PUBLICACIONES
En esta sección podrá consultar todas las publicaciones en las que
participa FUCOBI
participa FUCOBI
The FUCOBI Foundation contributed to a recent publication by our collaborator, Dr. Acacia Alcivar-Warren. The results are part of ‘The Shrimp Epigenome (ShrimpENCODE) Project’ of FUCOBI’s program ‘UNA SALUD / ONE HEALTH Epigenomics and Microbiomes: Somos lo que comemos / We are what we eat’
Bao W, Tang KFJ, Alcivar-Warren A. 2020. The Complete Genome of an Endogenous Nimavirus (Nimav-1_LVa) From the Pacific Whiteleg Shrimp Penaeus (Litopenaeus) Vannamei. Genes (Basel). 2020 Jan 14;11(1). pii: E94. doi: 10.3390/genes11010094.
Author information
Bao W1, Tang KFJ2, Alcivar-Warren A3,4.
1 Genetic Information Research Institute (GIRI), 20380 Town Center Lane, Suite 240, Cupertino, CA 95014, USA.
2 Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China.
3 Fundación para la Conservation de la Biodiversidad Acuática y Terrestre (FUCOBI), Quito EC1701, Ecuador.
4 Environmental Genomics Inc. (EGI), ONE HEALTH Epigenomics Educational Initiative, P. O. Box 196, Southborough, MA 01772, USA.
Bao W1, Tang KFJ2, Alcivar-Warren A3,4.
1 Genetic Information Research Institute (GIRI), 20380 Town Center Lane, Suite 240, Cupertino, CA 95014, USA.
2 Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China.
3 Fundación para la Conservation de la Biodiversidad Acuática y Terrestre (FUCOBI), Quito EC1701, Ecuador.
4 Environmental Genomics Inc. (EGI), ONE HEALTH Epigenomics Educational Initiative, P. O. Box 196, Southborough, MA 01772, USA.
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.
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.
Important information for the shrimp aquaculture industry worldwide: availability of a differential diagnostic tool useful for international trade certification and OIE regulations
Through a partnership with EGI and GIRI, we are helping to develop a diagnostic tool to differentiate the infectious WSSV virus from the non-infectious endogenous nimavirus (previously called DNAV-1_LVa and WSSV-EVE). This differential diagnostics tool will be valuable to the shrimp aquaculture industry worldwide for international trade health certification and compliance with OIE regulations.
Other publications by Dr. Alcivar-Warren and FUCOBI collaborators (highlighted)
Peer-reviewed publications:
Zhang X, Yuan J, Sun Y, Li S, Gao Y, Yu Y, Liu C, Wang Q, Lv X, Zhang X, Ma KY, Wang X, Lin W, Wang L, Zhu X, Zhang C, Zhang J, Jin S, Yu K, Kong J, Xu P, Chen J, Zhang H, Sorgeloos P, Sagi A, Alcivar-Warren A, Liu Z, Wang L, Ruan J, Chu KH, Liu B, Li F, Xiang J. Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nat Commun. 2019 Jan 21;10(1):356. doi: 10.1038/s41467-018-08197-4.
Aquaculture Genomics, Genetics and Breeding Workshop, Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, et al. 2017. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics. 2017 Feb 20;18(1):191. doi: 10.1186/s12864-017-3557-1. Review. Erratum in: BMC Genomics. 2017 Mar 16;18(1):235.
Alcivar-Warren A., Meehan-Meola D., Park S. W., Xu Z., Delaney M., Zuniga G. (2007). ShrimpMap: A low-density, microsatellite-based linkage map of the pacific whiteleg shrimp, Litopenaeus vannamei: Identification of sex-linked markers in linkage group 4. J. Shellfish Res. 26, 1259–1277.
Alcivar-Warren A., Xu Z., Meehan D., Zuniga G., Bell K. (2003). Over 150 polymorphic microsatellite markers available for parentage testing, pedigree tracing, genetic diversity and genome mapping of the Pacific White Shrimp, Penaeus (Litopenaeus) vannamei, in Aquaculture America (Louisville, KY: ).
Alcivar-Warren A, Meehan-Meola D, Wang Y, Guo X, Zhou L, Xiang J, Moss S, Arce S, Warren W, Xu Z, Bell K. 2006. Isolation and Mapping of Telomeric Pentanucleotide (TAACC)n Repeats of the Pacific Whiteleg Shrimp, Penaeus vannamei, Using Fluorescence In Situ Hybridization. Mar Biotechnol (NY) 8(5):467–480. doi: 10.1007/s10126-005-6031-z. Erratum in: Mar Biotechnol (NY). 2006 Nov-Dec;8(6):697-8.
Reville, C., Al-Beik, J., Meehan-Meola, D., Xu, Z., Goldsmith, M.L., Rand, W. and Alcivar-Warren, A. 2005. White Spot Syndrome Virus in Frozen Shrimp Sold at Massachusetts Supermarkets. J. Shellfish Res. 24 (1), 285-290.
Alcivar-Warren A, Overstreet RM, Dhar AK, Astrofsky K, Carr WH, Sweeney J, Lotz JM. Genetic susceptibility of cultured shrimp (Penaeus vannamei) to infectious hypodermal and hematopoietic necrosis virus and Baculovirus penaei: possible relationship with growth status and metabolic gene expression. J Invertebr Pathol. 1997;70(3):190–197. doi: 10.1006/jipa.1997.4692.
Alcivar-Warren A, Trasler JM, Awoniyi CA, Zirkin BR, Hecht NB. 1996. Differential expression of ornithine decarboxylase, poly(ADP)ribose polymerase, and mitochondrial mRNAs following testosterone administration to hypophysectomized rats.Mol Reprod Dev. 1996 Mar;43(3):283-9.
Dhar AK, Thompson MS, Paradis MR, Alcivar-Warren A. 2000. Determination of the cDNA sequence and mRNA expression of interleukin-1 receptor antagonist in horses. Am J Vet Res. 2000 Aug;61(8):920-4.
Eaton JK, Alcivar-Warren A, Kenny JE. 2012. Multidimensional fluorescence fingerprinting for classification of shrimp by location and species. Environ Sci Technol. 2012 Feb 21;46(4):2276-82. doi: 10.1021/es2037542. Epub 2012 Feb 9.
Garcia DK., Faggart MA., Rhoades L., Alcivar-Warren AA, Wyban JA, Carr WH, Sweeney JN, Ebert KM. 1994. Genetic diversity of cultured Penaeus vannamei shrimp using three molecular genetic techniques. Mol. Mar. Biol. Biotechnol. 3, 270–280.
Garcia DK, Dhar AK, Alcivar-Warren A. 1996. Molecular analysis of a RAPD marker (B20) reveals two microsatellites and differential mRNA expression in Penaeus vannamei. Mol Mar Biol Biotechnol. 1996 Mar;5(1):71-83.
Jue K, Benoit G, Alcivar-Warren AA, Trasler JM. 1995. Developmental and hormonal regulation of DNA methyltransferase in the rat testis. Biol Reprod. 1995 Jun;52(6):1364-71.
Meehan D, Xu Z, Zuniga G, Alcivar-Warren A. 2003. High frequency and large number of polymorphic microsatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei [Crustacea:Decapoda]. Mar Biotechnol (NY). 2003 Jul-Aug;5(4):311-30.
Pascual I, Dhar AK, Fan Y, Paradis MR, Arruga MV, Alcivar-Warren A. 2002. Isolation of expressed sequence tags from a Thoroughbred horse (Equus caballus) 5'-RACE cDNA library. Anim Genet. 2002 Jun;33(3):231-2.
Xu Z, Dhar AK, Wyrzykowski J, Alcivar-Warren A. 1888. Identification of abundant and informative microsatellites from shrimp (Penaeus monodon) genome. Anim Genet. 1999 Apr;30(2):150-6.
Xu Z., Primavera J. H., de la Pena L. D., Pettit P., Belak J., Alcivar-Warren A. 2001. Genetic diversity of wild and cultured black tiger shrimp (Penaeus monodon) in the Philippines using microsatellites. Aquaculture 199, 13–40.
Abstracts presented at ‘The Shrimp Epigenome (ShrimpENCODE) sessions and ‘ONE HEALTH Epigenomics and Microbiomes: From Soil to People’ workshops,co-chaired by Dr. Acacia Alcivar-Warren and Dr. Kathy Tang, at the annual meetings of the National Shellfisheries Association (NSA) from 2018 to 2020 (https://www.shellfish.org/publications-resources-public):
110th Annual Meeting, Seattle, Washington, March 2018 (this is not a citeable document)
111th Annual Meeting, New Orleans, Louisiana (Triennial), February 2019 available soon
112th Annual Meeting, Baltimore, Maryland (cancelled), March/April 2020 (this is not a citeable document)
Zhang X, Yuan J, Sun Y, Li S, Gao Y, Yu Y, Liu C, Wang Q, Lv X, Zhang X, Ma KY, Wang X, Lin W, Wang L, Zhu X, Zhang C, Zhang J, Jin S, Yu K, Kong J, Xu P, Chen J, Zhang H, Sorgeloos P, Sagi A, Alcivar-Warren A, Liu Z, Wang L, Ruan J, Chu KH, Liu B, Li F, Xiang J. Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nat Commun. 2019 Jan 21;10(1):356. doi: 10.1038/s41467-018-08197-4.
Aquaculture Genomics, Genetics and Breeding Workshop, Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, et al. 2017. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics. 2017 Feb 20;18(1):191. doi: 10.1186/s12864-017-3557-1. Review. Erratum in: BMC Genomics. 2017 Mar 16;18(1):235.
Alcivar-Warren A., Meehan-Meola D., Park S. W., Xu Z., Delaney M., Zuniga G. (2007). ShrimpMap: A low-density, microsatellite-based linkage map of the pacific whiteleg shrimp, Litopenaeus vannamei: Identification of sex-linked markers in linkage group 4. J. Shellfish Res. 26, 1259–1277.
Alcivar-Warren A., Xu Z., Meehan D., Zuniga G., Bell K. (2003). Over 150 polymorphic microsatellite markers available for parentage testing, pedigree tracing, genetic diversity and genome mapping of the Pacific White Shrimp, Penaeus (Litopenaeus) vannamei, in Aquaculture America (Louisville, KY: ).
Alcivar-Warren A, Meehan-Meola D, Wang Y, Guo X, Zhou L, Xiang J, Moss S, Arce S, Warren W, Xu Z, Bell K. 2006. Isolation and Mapping of Telomeric Pentanucleotide (TAACC)n Repeats of the Pacific Whiteleg Shrimp, Penaeus vannamei, Using Fluorescence In Situ Hybridization. Mar Biotechnol (NY) 8(5):467–480. doi: 10.1007/s10126-005-6031-z. Erratum in: Mar Biotechnol (NY). 2006 Nov-Dec;8(6):697-8.
Reville, C., Al-Beik, J., Meehan-Meola, D., Xu, Z., Goldsmith, M.L., Rand, W. and Alcivar-Warren, A. 2005. White Spot Syndrome Virus in Frozen Shrimp Sold at Massachusetts Supermarkets. J. Shellfish Res. 24 (1), 285-290.
Alcivar-Warren A, Overstreet RM, Dhar AK, Astrofsky K, Carr WH, Sweeney J, Lotz JM. Genetic susceptibility of cultured shrimp (Penaeus vannamei) to infectious hypodermal and hematopoietic necrosis virus and Baculovirus penaei: possible relationship with growth status and metabolic gene expression. J Invertebr Pathol. 1997;70(3):190–197. doi: 10.1006/jipa.1997.4692.
Alcivar-Warren A, Trasler JM, Awoniyi CA, Zirkin BR, Hecht NB. 1996. Differential expression of ornithine decarboxylase, poly(ADP)ribose polymerase, and mitochondrial mRNAs following testosterone administration to hypophysectomized rats.Mol Reprod Dev. 1996 Mar;43(3):283-9.
Dhar AK, Thompson MS, Paradis MR, Alcivar-Warren A. 2000. Determination of the cDNA sequence and mRNA expression of interleukin-1 receptor antagonist in horses. Am J Vet Res. 2000 Aug;61(8):920-4.
Eaton JK, Alcivar-Warren A, Kenny JE. 2012. Multidimensional fluorescence fingerprinting for classification of shrimp by location and species. Environ Sci Technol. 2012 Feb 21;46(4):2276-82. doi: 10.1021/es2037542. Epub 2012 Feb 9.
Garcia DK., Faggart MA., Rhoades L., Alcivar-Warren AA, Wyban JA, Carr WH, Sweeney JN, Ebert KM. 1994. Genetic diversity of cultured Penaeus vannamei shrimp using three molecular genetic techniques. Mol. Mar. Biol. Biotechnol. 3, 270–280.
Garcia DK, Dhar AK, Alcivar-Warren A. 1996. Molecular analysis of a RAPD marker (B20) reveals two microsatellites and differential mRNA expression in Penaeus vannamei. Mol Mar Biol Biotechnol. 1996 Mar;5(1):71-83.
Jue K, Benoit G, Alcivar-Warren AA, Trasler JM. 1995. Developmental and hormonal regulation of DNA methyltransferase in the rat testis. Biol Reprod. 1995 Jun;52(6):1364-71.
Meehan D, Xu Z, Zuniga G, Alcivar-Warren A. 2003. High frequency and large number of polymorphic microsatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei [Crustacea:Decapoda]. Mar Biotechnol (NY). 2003 Jul-Aug;5(4):311-30.
Pascual I, Dhar AK, Fan Y, Paradis MR, Arruga MV, Alcivar-Warren A. 2002. Isolation of expressed sequence tags from a Thoroughbred horse (Equus caballus) 5'-RACE cDNA library. Anim Genet. 2002 Jun;33(3):231-2.
Xu Z, Dhar AK, Wyrzykowski J, Alcivar-Warren A. 1888. Identification of abundant and informative microsatellites from shrimp (Penaeus monodon) genome. Anim Genet. 1999 Apr;30(2):150-6.
Xu Z., Primavera J. H., de la Pena L. D., Pettit P., Belak J., Alcivar-Warren A. 2001. Genetic diversity of wild and cultured black tiger shrimp (Penaeus monodon) in the Philippines using microsatellites. Aquaculture 199, 13–40.
Abstracts presented at ‘The Shrimp Epigenome (ShrimpENCODE) sessions and ‘ONE HEALTH Epigenomics and Microbiomes: From Soil to People’ workshops,co-chaired by Dr. Acacia Alcivar-Warren and Dr. Kathy Tang, at the annual meetings of the National Shellfisheries Association (NSA) from 2018 to 2020 (https://www.shellfish.org/publications-resources-public):
110th Annual Meeting, Seattle, Washington, March 2018 (this is not a citeable document)
111th Annual Meeting, New Orleans, Louisiana (Triennial), February 2019 available soon
112th Annual Meeting, Baltimore, Maryland (cancelled), March/April 2020 (this is not a citeable document)
Abstracts presented at ‘The Shrimp Epigenome (ShrimpENCODE) sessions and ‘ONE HEALTH Epigenomics and Microbiomes: From Soil to People’ workshops,co-chaired by Dr. Acacia Alcivar-Warren and Dr. Kathy Tang, at the annual meetings of the National Shellfisheries Association (NSA) from 2018 to 2020
Abstracts presented at the World Aquaculture Society meetings from 1993 to 2016 available soon, at sessions chaired by Dr. Acacia Alcivar-Warren.
Characterization of 35 new microsatellite genetic markers for the Pacific whiteleg shrimp, litopenaeus vannamei: their usefulness for Studying genetic diversity of wild and cultured stocks, tracing Pedigree in breeding programs, and linkage mapping proyecto UNSA SALUD / ONE HEALTH
Characterization and Mapping of Expressed Sequence Tags Isolated from a Subtracted Cdna Library Of Litopenaeus Vannamei Injected With White Spot Syndrome Virus
High frequency and large number of polymorphic Microsatellites in cultured shrimp, Penaeus (litopenaeus) vannamei [crustacea:decapoda]
Contributions To The International Marine Shrimp Environmental Genomics Initiative (Imsegi): Monitoring Ecosystem, Animals And Public Health, 2000–2006
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