González-Ortegón
- Instituto de Ciencias Marinas de Andalucía (ICMAN, CSIC), Campus Universitario Río San Pedro, 11510 Puerto Real, Cádiz, Spain.,International Campus of Excellence of the Sea (CEI-MAR), Edificio Hospital Real, 11003 Cádiz, Spain
| | - Ana M González-Tizón
- Grupo de Investigación en Biología Evolutiva (GIBE), Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira, 15071 A Coruña, Spain
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11
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Taju G, Madan N, Abdul Majeed S, Kumar TR, Thamizhvanan S, Otta SK, Sahul Hameed AS. Immune responses of whiteleg shrimp, Litopenaeus vannamei (Boone, 1931), to bacterially expressed dsRNA specific to VP28 gene of white spot syndrome virus. JOURNAL OF FISH DISEASES 2015; 38:451-465. [PMID: 24917208 DOI: 10.1111/jfd.12256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/07/2014] [Accepted: 04/16/2014] [Indexed: 06/03/2023]
Abstract
In this study, dsRNA specific to VP28 gene of white spot syndrome virus (WSSV) of shrimp was synthesized in Escherichia coli in large scale and studied the immune response of shrimp to dsRNA-VP28. The haematological parameters such as clotting time and total haemocytes counts, and immunological parameters such as prophenoloxidase (proPO), superoxide dismutase (SOD), superoxide anion (SOA) and malondialdehyde content, as well as the mRNA expression of ten immune-related genes were examined to estimate the effect of dsRNA-VP28 on the innate immunity of Litopenaeus vannamei. The activities of proPO, SOA and SOD significantly increased in haemocyte after dsRNA-VP28 treatment, whereas MDA content did not change significantly. Among the ten immune-related genes examined, only the mRNA expression of proPO, cMnSOD, haemocyanin, crustin, BGBP, lipopolysaccharides (LPs), lectin and lysozyme in haemocytes, gill and hepatopancreas of L. vannamei, was significantly upregulated at 12 h after dsRNA-VP28 treatment, while no significant expression changes were observed in Toll receptor and tumour receptor genes. The increase of proPO and SOD activities, and SOA level and mRNA expression level of proPO, cMnSOD, haemocyanin, crustin, BGBP, LPs, lectin and lysozyme after dsRNA-VP28 stimulation indicate that these immune-related genes were involved in dsRNA-VP28-induced innate immunity in shrimp.
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Affiliation(s)
- G Taju
- OIE Reference Laboratory for WTD, PG & Research Department of Zoology, C. Abdul Hakeem College, Melvisharam, Vellore District, Tamilnadu, India
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12
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Zhang Q, Liu Q, Liu S, Yang H, Liu S, Zhu L, Yang B, Jin J, Ding L, Wang X, Liang Y, Wang Q, Huang J. A new nodavirus is associated with covert mortality disease of shrimp. J Gen Virol 2014; 95:2700-2709. [DOI: 10.1099/vir.0.070078-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new nodavirus, named covert mortality nodavirus (CMNV), is associated with covert mortality disease of shrimp which has caused serious loss in China since 2009. Histopathological examination of shrimp suffering the disease revealed coagulative necrosis of striated muscle similar to typical histopathology features of infectious myonecrosis virus (IMNV), Penaeus vannamei nodavirus (PvNV) and Macrobrachium rosenbergii nodavirus (MrNV). However, shrimp suffering this disease tested negative for IMNV, MrNV and PvNV by reverse transcription (RT)-PCR. Additionally, eosinophilic inclusions were found in epithelium of the tubules in the hepatopancreas and lymphoid organ, and mass karyopyknotic nuclei existed in the muscle and lymphoid organ. The tubular epithelium of the hepatopancreas showed significant atrophy. A cDNA library was constructed from total RNA of infected shrimp. Sequencing and alignment analysis showed that one clone with an 1185 bp insert (designated CMNV-7) shared 54 , 53 and 39 % identity with the amino acid sequences of RNA-dependent RNA polymerase from Flock House virus, black beetle virus and MrNV. The results of fluorescence in situ hybridization showed that the hepatopancreas, striated muscle and lymphoid organ were positively reacting tissues. The mean size of negative-stained virus particles was 32 nm. In addition, a nested RT-PCR assay was developed for CMNV, and the RT-PCR detection results revealed that Fenneropenaeus chinensis, Litopenaeus vannamei and Marsupenaeus japonicus suffering from this disease were CMNV-positive.
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Affiliation(s)
- Qingli Zhang
- National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Qun Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Shuang Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Haolin Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Sun Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Luoluo Zhu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Bing Yang
- National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Jiting Jin
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Lixue Ding
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Xiuhua Wang
- National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Yan Liang
- National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Qintao Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
| | - Jie Huang
- National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China
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13
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Andriantahina F, Liu X, Feng T, Xiang J. Current status of genetics and genomics of reared penaeid shrimp: information relevant to access and benefit sharing. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:399-412. [PMID: 23529408 DOI: 10.1007/s10126-013-9500-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 01/16/2013] [Indexed: 06/02/2023]
Abstract
At present, research and progress in shrimp genomics and genetics show significant developments. Shrimp genetics and genomics also show immense potential for an increased production in a way that meets shrimp culture progress goals for the third millennium. This review article aims to provide an overview of its current status and future direction, discusses questions that need focused research to address them, and summarizes areas where genetics and genomics knowledge can make a positive difference to shrimp culture sustainability. Sustainable progress of penaeid shrimps will depend upon feasible solutions for environmental, research, economic, consumer problems, proper development, and planning policy enforcement. It is recommended that increased funding for biotechnology research and progress be directed to expand worldwide commercial shrimp culture and address environmental and public health issues. For any researcher or shrimp company member who has attempted to or whom would like to thoroughly search the literature to gain a complete understanding of the current state of shrimp genetics and genomics, this publication will be an invaluable source of reference materials, some of which is reported here for the first time.
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Affiliation(s)
- Farafidy Andriantahina
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
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Tassanakajon A, Somboonwiwat K, Supungul P, Tang S. Discovery of immune molecules and their crucial functions in shrimp immunity. FISH & SHELLFISH IMMUNOLOGY 2013; 34:954-967. [PMID: 23059654 DOI: 10.1016/j.fsi.2012.09.021] [Citation(s) in RCA: 277] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/21/2012] [Accepted: 09/24/2012] [Indexed: 06/01/2023]
Abstract
Several immune-related molecules in penaeid shrimps have been discovered, most of these via the analysis of expressed sequence tag libraries, microarray studies and proteomic approaches. These immune molecules include antimicrobial peptides, serine proteinases and inhibitors, phenoloxidases, oxidative enzymes, clottable protein, pattern recognition proteins, lectins, Toll receptors, and other humoral factors that might participate in the innate immune system of shrimps. These molecules have mainly been found in the hemolymph and hemocytes, which are the main sites where immune reactions take place, while some are found in other immune organs/tissues, such as the lymphoid organs, gills and intestines. Although the participation of some of these immune molecules in the shrimp innate immune defense against invading pathogens has been demonstrated, the functions of many molecules remain unclear. This review summarizes the current status of our knowledge concerning the discovery and functional characterization of the immune molecules in penaeid shrimps.
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Affiliation(s)
- Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand.
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15
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Trasviña-Arenas CH, Garcia-Triana A, Peregrino-Uriarte AB, Yepiz-Plascencia G. White shrimp Litopenaeus vannamei catalase: Gene structure, expression and activity under hypoxia and reoxygenation. Comp Biochem Physiol B Biochem Mol Biol 2013; 164:44-52. [DOI: 10.1016/j.cbpb.2012.10.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 11/28/2022]
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16
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Koyama T, Asakawa S, Katagiri T, Shimizu A, Fagutao FF, Mavichak R, Santos MD, Fuji K, Sakamoto T, Kitakado T, Kondo H, Shimizu N, Aoki T, Hirono I. Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus. BMC Genomics 2010; 11:141. [PMID: 20187930 PMCID: PMC2838849 DOI: 10.1186/1471-2164-11-141] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 02/26/2010] [Indexed: 11/30/2022] Open
Abstract
Background Higher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library. We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome. Results Mj024A04 BAC clone, which includes one redundant sequence, contained 27 putative genes and seemed to display a normal genomic DNA structure. Notably, of the putative genes, 3 genes encode homologous proteins to the inhibitor of apoptosis protein and 7 genes encode homologous proteins to white spot syndrome virus, a virulent pathogen known to affect crustaceans. Colony hybridization and PCR analysis of 381 BAC clones showed that almost half of the BAC clones maintain DNA segments whose sequences are homologous to the representative BAC clone Mj024A04. The Mj024A04 partial sequence was detected multiple times in the kuruma shrimp nuclear genome with a calculated copy number of at least 100. Microsatellites based BAC genotyping clearly showed that Mj024A04 homologous sequences were cloned from at least 48 different chromosomal loci. The absence of micro-syntenic relationships with the available genomic sequences of Daphnia and Drosophila suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences. Conclusions Our results demonstrate that hyper-expansion of large DNA segments took place in the kuruma shrimp genome. Although we analyzed only a part of the duplicated DNA segments, our result suggested that it is difficult to analyze the shrimp genome following normal analytical methodology. Hence, it is necessary to avoid repetitive sequence (such as segmental duplications) when studying the other unique structures in the shrimp genome.
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Affiliation(s)
- Takashi Koyama
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
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Du ZQ, Ciobanu DC, Onteru SK, Gorbach D, Mileham AJ, Jaramillo G, Rothschild MF. A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. Anim Genet 2009; 41:286-94. [PMID: 19968647 DOI: 10.1111/j.1365-2052.2009.02002.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r(2)), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r(2) increased with decreasing inter-marker distance from approximately 80 cm, and increased more rapidly from approximately 30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.
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Affiliation(s)
- Z-Q Du
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
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Piednoël M, Bonnivard E. DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms. BMC Evol Biol 2009; 9:86. [PMID: 19400949 PMCID: PMC2685390 DOI: 10.1186/1471-2148-9-86] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 04/28/2009] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. Considering their mutational abilities, TEs can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. DIRS1-like retrotransposons are a particular group of retrotransposons according to their mode of transposition that implies a tyrosine recombinase. To date, they have been described in a restricted number of species in comparison with the LTR retrotransposons. In this paper, we determine the distribution of DIRS1-like elements among 25 decapod species, 10 of them living in hydrothermal vents that correspond to particularly unstable environments. RESULTS Using PCR approaches, we have identified 15 new DIRS1-like families in 15 diverse decapod species (shrimps, lobsters, crabs and galatheid crabs). Hydrothermal organisms show a particularly great diversity of DIRS1-like elements with 5 families characterized among Alvinocarididae shrimps and 3 in the galatheid crab Munidopsis recta. Phylogenic analyses show that these elements are divergent toward the DIRS1-like families previously described in other crustaceans and arthropods and form a new clade called AlDIRS1. At larger scale, the distribution of DIRS1-like retrotransposons appears more or less patchy depending on the taxa considered. Indeed, a scattered distribution can be observed in the infraorder Brachyura whereas all the species tested in infraorders Caridea and Astacidea harbor some DIRS1-like elements. CONCLUSION Our results lead to nearly double both the number of DIRS1-like elements described to date, and the number of species known to harbor these ones. In this study, we provide the first degenerate primers designed to look specifically for DIRS1-like retrotransposons. They allowed for revealing for the first time a widespread distribution of these elements among a large phylum, here the order Decapoda. They also suggest some peculiar features of these retrotransposons in hydrothermal organisms where a great diversity of elements is already observed. Finally, this paper constitutes the first essential step which allows for considering further studies based on the dynamics of the DIRS1-like retrotransposons among several genomes.
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Affiliation(s)
- Mathieu Piednoël
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie Paris 6, Case 5, Bâtiment A, porte 427, 7 quai St Bernard, 75252 Paris Cedex 05, France
| | - Eric Bonnivard
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie Paris 6, Case 5, Bâtiment A, porte 427, 7 quai St Bernard, 75252 Paris Cedex 05, France
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Hizer SE, Tamulis WG, Robertson LM, Garcia DK. Evidence of multiple retrotransposons in two litopenaeid species. Anim Genet 2008; 39:363-73. [PMID: 18557973 DOI: 10.1111/j.1365-2052.2008.01739.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes. The impact of the varied types of retrotransposons on these genomes is just beginning to be deciphered. In a step towards understanding their role in litopenaeid shrimp, we have herein identified nine non-LTR retrotransposons, among which several appear to exist outside the standard defined clades. Two Litopenaeus stylirostris elements were discovered through degenerate PCR amplification using previously defined non-LTR degenerate primers, and through primers designed from a RAPD-derived sequence. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. In silico searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains found in our PCR-derived sequences. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group that included five of our nine sequences. This group, which included elements from both L. stylirostris and L. vannamei, appeared most closely related to the highly active RTE clade. Our remaining four sequences placed in the CR1 and I clades of retrotransposons, with one showing strong similarity to ancient Penelope elements. This research describes three newly discovered retrotransposons in the L. stylirostris genome. Phylogenetic analysis clusters these in a monophyletic grouping with retrotransposons previously described from two closely related species, L. vannamei and Penaeus monodon.
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Affiliation(s)
- S E Hizer
- Department of Biological Sciences, California State University, San Marcos, CA 920296, USA
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Sarathi M, Simon MC, Venkatesan C, Hameed ASS. Oral administration of bacterially expressed VP28dsRNA to protect Penaeus monodon from white spot syndrome virus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2008; 10:242-249. [PMID: 18202890 DOI: 10.1007/s10126-007-9057-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/13/2007] [Accepted: 09/27/2007] [Indexed: 05/25/2023]
Abstract
We explored the possibility of protecting Penaeus monodon against white spot syndrome virus (WSSV) infection via interference RNA technology by oral administration of bacterially expressed WSSV VP28dsRNA. Shrimp were given dsRNA orally via two methods. In the first method, pellet feed was coated with inactivated bacteria containing overexpressed dsRNA of the WSSV VP28 gene, and in the second method, pellet feed was coated with VP28dsRNA-chitosan complex nanoparticles. The treated shrimp were orally challenged with WSSV by feeding WSSV-infected tissue. The experiment was conducted for 30 days. The dsRNA-treated shrimp challenged with WSSV showed higher survival compared to control shrimp. Sixty-eight percent survival was observed in shrimp fed with feed coated with inactivated bacteria containing dsRNA of the WSSV VP28 gene whereas 37% survival was observed in shrimp fed with VP28dsRNA-chitosan complex nanoparticle-coated feed. The WSSV caused 100% mortality in shrimp fed with pellet feed coated with inactivated bacteria with empty LITMUS38i vector. At the end of the experiment, the tissue samples prepared from randomly selected shrimp that survived were analyzed via reverse transcriptase-polymerase chain reaction and Western blot analysis for WSSV. The samples were negative for WSSV. Based on the present data and the advantages of dsRNA, we believe that oral administration of crude extract of bacterially expressed VP28dsRNA is a potential therapeutic agent against WSSV infection of shrimp.
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Affiliation(s)
- M Sarathi
- Aquaculture Biotechnology Division, Department of Zoology, C. Abdul Hakeem College, Melvisharam -632 509, Vellore Dist., Tamil Nadu, India
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Sellars MJ, Lyons RE, Grewe PM, Vuocolo T, Leeton L, Coman GJ, Degnan BM, Preston NP. A PL10 vasa-like gene in the kuruma shrimp, Marsupenaeus japonicus, expressed during development and in adult gonad. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:377-87. [PMID: 17375354 DOI: 10.1007/s10126-007-6118-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Accepted: 01/15/2007] [Indexed: 05/14/2023]
Abstract
A PL10 vasa-like gene was isolated from the Kuruma shrimp Marsupenaeus japonicus and therefore called Mjpl10. It is differentially expressed during embryonic, larval, and postlarval development, and in female and male gonads. Using absolute real-time reverse transcriptase-polymerase chain reaction (RT-PCR), we demonstrate that Mjpl10 transcripts are present in the two-cell embryo, suggesting it is maternally expressed, and continually at low levels throughout embryogenesis. Mjpl10 expression increases significantly in the first 25 h after hatching (nauplii IV) and then decreases in a linear fashion by 316-fold over the next 52-day period. Its continued expression throughout embryonic and larval development is compatible with a conserved role in early germ cell specification. Transcript levels of Mjpl10 are also detected in the ovary and testes of mature adults.
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Affiliation(s)
- Melony J Sellars
- CSIRO Food Futures National Research Flagship, 5 Julius Avenue, North Ryde, NSW 2113, Australia.
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