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Incardona JP, Linbo TL, French BL, Cameron J, Peck KA, Laetz CA, Hicks MB, Hutchinson G, Allan SE, Boyd DT, Ylitalo GM, Scholz NL. Low-level embryonic crude oil exposure disrupts ventricular ballooning and subsequent trabeculation in Pacific herring. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 235:105810. [PMID: 33823483 DOI: 10.1016/j.aquatox.2021.105810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/18/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
There is a growing awareness that transient, sublethal embryonic exposure to crude oils cause subtle but important forms of delayed toxicity in fish. While the precise mechanisms for this loss of individual fitness are not well understood, they involve the disruption of early cardiogenesis and a subsequent pathological remodeling of the heart much later in juveniles. This developmental cardiotoxicity is attributable, in turn, to the inhibitory actions of crude oil-derived mixtures of polycyclic aromatic compounds (PACs) on specific ion channels and other proteins that collectively drive the rhythmic contractions of heart muscle cells via excitation-contraction coupling. Here we exposed Pacific herring (Clupea pallasi) embryos to oiled gravel effluent yielding ΣPAC concentrations as low as ~ 1 μg/L (64 ng/g in tissues). Upon hatching in clean seawater, and following the depuration of tissue PACs (as evidenced by basal levels of cyp1a gene expression), the ventricles of larval herring hearts showed a concentration-dependent reduction in posterior growth (ballooning). This was followed weeks later in feeding larvae by abnormal trabeculation, or formation of the finger-like projections of interior spongy myocardium, and months later with hypertrophy (overgrowth) of the spongy myocardium in early juveniles. Given that heart muscle cell differentiation and migration are driven by Ca2+-dependent intracellular signaling, the observed disruption of ventricular morphogenesis was likely a secondary (downstream) consequence of reduced calcium cycling and contractility in embryonic cardiomyocytes. We propose defective trabeculation as a promising phenotypic anchor for novel morphometric indicators of latent cardiac injury in oil-exposed herring, including an abnormal persistence of cardiac jelly in the ventricle wall and cardiomyocyte hyperproliferation. At a corresponding molecular level, quantitative expression assays in the present study also support biomarker roles for genes known to be involved in muscle contractility (atp2a2, myl7, myh7), cardiomyocyte precursor fate (nkx2.5) and ventricular trabeculation (nrg2, and hbegfa). Overall, our findings reinforce both proximal and indirect roles for dysregulated intracellular calcium cycling in the canonical fish early life stage crude oil toxicity syndrome. More work on Ca2+-mediated cellular dynamics and transcription in developing cardiomyocytes is needed. Nevertheless, the highly specific actions of ΣPAC mixtures on the heart at low, parts-per-billion tissue concentrations directly contravene classical assumptions of baseline (i.e., non-specific) crude oil toxicity.
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Affiliation(s)
- John P Incardona
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA.
| | - Tiffany L Linbo
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Barbara L French
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - James Cameron
- Earth Resources Technology, under contract to Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Karen A Peck
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Cathy A Laetz
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Mary Beth Hicks
- Oregon State University, Cooperative Institute for Marine Resources Studies, Hatfield Marine Science Center, Newport, OR, USA
| | - Greg Hutchinson
- Oregon State University, Cooperative Institute for Marine Resources Studies, Hatfield Marine Science Center, Newport, OR, USA
| | - Sarah E Allan
- National Oceanic and Atmospheric Administration, Office of Response and Restoration, Anchorage, AK, USA
| | - Daryle T Boyd
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Gina M Ylitalo
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Nathaniel L Scholz
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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Chou CH, Huang HY, Huang WC, Hsu SD, Hsiao CD, Liu CY, Chen YH, Liu YC, Huang WY, Lee ML, Chen YC, Huang HD. The aquatic animals' transcriptome resource for comparative functional analysis. BMC Genomics 2018; 19:103. [PMID: 29764375 PMCID: PMC5954267 DOI: 10.1186/s12864-018-4463-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. Results To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. Conclusion In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/. Electronic supplementary material The online version of this article (10.1186/s12864-018-4463-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsi-Yuan Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli, 320, Taiwan
| | - Chia-Yu Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Hung Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Chen Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Yun Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Meng-Lin Lee
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yi-Chang Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
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3
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Bich Vo TT. Identification and analysis of snps in population of Vietnamese catfish (pangasianodon hypophthalmus), using next generation sequencing and snp validation. ACTA ACUST UNITED AC 2018. [DOI: 10.15406/mojcrr.2018.01.00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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4
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Froehlich HE, Roberts SB, Essington TE. Evaluating hypoxia-inducible factor-1α mRNA expression in a pelagic fish, Pacific herring Clupea pallasii, as a biomarker for hypoxia exposure. Comp Biochem Physiol A Mol Integr Physiol 2015; 189:58-66. [DOI: 10.1016/j.cbpa.2015.07.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/28/2015] [Accepted: 07/28/2015] [Indexed: 11/29/2022]
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Raymond JA. Two potential fish glycerol-3-phosphate phosphatases. FISH PHYSIOLOGY AND BIOCHEMISTRY 2015; 41:811-818. [PMID: 25832176 DOI: 10.1007/s10695-015-0048-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/28/2015] [Indexed: 06/04/2023]
Abstract
Winter-acclimated rainbow smelt (Osmerus mordax Mitchill) produce high levels of glycerol as an antifreeze. A common pathway to glycerol involves the enzyme glycerol-3-phosphate phosphatase (GPP), but no GPP has yet been identified in fish or any other animal. Here, two phosphatases assembled from existing EST libraries (from winter-acclimated smelt and cold-acclimated smelt hepatocytes) were found to resemble a glycerol-associated phosphatase from a glycerol-producing alga, Dunaliella salina, and a recently discovered GPP from a bacterium, Mycobacterium tuberculosis. Recombinant proteins were generated and were found to have GPP activity on the order of a few μMol Pi/mg enzyme/min. The two enzymes have acidic pH optima (~5.5) similar to that previously determined for GPP activity in liver tissue, with about 1/3 of their peak activities at neutral pH. The two enzymes appear to account for the GPP activity of smelt liver, but due to their reduced activities at neutral pH, their contributions to glycerol production in vivo remain unclear. Similar enzymes may be active in a glycerol-producing insect, Dendroctonus ponderosae.
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Affiliation(s)
- James A Raymond
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA,
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6
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Huang LK, Yan HD, Zhao XX, Zhang XQ, Wang J, Frazier T, Yin G, Huang X, Yan DF, Zang WJ, Ma X, Peng Y, Yan YH, Liu W. Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerataL.) through transcriptome analysis. Mol Ecol Resour 2015; 15:1497-509. [DOI: 10.1111/1755-0998.12418] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/08/2015] [Accepted: 04/15/2015] [Indexed: 11/29/2022]
Affiliation(s)
- L. K. Huang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - H. D. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. X. Zhao
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. Q. Zhang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - J. Wang
- Agronomy Department; University of Florida; Gainesville FL 32611 USA
| | - T. Frazier
- Department of Horticulture; Virginia Tech; Blacksburg VA 24061 USA
| | - G. Yin
- Department of Crop, Soil, and Environmental Sciences; University of Arkansas; Fayetteville AR 72704 USA
| | - X. Huang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - D. F. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - W. J. Zang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. Ma
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - Y. Peng
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - Y. H. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - W. Liu
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
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Hemmer-Hansen J, Therkildsen NO, Pujolar JM. Population genomics of marine fishes: next-generation prospects and challenges. THE BIOLOGICAL BULLETIN 2014; 227:117-132. [PMID: 25411371 DOI: 10.1086/bblv227n2p117] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the past few years, technological advances have facilitated giant leaps forward in our ability to generate genome-wide molecular data, offering exciting opportunities for gaining new insights into the ecology and evolution of species where genomic information is still limited. Marine fishes are valuable organisms for advancing our understanding of evolution on historical and contemporary time scales, and here we highlight areas in which research on these species is likely to be particularly important in the near future. These include possibilities for gaining insights into processes on ecological time scales, identifying genomic signatures associated with population divergence under gene flow, and determining the genetic basis of phenotypic traits. We also consider future challenges pertaining to the implementation of genome-wide coverage through next-generation sequencing and genotyping methods in marine fishes. Complications associated with fast decay of linkage disequilibrium, as expected for species with large effective population sizes, and the possibility that adaptation is associated with both soft selective sweeps and polygenic selection, leaving complex genomic signatures in natural populations, are likely to challenge future studies. However, the combination of high genome coverage and new statistical developments offers promising solutions. Thus, the next generation of studies is likely to truly facilitate the transition from population genetics to population genomics in marine fishes. This transition will advance our understanding of basic evolutionary processes and will offer new possibilities for conservation and management of valuable marine resources.
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Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark;
| | | | - José Martin Pujolar
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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Emmenegger EJ, Glenn JA, Winton JR, Batts WN, Gregg JL, Hershberger PK. Molecular identification of erythrocytic necrosis virus (ENV) from the blood of Pacific herring (Clupea pallasii). Vet Microbiol 2014; 174:16-26. [PMID: 25263493 DOI: 10.1016/j.vetmic.2014.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/05/2014] [Accepted: 08/26/2014] [Indexed: 10/24/2022]
Abstract
Viral erythrocytic necrosis (VEN) is a condition affecting the red blood cells of more than 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. Among populations of Pacific herring (Clupea pallasii) on the west coast of North America the disease causes anemia and elevated mortality in periodic epizootics. Presently, VEN is diagnosed by observation of typical cytoplasmic inclusion bodies in stained blood smears from infected fish. The causative agent, erythrocytic necrosis virus (ENV), is unculturable and a presumed iridovirus by electron microscopy. In vivo amplification of the virus in pathogen-free laboratory stocks of Pacific herring with subsequent virus concentration, purification, DNA extraction, and high-throughput sequencing were used to obtain genomic ENV sequences. Fragments with the highest sequence identity to the family Iridoviridae were used to design four sets of ENV-specific polymerase chain reaction (PCR) primers. Testing of blood and tissue samples from experimentally and wild infected Pacific herring as well as DNA extracted from other amphibian and piscine iridoviruses verified the assays were specific to ENV with a limit of detection of 0.0003 ng. Preliminary phylogenetic analyses of a 1448 bp fragment of the putative DNA polymerase gene supported inclusion of ENV in a proposed sixth genus of the family Iridoviridae that contains other erythrocytic viruses from ectothermic hosts. This study provides the first molecular evidence of ENV's inclusion within the Iridoviridae family and offers conventional PCR assays as a means of rapidly surveying the ENV-status of wild and propagated Pacific herring stocks.
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Affiliation(s)
- Eveline J Emmenegger
- U.S. Geological Survey, Western Fisheries Research Center (WFRC), 6505 NE 65th St., Seattle, WA 98115, USA.
| | - Jolene A Glenn
- U.S. Geological Survey, Western Fisheries Research Center (WFRC), 6505 NE 65th St., Seattle, WA 98115, USA
| | - James R Winton
- U.S. Geological Survey, Western Fisheries Research Center (WFRC), 6505 NE 65th St., Seattle, WA 98115, USA
| | - William N Batts
- U.S. Geological Survey, Western Fisheries Research Center (WFRC), 6505 NE 65th St., Seattle, WA 98115, USA
| | - Jacob L Gregg
- U.S. Geological Survey, WFRC, Marrowstone Marine Field Station, 616 Marrowstone Point Road, Nordland, WA 98358, USA
| | - Paul K Hershberger
- U.S. Geological Survey, WFRC, Marrowstone Marine Field Station, 616 Marrowstone Point Road, Nordland, WA 98358, USA
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9
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Wang J, Qi H, Li L, Que H, Wang D, Zhang G. Discovery and validation of genic single nucleotide polymorphisms in the Pacific oyster Crassostrea gigas. Mol Ecol Resour 2014; 15:123-35. [PMID: 24823694 DOI: 10.1111/1755-0998.12278] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 12/01/2022]
Abstract
The economic and ecological importance of the oyster necessitates further research on the molecular mechanisms, which both regulate the commercially important traits of the oyster and help it to survive in the variable marine environment. Single nucleotide polymorphisms (SNPs) have been widely used to assess genetic variation and identify genes underlying target traits. In addition, high-resolution melting (HRM) analysis is a potentially powerful method for validating candidate SNPs. In this study, we adopted a rapid and efficient pipeline for the screening and validation of SNPs in the genic region of Crassostrea gigas based on transcriptome sequencing and HRM analysis. Transcriptomes of three wild oyster populations were sequenced using Illumina sequencing technology. In total, 50-60 million short reads, corresponding to 4.5-5.4 Gbp, from each population were aligned to the oyster genome, and 5.8 × 10(5) SNPs were putatively identified, resulting in a predicted SNP every 47 nucleotides on average. The putative SNPs were unevenly distributed in the genome and high-density (≥2%), nonsynonymous coding SNPs were enriched in genes related to apoptosis and responses to biotic stimuli. Subsequently, 1,671 loci were detected by HRM analysis, accounting for 64.7% of the total selected candidate primers, and finally, 1,301 polymorphic SNP markers were developed based on HRM analysis. All of the validated SNPs were distributed into 897 genes and located in 672 scaffolds, and 275 of these genes were stress inducible under unfavourable salinity, temperature, and exposure to air and heavy metals. The validated SNPs in this study provide valuable molecular markers for genetic mapping and characterization of important traits in oysters.
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Affiliation(s)
- Jiafeng Wang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Affiliated Hospital of Guangdong Medical College, Guangdong, 524001, China
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10
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Zhu G, Zhong D, Cao J, Zhou H, Li J, Liu Y, Bai L, Xu S, Wang MH, Zhou G, Chang X, Gao Q, Yan G. Transcriptome profiling of pyrethroid resistant and susceptible mosquitoes in the malaria vector, Anopheles sinensis. BMC Genomics 2014; 15:448. [PMID: 24909924 PMCID: PMC4070547 DOI: 10.1186/1471-2164-15-448] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 05/28/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Anopheles sinensis is a major malaria vector in China and other Southeast Asian countries, and it is becoming increasingly resistant to the insecticides used for agriculture, net impregnation, and indoor residual spray. Very limited genomic information on this species is available, which has hindered the development of new tools for resistance surveillance and vector control. We used the 454 GS FLX system and generated expressed sequence tag (EST) databases of various life stages of An. sinensis, and we determined the transcriptional differences between deltamethrin resistant and susceptible mosquitoes. RESULTS The 454 GS FLX transcriptome sequencing yielded a total of 624,559 reads (average length of 290 bp) with the pooled An. sinensis mosquitoes across various development stages. The de novo assembly generated 33,411 contigs with average length of 493 bp. A total of 8,057 ESTs were generated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. A total of 2,131 ESTs were differentially expressed between deltamethrin resistant and susceptible mosquitoes collected from the same field site in Jiangsu, China. Among these differentially expressed ESTs, a total of 294 pathways were mapped to the KEGG database, with the predominant ESTs belonging to metabolic pathways. Furthermore, a total of 2,408 microsatellites and 15,496 single nucleotide polymorphisms (SNPs) were identified. CONCLUSIONS The annotated EST and transcriptome databases provide a valuable genomic resource for further genetic studies of this important malaria vector species. The differentially expressed ESTs associated with insecticide resistance identified in this study lay an important foundation for further functional analysis. The identified microsatellite and SNP markers will provide useful tools for future population genetic and comparative genomic analyses of malaria vectors.
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Affiliation(s)
- Guoding Zhu
- />Department of Parasitology, Medical College of Soochow University, Suzhou, 215123 PR China
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Daibin Zhong
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Jun Cao
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Huayun Zhou
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Julin Li
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Yaobao Liu
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Liang Bai
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Sui Xu
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Mei-Hui Wang
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Guofa Zhou
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Xuelian Chang
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Qi Gao
- />Department of Parasitology, Medical College of Soochow University, Suzhou, 215123 PR China
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Guiyun Yan
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
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11
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Effect of photosynthetic bacteria on water quality and microbiota in grass carp culture. World J Microbiol Biotechnol 2014; 30:2523-31. [DOI: 10.1007/s11274-014-1677-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 05/24/2014] [Indexed: 10/25/2022]
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Gomez-Uchida D, Seeb LW, Warheit KI, McKinney GJ, Seeb JE. Deep sequencing of the transcriptome and mining of single nucleotide polymorphisms (SNPs) provide genomic resources for applied studies in Chinook salmon (Oncorhynchus tshawytscha). CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0235-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhang J, Ruhlman TA, Mower JP, Jansen RK. Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. BMC PLANT BIOLOGY 2013; 13:228. [PMID: 24373163 PMCID: PMC3880972 DOI: 10.1186/1471-2229-13-228] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/20/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum. RESULTS Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional. CONCLUSIONS The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition, results indicated no major improvements in breadth of coverage with data sets larger than six billion nucleotides or when sampling RNA from four tissue types rather than from a single tissue. Finally, this work demonstrates the power of cross-compartmental genomic analyses to deepen our understanding of the correlated evolution of the nuclear, plastid, and mitochondrial genomes in plants.
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Affiliation(s)
- Jin Zhang
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Robert K Jansen
- Department of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 205 W. 24th St. Stop C0930, Austin, TX 78712, USA
- Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Bilyk KT, Cheng CHC. Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki. BMC Genomics 2013; 14:634. [PMID: 24053439 PMCID: PMC3856495 DOI: 10.1186/1471-2164-14-634] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 06/26/2013] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Among the cold-adapted Antarctic notothenioid fishes, the high-latitude bald notothen Pagothenia borchgrevinki is particularly notable as the sole cryopelagic species, exploiting the coldest and iciest waters of the Southern Ocean. Because P. borchgrevinki is a frequent model for investigating notothenioid cold-adaptation and specialization, it is imperative that "omic" tools be developed for this species. In the absence of a sequenced genome, a well annotated reference transcriptome of the bald notothen will serve as a model of gene expression in the coldest and harshest of all polar marine environments, useful for future comparative studies of cold adaptation and thermal responses in polar teleosts and ectotherms. RESULTS We sequenced and annotated a reference transcriptome for P. borchgrevinki, with added attention to capturing the transcriptional responses to acute and chronic heat exposures. We sequenced by Roche 454 a normalized cDNA library constructed from pooled mRNA encompassing multiple tissues taken from environmental, warm acclimating, and acute heat stressed specimens. The resulting reads were assembled into 42,620 contigs, 17,951 of which could be annotated. We utilized this annotated portion of the reference transcriptome to map short Illumina reads sequenced from the gill and liver of environmental specimens, and also compared the gene expression profiles of these two tissue transcriptomes with those from the temperate model fish Danio rerio. From this, we identified a conserved group of 58 GO terms, in which terms related to transcription and its regulation, ubiquitin-protein ligase activity, protein ubiquitination, and protein binding among others are more prevalent in the bald notothen, suggesting the pertinent genes play essential roles in cold temperature functioning. CONCLUSION We sequenced multiple tissue transcriptomes from native and heat-exposed experimental specimens of the high Antarctic, cryopelagic notothenioid P. borchgrevinki to construct a reference transcriptome. In a proof of concept, we utilized the annotated reference transcriptome to profile the gene expression patterns of gill and liver, and identified a suite of over and under-represented GO terms when compared to the tropical water zebrafish suggesting these functions may be important for surviving in freezing waters. The transcriptome resource from this study will aid future investigations of cold adaptation and thermal response of polar ectothermic species.
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Affiliation(s)
- Kevin T Bilyk
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, 515 Morrill Hall, 505 South Goodwin Ave., Urbana, IL 61801, USA
- Current Address: College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucenghuan Rd, Shanghai 201306, China
| | - C-H Christina Cheng
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, 515 Morrill Hall, 505 South Goodwin Ave., Urbana, IL 61801, USA
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15
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SNP discovery in European anchovy (Engraulis encrasicolus, L) by high-throughput transcriptome and genome sequencing. PLoS One 2013; 8:e70051. [PMID: 23936375 PMCID: PMC3731364 DOI: 10.1371/journal.pone.0070051] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/13/2013] [Indexed: 11/29/2022] Open
Abstract
Increased throughput in sequencing technologies has facilitated the acquisition of detailed genomic information in non-model species. The focus of this research was to discover and validate SNPs derived from the European anchovy (Engraulis encrasicolus) transcriptome, a species with no available reference genome, using next generation sequencing technologies. A cDNA library was constructed from four tissues of ten fish individuals corresponding to three populations of E. encrasicolus, and Roche 454 GS FLX Titanium sequencing yielded 19,367 contigs. Additionally, the European anchovy genome was sequenced for the same ten individuals using an Illumina HiSeq2000. Using a computational pipeline for combining transcriptome and genome information, a total of 18,994 SNPs met the necessary minor allele frequency and depth filters. A series of further stringent filters were applied to identify those SNPs likely to succeed in genotyping assays, and for filtering of those in potential duplicated genome regions. A novel method for detecting potential intron-exon boundaries in areas of putative SNPs has also been applied in silico to improve genotyping success. In all, 2,317 filtered putative transcriptome SNPs suitable for genotyping primer design were identified. From those, a subset of 530 were selected, with the genotyping results showing the highest reported conversion and validation rates (91.3% and 83.2%, respectively) reported to date for a non-model species. This study represents a promising strategy to discover genotypable SNPs in the exome of non-model organisms. The genomic resource generated for E. encrasicolus, both in terms of sequences and novel markers, will be informative for research into this species with applications including traceability studies, population genetic analyses and aquaculture.
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16
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Zhou ZC, Dong Y, Sun HJ, Yang AF, Chen Z, Gao S, Jiang JW, Guan XY, Jiang B, Wang B. Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers. Mol Ecol Resour 2013; 14:127-38. [PMID: 23855518 DOI: 10.1111/1755-0998.12147] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/23/2013] [Accepted: 06/25/2013] [Indexed: 11/30/2022]
Abstract
Sea cucumber (Apostichopus japonicus) is an ecologically and economically important species in East and South-East Asia. This project aimed to identify large numbers of gene-associated markers and differentially expressed genes (DEGs) after lipopolysaccharides (LPS) challenge in A. japonicus using high-throughput transcriptome sequencing. A total of 162 million high-quality reads of 174 million raw reads were obtained by deep sequencing using Illumina HiSeq™ 2000 platform. Assembly of these reads generated 94 704 unigenes, with read length ranging from 200 to 16 153 bp (average length of 810 bp). A total of 36 005 were identified as coding sequences (CDSs), 32 479 of which were successfully annotated. Based on the assembly transcriptome, we identified 142 511 high-quality single nucleotide polymorphisms (SNPs). Among them, 33 775, 63 120 and 45 616 were located in sequences without predicted CDS (non-CDSs), CDSs and untranslated regions (UTRs), respectively. These putative SNPs included 82 664 transitions and 59 847 transversions. Totally, 89 375 (59.1%) were distributed in 15 473 known genes. A total of 6417 microsatellites were detected in 5970 unigenes, 3216 of which were annotated and 2481 were successfully subjected for primer design. The numbers of simple sequence repeats (SSRs) identified in non-CDSs, CDSs and UTRs were 2367, 2316 and 1734. These potential SNPs and SSRs are expected to provide abundant resources for genetic, evolutionary and ecological studies in sea cucumber. Transcriptome comparison revealed 1330, 1347 and 1291 DEGs in the coelomocytes of A. japonicus at 4 h, 24 h and 72 h after LPS challenge, respectively. Approximately 58.4% (1802) of total DEGs have been successfully annotated.
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Affiliation(s)
- Z C Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
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17
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Zhang X, Fu L, Deng B, Liang Q, Zheng J, Sun J, Zhu H, Peng L, Wang Y, Wenying S, Li W. Bacillus subtilis SC02 supplementation causes alterations of the microbial diversity in grass carp water. World J Microbiol Biotechnol 2013; 29:1645-53. [DOI: 10.1007/s11274-013-1327-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/18/2013] [Indexed: 10/27/2022]
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Corander J, Majander KK, Cheng L, Merilä J. High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Mol Ecol 2013; 22:2931-40. [PMID: 23294045 DOI: 10.1111/mec.12174] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 11/01/2012] [Accepted: 11/06/2012] [Indexed: 12/27/2022]
Abstract
Marine fish species are characterized by a low degree of population differentiation at putatively neutral marker genes. This has been traditionally attributed to ecological homogeneity and a lack of obvious dispersal barriers in marine habitats, as well as to the large (effective) population sizes of most marine fish species. The herring (Clupea harengus) is a case in point - the levels of population differentiation at neutral markers, even across vast geographic areas, are typically very low (FST ≈ 0.005). We used a RAD-sequencing approach to identify 5985 novel single-nucleotide polymorphism markers (SNPs) in herring and estimated genome-wide levels of divergence using pooled DNA samples between two Baltic Sea populations separated by 387 km. We found a total of 4756 divergent SNPs (79% of all SNPs) between the populations, of which 117 showed evidence of substantial divergence, corresponding to F(ST) = 0.128 (0.125, 0.131) after accounting for possible biases due to minor alleles and uneven DNA amplification over the pooled samples. This estimate - based on screening many genomic polymorphisms - suggests the existence of hitherto unrecognized levels of genetic differentiation in this commercially important species, challenging the view of genetic homogeneity in marine fish species, and in that of the Baltic Sea herring in particular.
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Affiliation(s)
- Jukka Corander
- Department of Mathematics and Statistics, University Helsinki, FI-00014, Helsinki, Finland
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Timmins‐Schiffman EB, Friedman CS, Metzger DC, White SJ, Roberts SB. Genomic resource development for shellfish of conservation concern. Mol Ecol Resour 2012; 13:295-305. [DOI: 10.1111/1755-0998.12052] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/16/2012] [Accepted: 11/20/2012] [Indexed: 01/23/2023]
Affiliation(s)
| | - Carolyn S. Friedman
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Dave C. Metzger
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Samuel J. White
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Steven B. Roberts
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
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Speller CF, Hauser L, Lepofsky D, Moore J, Rodrigues AT, Moss ML, McKechnie I, Yang DY. High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation. PLoS One 2012; 7:e51122. [PMID: 23226474 PMCID: PMC3511397 DOI: 10.1371/journal.pone.0051122] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 10/29/2012] [Indexed: 11/21/2022] Open
Abstract
Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation.
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Affiliation(s)
- Camilla F. Speller
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Archaeology, University of York, University of York, Heslington, York, United Kingdom
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Dana Lepofsky
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jason Moore
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Antonia T. Rodrigues
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Madonna L. Moss
- Department of Anthropology, University of Oregon, Eugene, Oregon, United States of America
| | - Iain McKechnie
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dongya Y. Yang
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
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Graham LA, Li J, Davidson WS, Davies PL. Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes. BMC Evol Biol 2012; 12:190. [PMID: 23009612 PMCID: PMC3499448 DOI: 10.1186/1471-2148-12-190] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/20/2012] [Indexed: 12/26/2022] Open
Abstract
Background Type II antifreeze protein (AFP) from the rainbow smelt, Osmerus mordax, is a calcium-dependent C-type lectin homolog, similar to the AFPs from herring and sea raven. While C-type lectins are ubiquitous, type II AFPs are only found in a few species in three widely separated branches of teleost fishes. Furthermore, several other non-homologous AFPs are found in intervening species. We have previously postulated that this sporadic distribution has resulted from lateral gene transfer. The alternative hypothesis, that the AFP evolved from a lectin present in a shared ancestor and that this gene was lost in most species, is not favored because both the exon and intron sequences are highly conserved. Results Here we have sequenced and annotated a 160 kb smelt BAC clone containing a centrally-located AFP gene along with 14 other genes. Quantitative PCR indicates that there is but a single copy of this gene within the smelt genome, which is atypical for fish AFP genes. The corresponding syntenic region has been identified and searched in a number of other species and found to be devoid of lectin or AFP sequences. Unlike the introns of the AFP gene, the intronic sequences of the flanking genes are not conserved between species. As well, the rate and pattern of mutation in the AFP gene are radically different from those seen in other smelt and herring genes. Conclusions These results provide stand-alone support for an example of lateral gene transfer between vertebrate species. They should further inform the debate about genetically modified organisms by showing that gene transfer between ‘higher’ eukaryotes can occur naturally. Analysis of the syntenic regions from several fishes strongly suggests that the smelt acquired the AFP gene from the herring.
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Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
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