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Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii). Genes (Basel) 2023; 14:genes14030620. [PMID: 36980892 PMCID: PMC10048070 DOI: 10.3390/genes14030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Simple sequence repeats (SSRs), the markers with the highest polymorphism and co-dominance degrees, offer a crucial genetic research resource. Limited SSR markers in blackhead seabream have been reported. The availability of the blackhead seabream genome assembly provided the opportunity to carry out genome-wide identification for all microsatellite markers, and bioinformatic analyses open the way for developing a microsatellite genome-wide database in blackhead seabream. In this study, a total of 412,381 SSRs were identified in the 688.08 Mb genome by Krait software. Whole-genome sequences (10×) of 42 samples were aligned against the reference genome and genotyped using the HipSTR tools by comparing and counting repeat number variation across the SSR loci. A total of 156,086 SSRs with a 2–4 bp repeat were genotyped by HipSTR tools, which accounted for 55.78% of the 2–4 bp SSRs in the reference genome. High accuracy of genotyping was observed by comparing HipSTR tools and PCR amplification. A set of 109,131 loci with a number of alleles ≥ 3 and with a number of genotyped individuals ≥ 6 were reserved to constitute the polymorphic SSR database. Fifty-one polymorphic SSR loci were identified through PCR amplification. This strategy to develop polymorphic SSR markers not only obtained a large set of polymorphic SSRs but also eliminated the need for laborious experimental screening. SSR markers developed in this study may facilitate blackhead seabream research, which lays a certain foundation for further gene tagging and genetic linkage analysis, such as marker-assisted selection, genetic mapping, as well as comparative genomic analysis.
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Nie Z, Ren Y, Zhang L, Ge R, Wei J. Analysis of Population Genetic Diversity and Genetic Structure of Schizothorax biddulphi Based on 20 Newly Developed SSR Markers. Front Genet 2022; 13:908367. [PMID: 35769984 PMCID: PMC9234283 DOI: 10.3389/fgene.2022.908367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 11/23/2022] Open
Abstract
To protect the germplasm resources of Schizothorax biddulphi, we developed and used 20 pairs of polymorphic microsatellite primers to analyze the genetic diversity and structure of populations. A total of 126 samples were collected from the Qarqan River (CEC), Kizil River (KZL), and Aksu River (AKS) in Xinjiang, China. The results showed that 380 alleles were detected in 20 pairs of primers and the average number of alleles was 19.0. The effective allele numbers and Nei’s gene diversity ranged from 1.1499 to 1.1630 and 0.0962 to 0.1136, respectively. The Shannon index range suggested low levels of genetic diversity in all populations. The genetic distance between the CEC and AKS populations was the largest, and the genetic similarity was the smallest. There was a significant genetic differentiation between CEC and the other two populations. The UPGMA clustering tree was constructed based on population genetic distance, and the clustering tree constructed by individuals showed that the AKS population and KZL population were clustered together, and the CEC population was clustered separately. Also, the group structure analysis also got the same result. It can be seen that although the three populations of S. biddulphi do not have high genetic diversity, the differentiation between the populations was high and the gene flow was limited, especially the differentiation between the CEC population and the other two populations. This study not only provided genetic markers for the research of S. biddulphi but the results of this study also suggested the need for enhanced management of S. biddulphi populations.
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Affiliation(s)
- Zhulan Nie
- College of Animal Science and Technology, Tarim University, Alar, China
- Key Laboratory of Tarim Animal Husbandry and Science Technology of Xinjiang Production and Construction Corps., Alar, China
- State Key Laboratory Breeding Base of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Crops and Ministry of Science and Technology, Alar, China
- College of Life Science, Tarim University, Alar, China
| | - Yongli Ren
- College of Animal Science and Technology, Tarim University, Alar, China
- Key Laboratory of Tarim Animal Husbandry and Science Technology of Xinjiang Production and Construction Corps., Alar, China
- State Key Laboratory Breeding Base of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Crops and Ministry of Science and Technology, Alar, China
| | - Lirong Zhang
- Key Laboratory of Tarim Animal Husbandry and Science Technology of Xinjiang Production and Construction Corps., Alar, China
- State Key Laboratory Breeding Base of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Crops and Ministry of Science and Technology, Alar, China
- College of Life Science, Tarim University, Alar, China
| | - Rui Ge
- Key Laboratory of Tarim Animal Husbandry and Science Technology of Xinjiang Production and Construction Corps., Alar, China
- State Key Laboratory Breeding Base of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Crops and Ministry of Science and Technology, Alar, China
- College of Life Science, Tarim University, Alar, China
| | - Jie Wei
- College of Animal Science and Technology, Tarim University, Alar, China
- Key Laboratory of Tarim Animal Husbandry and Science Technology of Xinjiang Production and Construction Corps., Alar, China
- State Key Laboratory Breeding Base of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Crops and Ministry of Science and Technology, Alar, China
- College of Life Science, Tarim University, Alar, China
- *Correspondence: Jie Wei,
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Development of Disease-Resistance-Associated Microsatellite DNA Markers for Selective Breeding of Tilapia (Oreochromis spp.) Farmed in Taiwan. Genes (Basel) 2021; 13:genes13010099. [PMID: 35052439 PMCID: PMC8774982 DOI: 10.3390/genes13010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 12/13/2022] Open
Abstract
There are numerous means to improve the tilapia aquaculture industry, and one is to develop disease resistance through selective breeding using molecular markers. In this study, 11 disease-resistance-associated microsatellite markers including 3 markers linked to hamp2, 4 linked to hamp1, 1 linked to pgrn2, 2 linked to pgrn1, and 1 linked to piscidin 4 (TP4) genes were established for tilapia strains farmed in Taiwan after challenge with Streptococcus inae. The correlation analysis of genotypes and survival revealed a total of 55 genotypes related to survival by the chi-square and Z-test. Although fewer markers were found in B and N2 strains compared with A strain, they performed well in terms of disease resistance. It suggested that this may be due to the low potency of some genotypes and the combinatorial arrangement between them. Therefore, a predictive model was built by the genotypes of the parental generation and the mortality rate of different combinations was calculated. The results show the same trend of predicted mortality in the offspring of three new disease-resistant strains as in the challenge experiment. The present findings is a nonkilling method without requiring the selection by challenge with bacteria or viruses and might increase the possibility of utilization of selective breeding using SSR markers in farms.
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Maduna SN, Vivian-Smith A, Jónsdóttir ÓDB, Imsland AKD, Klütsch CFC, Nyman T, Eiken HG, Hagen SB. Genome- and transcriptome-derived microsatellite loci in lumpfish Cyclopterus lumpus: molecular tools for aquaculture, conservation and fisheries management. Sci Rep 2020; 10:559. [PMID: 31953426 PMCID: PMC6968997 DOI: 10.1038/s41598-019-57071-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.
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Affiliation(s)
- Simo N Maduna
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway.
| | - Adam Vivian-Smith
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Forestry and Forest Resources, P.O. Box 115, NO-1431, Ås, Norway
| | | | - Albert K D Imsland
- Akvaplan-niva, Iceland Office, Akralind 4, 201, Kópavogur, Iceland.,Department of Biosciences, University of Bergen, 5020, Bergen, Norway
| | - Cornelya F C Klütsch
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Tommi Nyman
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Snorre B Hagen
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway.
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Song J, Li Q, Yu Y, Wan S, Han L, Du S. Mapping Genetic Loci for Quantitative Traits of Golden Shell Color, Mineral Element Contents, and Growth-Related Traits in Pacific Oyster (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:666-675. [PMID: 29931607 DOI: 10.1007/s10126-018-9837-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
Golden shell color and mineral content are important economic traits of Pacific oyster (Crassostrea gigas). In this study, we mapped a series of quantitative trait loci (QTLs) that control zinc (Zn) and magnesium (Mg) content, shell color and growth performance to two sex-averaged linkage maps from the FAM-A and FAM-B families. In total, ten QTLs were identified in seven linkage groups (LGs) in the FAM-B family, and seven QTLs were identified in four linkage groups in the FAM-A family. Two QTLs affecting the trait of golden shell color were identified in LG8 of the FAM-A and LG10 of the FAM-B families, which could explain 20.2 and 10.5% of the phenotypic variations, respectively. Two QTLs for Zn content were identified that could contribute to 17.9 and 34.44% of the phenotypic variations in FAM-A. Six QTLs for Zn and Mg contents were identified in four LGs (LG1, LG2, LG5, and LG9) in FAM-B, which explained 13.5-26.7% of the phenotypic variations. In addition, seven QTLs related to oyster growth were recognized in both FAM-A and FAM-B families accounting for 14.6-36.7% of the phenotypic variations. All of the DNA markers in QTL regions were blasted and 14 genes associated with above traits were identified. The mRNA expression of these genes was determined by quantitative RT-PCR. These QTLs and candidate genes could be used as potential targets for marker-assisted selection in C. gigas breeding.
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Affiliation(s)
- Junlin Song
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Qingdao Agricultural University, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Sai Wan
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lichen Han
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
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Yuan Z, Zhou T, Bao L, Liu S, Shi H, Yang Y, Gao D, Dunham R, Waldbieser G, Liu Z. The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus). PLoS One 2018; 13:e0197371. [PMID: 29763462 PMCID: PMC5953449 DOI: 10.1371/journal.pone.0197371] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 05/01/2018] [Indexed: 11/18/2022] Open
Abstract
Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposons are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalence of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported Xba elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions.
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Affiliation(s)
- Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Dongya Gao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Geoff Waldbieser
- USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, Mississippi, United States of America
| | - Zhanjiang Liu
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
- * E-mail:
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Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence. Sci Rep 2017; 7:40347. [PMID: 28079141 PMCID: PMC5228154 DOI: 10.1038/srep40347] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/05/2016] [Indexed: 02/02/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence. Here we also report linkage mapping using the 690 K array, which allowed mapping of over 250,000 SNPs on the linkage map, the highest marker density among all the constructed linkage maps. These markers were mapped to 29 linkage groups (LGs) with 30,591 unique marker positions. This linkage map anchored 1,602 scaffolds of the reference genome sequence to LGs, accounting for over 97% of the total genome assembly. A total of 1,007 previously unmapped scaffolds were placed to LGs, allowing validation and in few instances correction of the reference genome sequence assembly. This linkage map should serve as a valuable resource for various genetic and genomic analyses, especially for GWAS and QTL mapping for genes associated with economically important traits.
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CHEN MENG, GAO LINLIN, ZHANG WEIJIE, YOU HONGZHENG, SUN QIAN, CHANG YAQING. Identification of forty-five gene-derived polymorphic microsatellite loci for the sea cucumber, Apostichopus japonicus. J Genet 2016. [DOI: 10.1007/s12041-013-0234-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nakharuthai C, Areechon N, Srisapoome P. Molecular characterization, functional analysis, and defense mechanisms of two CC chemokines in Nile tilapia (Oreochromis niloticus) in response to severely pathogenic bacteria. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 59:207-228. [PMID: 26853931 DOI: 10.1016/j.dci.2016.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 02/03/2016] [Accepted: 02/03/2016] [Indexed: 06/05/2023]
Abstract
Two full-length cDNAs encoding CC chemokine genes in Nile tilapia (Oreochromis niloticus) (On-CC1 and On-CC2) were cloned and characterized. On-CC1 and On-CC2 showed signature cysteine motifs consisting of four cysteines. The expression levels of On-CC1 and On-CC2 were analyzed by RT-PCR, which showed that low expression of these two genes was only observed in the peripheral blood leukocytes (PBLs) and spleen of normal fish. Expression levels of these two molecules were quantified in 13 tissues of fish infected with virulent strains of Streptococcus agalactiae and Flavobacterium columnare. Most tissues, especially PBLs, the spleen and the liver, expressed significantly higher mRNA levels than the controls, particularly at 12 and 24 h after infection (P < 0.05). The current study strongly indicates that CC chemokine genes in Nile tilapia are crucially involved in the early immune responses to pathogens. Functional analyses clearly demonstrated that 10 and 100 μg/ml of recombinant rOn-CC1 and rOn-CC2 proteins efficiently enhanced the phagocytic activity (in vitro) of Nile tilapia phagocytes. Finally, Southern blot analysis and searching in Ensembl databases demonstrated that two different functional CC chemokine genes and other pseudogene fragments were discovered in the Nile tilapia genome.
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Affiliation(s)
- Chatsirin Nakharuthai
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Thailand; Center of Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
| | - Nontawith Areechon
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Thailand; Center of Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
| | - Prapansak Srisapoome
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Thailand; Center of Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand.
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Lee E, Kim SH, Kim BG, Yoon JT. Characterization of EST Gene in the Bovine Corpus Luteum during the Estrous Cycle. Dev Reprod 2016; 19:227-34. [PMID: 26973974 PMCID: PMC4786484 DOI: 10.12717/dr.2015.19.4.227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The objective of this study was to investigate the expression of bovine luteum expressed sequence tags (ESTs), vascular endothelial growth factor (VEGF), and tumor necrosis factor receptor 1 (TNFR1) and the presence of functional ESTs in the bovine corpus luteum (CL) during different stages of the estrus cycle. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed a difference in the expression of ESTs during the CL stage. Concentration of ESTs in the CL tissue increased significantly from the mid-luteal stage and decreased thereafter. RT-PCR analysis showed higher levels of the EST genes in the CL of the mid-luteal stage than in other stages, and the same level of expression of VEGF. Immunohistochemistry analysis of the tissue from CL formation to regression showed low cytosol and aggregation of the nucleus. And activity caspase 3 (apoptosis detector) was most strongly detected in the CL1 stage of bovine. During the estrous cycle, the cytosol was magnified and differentiation of the nucleus was clearly manifested. The ESTs affected the CL, and the relationship between VEGF and TNFR1 played a pivotal role for CL development and activation, dependent on the stage of CL. These results suggest local production of ESTs, the presence of functional ESTs in the bovine CL, and that ESTs play a role in regulating the function of cell death in bovine CL.
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Affiliation(s)
- Eunyoung Lee
- Dept. of Animal Life Science, Hankyong National University, Ansung 456-749, Korea
| | - Sang Hwan Kim
- Dept. of Animal Life Science, Hankyong National University, Ansung 456-749, Korea
| | - Byung-Gak Kim
- Dept. of Animal Life Science, Hankyong National University, Ansung 456-749, Korea
| | - Jong Taek Yoon
- Dept. of Animal Life Science, Hankyong National University, Ansung 456-749, Korea
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Xiao S, Han Z, Wang P, Han F, Liu Y, Li J, Wang ZY. Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing. PLoS One 2015; 10:e0124432. [PMID: 25909910 PMCID: PMC4409302 DOI: 10.1371/journal.pone.0124432] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/15/2015] [Indexed: 01/08/2023] Open
Abstract
Large yellow croaker (Larimichthys crocea) is an important economic fish in China and Eastern Asia. Because of the exhaustive fishing and overdense aquaculture, the wild population and the mariculture of the species are facing serious challenges on germplasm degeneration and susceptibility to infectious disease agents. However, a comprehensive transcriptome from multi-tissues of the species has not been reported and functional molecular markers have not yet been detected and analyzed. In this work, we applied RNA-seq with the Illumina Hiseq2000 platform for a multi-tissue sample of large yellow croaker and assembled the transcriptome into 88,103 transcripts. Of them, 52,782 transcripts have been successfully annotated by nt/nr, InterPro, GO and KEGG database. Comparing with public fish proteins, we have found that 34,576 protein coding transcripts are shared in large yellow croaker with zebrafish, medaka, pufferfish, and stickleback. For functional markers, we have discovered 1,276 polymorphic SSRs and 261, 000 SNPs. The functional impact analysis of SNPs showed that the majority (~75%) of small variants cause synonymous mutations in proteins, followed by variations in 3' UTR region. The functional enrichment analysis illuminated that transcripts involved in DNA bindings, enzyme activities, and signal pathways prominently exhibit less single-nucleotide variants but genes for the constituent of the muscular tissue, the cytoskeleton, and the immunity system contain more frequent SNP mutations, which may reflect the structural and functional selections of the translated proteins. This is the first work for the high-throughput detection and analysis of functional polymorphic SSR and SNP markers in a comprehensive transcriptome of large yellow croaker. Our study provides valuable transcript sequence and functional marker resources for the quantitative trait locus (QTL) identification and molecular selection of the species in the research community.
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Affiliation(s)
- Shijun Xiao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Zhaofang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Panpan Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Yang Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Jiongtang Li
- Chinese Academy of Fishery Sciences, Beijing, China
| | - Zhi Yong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
- * E-mail:
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12
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Geng X, Feng J, Liu S, Wang Y, Arias C, Liu Z. Transcriptional regulation of hypoxia inducible factors alpha (HIF-α) and their inhibiting factor (FIH-1) of channel catfish (Ictalurus punctatus) under hypoxia. Comp Biochem Physiol B Biochem Mol Biol 2013; 169:38-50. [PMID: 24384398 DOI: 10.1016/j.cbpb.2013.12.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/22/2013] [Accepted: 12/27/2013] [Indexed: 12/22/2022]
Abstract
Hypoxia inducible factors (HIFs) are considered to be the master switch of oxygen-dependent gene expression with mammalian species. In most cases, regulation of HIF has been believed at posttranslational levels. However, little is known of HIF regulation in channel catfish, a species highly tolerant to low oxygen condition. Here we report the identification and characterization of HIF-1α, HIF-2αa, HIF-2αb, HIF-3α, and FIH-1 genes, and their mRNA expression under hypoxia conditions. The transcripts of the five genes were found to be regulated temporally and spatially after low oxygen challenge, suggesting regulation of HIF-α genes at pre-translational levels. In most tissues, the HIF-α mRNAs were down-regulated 1.5h but up-regulated 5h after hypoxia treatment. Of these HIF-α mRNAs, the expression of HIF-3α mRNA was induced in the most dramatic fashion, both in the speed of induction and the extent of induction, compared to HIF-1α and HIF-2α genes, suggesting its importance in responses to hypoxia.
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Affiliation(s)
- Xin Geng
- Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Jianbin Feng
- Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Shikai Liu
- Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Yaping Wang
- Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Covadonga Arias
- Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA.
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Immunological role of C4 CC chemokine-1 from snakehead murrel Channa striatus. Mol Immunol 2013; 57:292-301. [PMID: 24231766 DOI: 10.1016/j.molimm.2013.10.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/09/2013] [Accepted: 10/15/2013] [Indexed: 11/22/2022]
Abstract
In this study, we have reported a cDNA sequence of C4 CC chemokine identified from snakehead murrel (also known as striped murrel) Channa striatus (named as CsCC-Chem-1) normalized cDNA library constructed by Genome Sequencing FLX™ Technology (GS-FLX™). CsCC-Chem-1 is 641 base pairs (bp) long that contain 438 bp open reading frame (ORF). The ORF encodes a polypeptide of 146 amino acids with a molecular mass of 15 kDa. The polypeptide contains a small cytokine domain at 30-88. The domain carries the CC motif at Cys(33)-Cys(34). In addition, CsCC-Chem-1 consists of another two cysteine residues at C(59) and C(73), which, together with C(33) and C(34), make CsCC-Chem-1 as a C4-CC chemokine. CsCC-Chem-1 also contains a 'TCCT' motif at 32-35 as CC signature motif; this new motif may represent new characteristic features, which may lead to some unknown function that needs to be further focused on. Phylogenitically, CsCC-Chem-1 clustered together with CC-Chem-1 from rock bream Oplegnathus fasciatus and European sea bass Dicentrarchus labrax. Significantly (P<0.05) highest gene expression was noticed in spleen and is up-regulated upon fungus (Aphanomyces invadans), bacteria (Aeromonas hydrophila) and virus (poly I:C) infection at various time points. The gene expression results indicate the influence of CsCC-Chem-1 in the immune system of murrel. Overall, the gene expression study showed that the CsCC-Chem-1 is a capable gene to increase the cellular response against various microbial infections. Further, we cloned the coding sequence of CsCC-Chem-1 in pMAL vector and purified the recombinant protein to study the functional properties. The cell proliferation activity of recombinant CsCC-Chem-1 protein showed a significant metabolic activity in a concentration dependent manner. Moreover, the chemotaxis assay showed the capability of recombinant CsCC-Chem-1 protein which can induce the migration of spleen leukocytes in C. striatus. However, this remains to be verified further at molecular and proteomic level.
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Zhang Y, Liu S, Lu J, Jiang Y, Gao X, Ninwichian P, Li C, Waldbieser G, Liu Z. Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements. BMC Genomics 2013; 14:387. [PMID: 23758806 PMCID: PMC3691659 DOI: 10.1186/1471-2164-14-387] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 05/24/2013] [Indexed: 12/02/2022] Open
Abstract
Background Comparative genomics is a powerful tool to transfer genomic information from model species to related non-model species. Channel catfish (Ictalurus punctatus) is the primary aquaculture species in the United States. Its existing genome resources such as genomic sequences generated from next generation sequencing, BAC end sequences (BES), physical maps, linkage maps, and integrated linkage and physical maps using BES-associated markers provide a platform for comparative genomic analysis between catfish and other model teleost fish species. This study aimed to gain understanding of genome organizations and similarities among catfish and several sequenced teleost genomes using linkage group 8 (LG8) as a pilot study. Results With existing genome resources, 287 unique genes were identified in LG8. Comparative genome analysis indicated that most of these 287 genes on catfish LG8 are located on two homologous chromosomes of zebrafish, medaka, stickleback, and three chromosomes of green-spotted pufferfish. Large numbers of conserved syntenies were identified. Detailed analysis of the conserved syntenies in relation to chromosome level similarities revealed extensive inter-chromosomal and intra-chromosomal rearrangements during evolution. Of the 287 genes, 35 genes were found to be duplicated in the catfish genome, with the vast majority of the duplications being interchromosomal. Conclusions Comparative genome analysis is a powerful tool even in the absence of a well-assembled whole genome sequence. In spite of sequence stacking due to low resolution of the linkage and physical maps, conserved syntenies can be identified although the exact gene order and orientation are unknown at present. Through chromosome-level comparative analysis, homologous chromosomes among teleosts can be identified. Syntenic analysis should facilitate annotation of the catfish genome, which in turn, should facilitate functional inference of genes based on their orthology.
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Affiliation(s)
- Yu Zhang
- Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, The Fish Molecular Genetics and Biotechnology Laboratory, Auburn University, Auburn, AL 36849, USA
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15
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Cardoso SD, Gonçalves D, Robalo JI, Almada VC, Canário AVM, Oliveira RF. Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats. Mar Genomics 2013; 11:11-6. [PMID: 23665344 DOI: 10.1016/j.margen.2013.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 12/12/2022]
Abstract
Transcriptome data are a good resource to develop microsatellites due to their potential in targeting candidate genes. However, developing microsatellites can be a time-consuming enterprise due to the numerous primer pairs to be tested. Therefore, the use of methodologies that make it efficient to identify polymorphic microsatellites is desirable. Here we used a 62,038 contigs transcriptome assembly, obtained from pyrosequencing a peacock blenny (Salaria pavo) multi-tissue cDNA library, to mine for microsatellites and in silico evaluation of their polymorphism. A total of 4190 microsatellites were identified in 3670 unique unigenes, and from these microsatellites, in silico polymorphism was detected in 733. We selected microsatellites based either on their in silico polymorphism and annotation results or based only on their number of repeats. Using these two approaches, 28 microsatellites were successfully amplified in twenty-six individuals, and all but 2 were found to be polymorphic, being the first genetic markers for this species. Our results showed that the strategy of selection based on number of repeats is more efficient in obtaining polymorphic microsatellites than the strategy of in silico polymorphism (allelic richness was 8.2±3.85 and 4.56±2.45 respectively). This study demonstrates that combining the knowledge of number of repeats with other predictors of variability, for example in silico microsatellite polymorphism, improves the rates of polymorphism, yielding microsatellites with higher allelic richness, and decreases the number of monomorphic microsatellites obtained.
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Affiliation(s)
- Sara D Cardoso
- Unidade de Investigação em Eco-Etologia, Instituto Superior de Psicologia Aplicada - Instituto Universitário, Rua Jardim do Tabaco, 34, 1149-041 Lisboa, Portugal.
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16
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Vera M, Alvarez-Dios JA, Fernandez C, Bouza C, Vilas R, Martinez P. Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping. Int J Mol Sci 2013; 14:5694-711. [PMID: 23481633 PMCID: PMC3634403 DOI: 10.3390/ijms14035694] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/17/2013] [Accepted: 02/22/2013] [Indexed: 11/16/2022] Open
Abstract
The turbot (Scophthalmus maximus) is a commercially valuable flatfish and one of the most promising aquaculture species in Europe. Two transcriptome 454-pyrosequencing runs were used in order to detect Single Nucleotide Polymorphisms (SNPs) in genes related to immune response and gonad differentiation. A total of 866 true SNPs were detected in 140 different contigs representing 262,093 bp as a whole. Only one true SNP was analyzed in each contig. One hundred and thirteen SNPs out of the 140 analyzed were feasible (genotyped), while Ш were polymorphic in a wild population. Transition/transversion ratio (1.354) was similar to that observed in other fish studies. Unbiased gene diversity (He) estimates ranged from 0.060 to 0.510 (mean = 0.351), minimum allele frequency (MAF) from 0.030 to 0.500 (mean = 0.259) and all loci were in Hardy-Weinberg equilibrium after Bonferroni correction. A large number of SNPs (49) were located in the coding region, 33 representing synonymous and 16 non-synonymous changes. Most SNP-containing genes were related to immune response and gonad differentiation processes, and could be candidates for functional changes leading to phenotypic changes. These markers will be useful for population screening to look for adaptive variation in wild and domestic turbot.
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Affiliation(s)
- Manuel Vera
- Laboratory of Genetics Ichthyology, Department of Biology, Faculty of Sciences, University of Girona, Campus of Montilivi s/n, Girona 17071, Spain
- Department of Genetics, Faculty of Veterinary, University of Santiago de Compostela, Campus of Lugo, Lugo 27002, Spain; E-Mails: (C.F.); (C.B.); (R.V.); (P.M.)
| | - Jose-Antonio Alvarez-Dios
- Department of Applied Mathematics, Faculty of Mathematics, University of Santiago de Compostela, Santiago de Compostela 15782, Spain; E-Mail:
| | - Carlos Fernandez
- Department of Genetics, Faculty of Veterinary, University of Santiago de Compostela, Campus of Lugo, Lugo 27002, Spain; E-Mails: (C.F.); (C.B.); (R.V.); (P.M.)
| | - Carmen Bouza
- Department of Genetics, Faculty of Veterinary, University of Santiago de Compostela, Campus of Lugo, Lugo 27002, Spain; E-Mails: (C.F.); (C.B.); (R.V.); (P.M.)
| | - Roman Vilas
- Department of Genetics, Faculty of Veterinary, University of Santiago de Compostela, Campus of Lugo, Lugo 27002, Spain; E-Mails: (C.F.); (C.B.); (R.V.); (P.M.)
| | - Paulino Martinez
- Department of Genetics, Faculty of Veterinary, University of Santiago de Compostela, Campus of Lugo, Lugo 27002, Spain; E-Mails: (C.F.); (C.B.); (R.V.); (P.M.)
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17
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Hunter ME, Hart KM. Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python-Python molurus bivittatus-Management. Int J Mol Sci 2013; 14:4793-804. [PMID: 23449030 PMCID: PMC3634432 DOI: 10.3390/ijms14034793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/06/2013] [Accepted: 02/13/2013] [Indexed: 01/29/2023] Open
Abstract
Invasive species represent an increasing threat to native ecosystems, harming indigenous taxa through predation, habitat modification, cross-species hybridization and alteration of ecosystem processes. Additionally, high economic costs are associated with environmental damage, restoration and control measures. The Burmese python, Python molurus bivittatus, is one of the most notable invasive species in the US, due to the threat it poses to imperiled species and the Greater Everglades ecosystem. To address population structure and relatedness, next generation sequencing was used to rapidly produce species-specific microsatellite loci. The Roche 454 GS-FLX Titanium platform provided 6616 di-, tri- and tetra-nucleotide repeats in 117,516 sequences. Using stringent criteria, 24 of 26 selected tri- and tetra-nucleotide loci were polymerase chain reaction (PCR) amplified and 18 were polymorphic. An additional six cross-species loci were amplified, and the resulting 24 loci were incorporated into eight PCR multiplexes. Multi-locus genotypes yielded an average of 61% (39%–77%) heterozygosity and 3.7 (2–6) alleles per locus. Population-level studies using the developed microsatellites will track the invasion front and monitor population-suppression dynamics. Additionally, cross-species amplification was detected in the invasive Ball, P. regius, and Northern African python, P. sebae. These markers can be used to address the hybridization potential of Burmese pythons and the larger, more aggressive P. sebae.
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Affiliation(s)
- Margaret E. Hunter
- U.S. Geological Survey, Southeast Ecological Science Center, 7920 NW 71st Street, Gainesville, FL 32653, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-352-264-3484; Fax: +1-352-374-8080
| | - Kristen M. Hart
- U.S. Geological Survey, Southeast Ecological Science Center, 3205 College Avenue, Davie, FL 33314, USA; E-Mail:
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Jing S, Liu B, Peng L, Peng X, Zhu L, Fu Q, He G. Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugens Stål). BULLETIN OF ENTOMOLOGICAL RESEARCH 2012; 102:113-122. [PMID: 21896240 DOI: 10.1017/s0007485311000435] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
To assess genetic diversity in populations of the brown planthopper (Nilaparvata lugens Stål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopper N. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.
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Affiliation(s)
- S Jing
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, People's Republic of China
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Ong WD, Voo CLY, Kumar SV. Development of ESTs and data mining of pineapple EST-SSRs. Mol Biol Rep 2011; 39:5889-96. [PMID: 22207174 DOI: 10.1007/s11033-011-1400-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 12/17/2011] [Indexed: 11/28/2022]
Abstract
Improving the quality of the non-climacteric fruit, pineapple, is possible with information on the expression of genes that occur during the process of fruit ripening. This can be made known though the generation of partial mRNA transcript sequences known as expressed sequence tags (ESTs). ESTs are useful not only for gene discovery but also function as a resource for the identification of molecular markers, such as simple sequence repeats (SSRs). This paper reports on firstly, the construction of a normalized library of the mature green pineapple fruit and secondly, the mining of EST-SSRs markers using the newly obtained pineapple ESTs as well as publically available pineapple ESTs deposited in GenBank. Sequencing of the clones from the EST library resulted in 282 good sequences. Assembly of sequences generated 168 unique transcripts (UTs) consisting of 34 contigs and 134 singletons with an average length of ≈500 bp. Annotation of the UTs categorized the known proteins transcripts into the three ontologies as: molecular function (34.88%), biological process (38.43%), and cellular component (26.69%). Approximately 7% (416) of the pineapple ESTs contained SSRs with an abundance of trinucleotide SSRs (48.3%) being identified. This was followed by dinucleotide and tetranucleotide SSRs with frequency of 46 and 57%, respectively. From these EST-containing SSRs, 355 (85.3%) matched to known proteins while 133 contained flanking regions for primer design. Both the ESTs were sequenced and the mined EST-SSRs will be useful in the understanding of non-climacteric ripening and the screening of biomarkers linked to fruit quality traits.
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Affiliation(s)
- W D Ong
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
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20
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Mohindra V, Singh A, Barman AS, Tripathi R, Sood N, Lal KK. Development of EST derived SSRs and SNPs as a genomic resource in Indian catfish, Clarias batrachus. Mol Biol Rep 2011; 39:5921-31. [PMID: 22207175 DOI: 10.1007/s11033-011-1404-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 12/17/2011] [Indexed: 01/19/2023]
Abstract
Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential cultivable species. The genomic resources in C. batrachus in the form of ESTs containing microsatellite repeats (EST-SSR) and single nucleotide polymorphisms (SNPs) that are associated with the expressed genes from spleen were mined. From a total of 1,937 ESTs generated, 1,698 unique sequences were obtained, out of which 221 EST-SSRs were identified and 54% could be functionally annotated by similarity searches. A total of 23 contigs containing 3 or more ESTs were found to contain 31 SNP loci, out of which 8 ESTs showed similarity to genes of known function and 1 for hypothetical protein. Nine ESTs with SSRs and/or SNPs identified in this study were reported to be associated with diseases in human and animals. These identified loci can be developed into markers in C. batrachus, which can be useful in linkage mapping, comparative genomics studies and for its genetic improvement programmes.
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Affiliation(s)
- Vindhya Mohindra
- National Bureau of Fish Genetic Resources, Canal Ring Road, PO Dilkusha, Lucknow, 226 002, UP, India.
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21
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Hamarsheh O, Amro A. Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs). Parasit Vectors 2011; 4:189. [PMID: 21958493 PMCID: PMC3191335 DOI: 10.1186/1756-3305-4-189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 09/29/2011] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND Phlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs), or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers. RESULTS Simple sequence repeats (SSRs) were characterized in P. papatasi expressed sequence tags (ESTs) derived from a public database, National Center for Biotechnology Information (NCBI). A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AX)n repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation. CONCLUSION The first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.
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Affiliation(s)
- Omar Hamarsheh
- Department of Biological Sciences, Faculty of Science and Technology, Al-Quds University, PO Box 51000, Jerusalem, Palestine.
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22
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Ma H, Ma C, Ma L. Identification of type I microsatellite markers associated with genes and ESTs in Scylla paramamosain. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Ma H, Ma Q, Ma C, Ma L. Isolation and characterization of gene-derived single nucleotide polymorphism (SNP) markers in Scylla paramamosain. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Cheng YZ, Wang RX, Sun YN, Xu TJ. Molecular characterization of miiuy croaker CC chemokine gene and its expression following Vibrio anguillarum injection. FISH & SHELLFISH IMMUNOLOGY 2011; 31:148-154. [PMID: 21414411 DOI: 10.1016/j.fsi.2011.02.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 02/24/2011] [Accepted: 02/26/2011] [Indexed: 05/30/2023]
Abstract
A CC chemokine gene was isolated from miiuy croaker (Miichthys miiuy) by expressed sequence tag analysis. The Mimi-CC cDNA contains an open reading frame of 429 nucleotides encoding 142 amino acid residues. The deduced Mimi-CC possesses the typical arrangement of four cysteines as found in other known CC chemokines (C³¹, C³², C⁵⁶, and C⁷⁰). It shares 15.3%-37.4% identity to CC chemokines of mammal and teleost. Phylogenetic analysis showed that miiuy croaker was most closely related to Atlantic cod. Genomic analysis revealed that Mimi-CC gene consists of four exons and three introns, which is not typical of CC chemokines but resembles that of CXC chemokines. Real-time quantitative RT-PCR demonstrated that Mimi-CC is constitutively expressed in most tissues including lymphoid organs, and the highest expression of Mimi-CC transcripts in normal tissues was observed in muscle. Challenge of miiuy croaker with Vibrio anguillarum resulted in significant changes in the expression of CC chemokine transcripts in four tissues, especially in kidney and spleen.
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Affiliation(s)
- Yuan-zhi Cheng
- Key Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, Zhejiang province 316000, PR China
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25
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Development, characterization, and inheritance of 113 novel EST-SSR markers in the Pacific oyster (Crassostrea gigas). Genes Genomics 2011. [DOI: 10.1007/s13258-011-0021-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Quinn NL, McGowan CR, Cooper GA, Koop BF, Davidson WS. Identification of genes associated with heat tolerance in Arctic charr exposed to acute thermal stress. Physiol Genomics 2011; 43:685-96. [PMID: 21467159 DOI: 10.1152/physiolgenomics.00008.2011] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids and is bred and grown at inland freshwater tank farms year round. It is of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change and to enable production in more southern regions. We used a genomics approach that takes advantage of the well-studied Atlantic salmon genome to identify genes that are associated with UTT in Arctic charr. Specifically, we conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals, which were subject to microarray and qPCR analysis to identify candidate UTT genes. These were compared with genes annotated in a quantitative trait locus (QTL) region that was previously identified as associated with UTT in rainbow trout and Arctic charr and that we sequenced in Atlantic salmon. Our results suggest that small heat shock proteins as well as HSP-90 genes are associated with UTT. Furthermore, hemoglobin expression was significantly downregulated in tolerant compared with intolerant fish. Finally, QTL analysis and expression profiling identified COUP-TFII as a candidate UTT gene, although its specific role is unclear given the identification of two transcripts, which appear to have different expression patterns. Our results highlight the importance of using more than one approach to identify candidate genes, particularly when examining a complicated trait such as UTT in a highly complex genome for which there is no reference genome.
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Affiliation(s)
- Nicole L Quinn
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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Kim WJ, Jung H, Gaffney PM. Development of type I genetic markers from expressed sequence tags in highly polymorphic species. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:127-132. [PMID: 20309599 DOI: 10.1007/s10126-010-9280-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 01/19/2010] [Indexed: 05/29/2023]
Abstract
Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: 1) priming site polymorphism in the template leads to inferior or erratic amplification; 2) introns in the target amplicon are too large and/or numerous to allow effective amplification under standard screening conditions; and 3) at least occasionally, a PCR primer straddles an exon-intron junction and is unable to bind to genomic DNA template. The first is only a minor issue for species or strains with low heterozygosity but becomes a significant problem for species with high genomic variation, such as marine organisms with extremely large effective population sizes. Problems arising from unanticipated introns are unavoidable but are most pronounced in intron-rich species, such as vertebrates and lophotrochozoans. We present an approach to marker development in the Pacific oyster Crassostrea gigas, a highly polymorphic and intron-rich species, which minimizes these problems, and should be applicable to other non-model species for which EST databases are available. Placement of PCR primers in the 3' end of coding sequence and 3' UTR improved PCR success rate from 51% to 97%. Almost all (37 of 39) markers developed for the Pacific oyster were polymorphic in a small test panel of wild and domesticated oysters.
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Affiliation(s)
- Woo-Jin Kim
- Biotechnology Research Institute, National Fisheries Research and Development Institute, 408-1 Sirang-ri, Gijang-eup, Gijang-gun, Busan, 619-705, South Korea
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Vogiatzi E, Lagnel J, Pakaki V, Louro B, Canario AVM, Reinhardt R, Kotoulas G, Magoulas A, Tsigenopoulos CS. In silico mining and characterization of simple sequence repeats from gilthead sea bream (Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays. Mar Genomics 2011; 4:83-91. [PMID: 21620329 DOI: 10.1016/j.margen.2011.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/09/2011] [Accepted: 01/12/2011] [Indexed: 12/30/2022]
Abstract
We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95 kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number. EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs.
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Affiliation(s)
- Emmanouella Vogiatzi
- Institute of Marine Biology and Genetics (IMBG), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
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Sathishkumar R, Lakshmi PTV, Annamalai A, Arunachalam V. Mining of simple sequence repeats in the Genome of Gentianaceae. Pharmacognosy Res 2011; 3:19-29. [PMID: 21731391 PMCID: PMC3119266 DOI: 10.4103/0974-8490.79111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 09/25/2010] [Accepted: 04/07/2011] [Indexed: 11/06/2022] Open
Abstract
Simple sequence repeats (SSRs) or short tandem repeats are short repeat motifs that show high level of length polymorphism due to insertion or deletion mutations of one or more repeat types. Here, we present the detection and abundance of microsatellites or SSRs in nucleotide sequences of Gentianaceae family. A total of 545 SSRs were mined in 4698 nucleotide sequences downloaded from the National Center for Biotechnology Information (NCBI). Among the SSR sequences, the frequency of repeat type was about 429 -mono repeats, 99 -di repeats, 15 -tri repeats, and 2 --hexa repeats. Mononucleotide repeats were found to be abundant repeat types, about 78%, followed by dinucleotide repeats (18.16%) among the SSR sequences. An attempt was made to design primer pairs for 545 identified SSRs but these were found only for 169 sequences.
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Affiliation(s)
- R. Sathishkumar
- Phytomatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
| | - P. T. V. Lakshmi
- Phytomatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India.
| | - A. Annamalai
- Plant Cell and Molecular Biology Laboratory, Department of Biotechnology, Karunya University, Coimbatore, Tamil Nadu, India.
| | - V. Arunachalam
- Molecular Biology and Bioinformatics Laboratory, Central Plantation Crops Research Institute, Kasaragod, Kerala, India.
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Xu B, Wang S, Jiang Y, Yang L, Li P, Xie C, Xing J, Ke Z, Li J, Gai J, Yang G, Bao B, Liu Z. Generation and Analysis of ESTs from the Grass Carp,Ctenopharyngodon idellus. Anim Biotechnol 2010; 21:217-25. [DOI: 10.1080/10495398.2010.505843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Lu J, Peatman E, Yang Q, Wang S, Hu Z, Reecy J, Kucuktas H, Liu Z. The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish. Nucleic Acids Res 2010; 39:D815-21. [PMID: 20935046 PMCID: PMC3013753 DOI: 10.1093/nar/gkq765] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome.org.
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Affiliation(s)
- Jianguo Lu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, AL 36849, USA
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Louro B, Passos ALS, Souche EL, Tsigenopoulos C, Beck A, Lagnel J, Bonhomme F, Cancela L, Cerdà J, Clark MS, Lubzens E, Magoulas A, Planas JV, Volckaert FA, Reinhardt R, Canario AV. Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers. Mar Genomics 2010; 3:179-91. [DOI: 10.1016/j.margen.2010.09.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Revised: 09/17/2010] [Accepted: 09/21/2010] [Indexed: 12/22/2022]
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Lee BY, Howe AE, Conte MA, D'Cotta H, Pepey E, Baroiller JF, di Palma F, Carleton KL, Kocher TD. An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags. BMC Genomics 2010; 11:278. [PMID: 20433739 PMCID: PMC2874815 DOI: 10.1186/1471-2164-11-278] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 04/30/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research. RESULTS The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10(-10)) to the UniProt database. CONCLUSION Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.
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Affiliation(s)
- Bo-Young Lee
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA
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Liu Z. Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 6:11-7. [PMID: 20430707 DOI: 10.1016/j.cbd.2010.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 12/11/2022]
Abstract
Major progress has been made in catfish genomics including construction of high-density genetic linkage maps, BAC-based physical maps, and integration of genetic linkage and physical maps. Large numbers of ESTs have been generated from both channel catfish and blue catfish. Microarray platforms have been developed for the analysis of genome expression. Genome repeat structures are studied, laying grounds for whole genome sequencing. USDA recently approved funding of the whole genome sequencing project of catfish using the next generation sequencing technologies. Generation of the whole genome sequence is a historical landmark of catfish research as it opens the real first step of the long march toward genetic enhancement. The research community needs to be focused on aquaculture performance and production traits, take advantage of the unprecedented genome information and technology, and make real progress toward genetic improvements of aquaculture brood stocks.
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Affiliation(s)
- Zhanjiang Liu
- Department of Fisheries and Allied Aquacultures, Auburn University, AL 36849, USA.
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Development and characterization of polymorphic microsatellite loci for a threatened reef fish Plectropomus leopardus. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9210-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zhou P, Zhang Z, Wang Y, Zou Z, Xie F. EST analysis and identification of gonad-related genes from the normalized cDNA library of large yellow croaker, Larimichthys crocea. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 5:89-97. [PMID: 20403775 DOI: 10.1016/j.cbd.2010.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 01/24/2010] [Accepted: 01/24/2010] [Indexed: 12/01/2022]
Abstract
On grounds of the especially limited numbers of identified gonad-specific or gonad-related genes of large yellow croaker Larimichthys crocea which may represent a major obstacle for the study of gonad development and sex differentiation, we initiated a sequencing program of Expressed Sequence Tags (ESTs) in large yellow croaker. In this study, we firstly constructed a normalized gonad cDNA library using the combination of SMART technique and DSN treatment. The titer of amplified cDNA library was 4.8x10(11) and the percentage of unique cDNA sequences of the library was 82.49%. 2916 unique cDNAs were clustered from the 3535 high quality ESTs. Among the 1785 ESTs which had significant homology with known genes in the NCBI database, about 64 significant gonad-related genes were found, accounting for 3.59% of the total unique cDNAs. Specifically, the testis-specific LRR gene and testis-specific chromodomain Y-like protein gene were identified from fish for the first time. Six gonad-related microsatellite-containing ESTs were identified from the 129 ESTs containing 149 microsatellites. Expression patterns of 10 of these gonad-related gene homologues in ovaries and testes were examined by qRT-PCR. The results will be powerful resources for our further investigation to establish the molecular mechanisms of gonad development and sex differentiation in large yellow croaker.
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Affiliation(s)
- Peng Zhou
- Key Laboratory of Science and Technology for Aquaculture and Food Safety of Fujian Province University, Fisheries College/Fisheries Biotechnology Institute, Jimei University, Xiamen, China
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Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock C, Small BC, Wilson M, Liu H, Jiang Y, Lee Y, Chen F, Lu J, Wang W, Xu P, Somridhivej B, Baoprasertkul P, Quilang J, Sha Z, Bao B, Wang Y, Wang Q, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rokhsar D, Liu Z. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol 2010; 11:R8. [PMID: 20096101 PMCID: PMC2847720 DOI: 10.1186/gb-2010-11-1-r8] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 01/14/2010] [Accepted: 01/22/2010] [Indexed: 12/13/2022] Open
Abstract
Twelve cDNA libraries from two species of catfish have been sequenced, resulting in the generation of nearly 500,000 ESTs. Background Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.
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Affiliation(s)
- Shaolin Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, 203 Swingle Hall, Auburn University, Auburn, AL 36849, USA.
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Liu H, Jiang Y, Wang S, Ninwichian P, Somridhivej B, Xu P, Abernathy J, Kucuktas H, Liu Z. Comparative analysis of catfish BAC end sequences with the zebrafish genome. BMC Genomics 2009; 10:592. [PMID: 20003258 PMCID: PMC2796685 DOI: 10.1186/1471-2164-10-592] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 12/10/2009] [Indexed: 01/09/2023] Open
Abstract
Background Comparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish. Results We reported the generation of 43,000 BAC end sequences and their applications for comparative genome analysis in catfish. Using these and the additional 20,000 existing BAC end sequences as a resource along with linkage mapping and existing physical map, conserved syntenic regions were identified between the catfish and zebrafish genomes. A total of 10,943 catfish BAC end sequences (17.3%) had significant BLAST hits to the zebrafish genome (cutoff value ≤ e-5), of which 3,221 were unique gene hits, providing a platform for comparative mapping based on locations of these genes in catfish and zebrafish. Genetic linkage mapping of microsatellites associated with contigs allowed identification of large conserved genomic segments and construction of super scaffolds. Conclusion BAC end sequences and their associated polymorphic markers are great resources for comparative genome analysis in catfish. Highly conserved chromosomal regions were identified to exist between catfish and zebrafish. However, it appears that the level of conservation at local genomic regions are high while a high level of chromosomal shuffling and rearrangements exist between catfish and zebrafish genomes. Orthologous regions established through comparative analysis should facilitate both structural and functional genome analysis in catfish.
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Affiliation(s)
- Hong Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA.
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Development of Fifty-one novel EST-SSR loci in the Pacific oyster, Crassostrea gigas by data mining from the public EST database. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9127-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Kucuktas H, Wang S, Li P, He C, Xu P, Sha Z, Liu H, Jiang Y, Baoprasertkul P, Somridhivej B, Wang Y, Abernathy J, Guo X, Liu L, Muir W, Liu Z. Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics 2009; 181:1649-60. [PMID: 19171943 PMCID: PMC2666527 DOI: 10.1534/genetics.108.098855] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 01/20/2009] [Indexed: 01/01/2023] Open
Abstract
A genetic linkage map of the channel catfish genome (N=29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3-18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.
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Affiliation(s)
- Huseyin Kucuktas
- Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures Program of Cell and Molecular Sciences, Auburn University, Auburn, AL 36849, USA
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Venier P, De Pittà C, Bernante F, Varotto L, De Nardi B, Bovo G, Roch P, Novoa B, Figueras A, Pallavicini A, Lanfranchi G. MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences. BMC Genomics 2009; 10:72. [PMID: 19203376 PMCID: PMC2657158 DOI: 10.1186/1471-2164-10-72] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 02/09/2009] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Although bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues of Mytilus galloprovincialis (the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria. RESULTS We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundant M. galloprovincialis sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database http://mussel.cribi.unipd.it. CONCLUSION We defined the first species-specific catalogue of M. galloprovincialis ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels.
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Affiliation(s)
- Paola Venier
- Department of Biology, University of Padova, Via U Bassi 58/B, Padova, Italy.
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Zhan A, Wang Y, Brown B, Wang HP. Isolation and characterization of novel microsatellite markers for yellow perch (Perca flavescens). Int J Mol Sci 2008; 10:18-27. [PMID: 19333432 PMCID: PMC2662453 DOI: 10.3390/ijms10010018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 12/15/2008] [Accepted: 12/18/2008] [Indexed: 11/20/2022] Open
Abstract
To perform whole genome scanning for complex trait analysis, we isolated and characterized a total of 21 novel genomic-SSRs and EST-SSRs for yellow perch (Perca flavescens), using the methods of construction of SSR-enrichment libraries and EST database mining of a related species P. fluviatilis. Of 16 genomic-SSR primer pairs examined, eight successfully amplified scorable products. The number of alleles at these informative loci varied from 3 – 14 with an average of 8.5 alleles per locus. When tested on wild perch from a population in Pennsylvania, observed and expected heterozygosities ranged from 0.07 – 0.81 and from 0.37 – 0.95, respectively. Of 2,226 EST sequences examined, only 110 (4.93%) contained microsatellites and for those, 13 markers were tested, 12 of which exhibited polymorphism. Compared with genomic-SSRs, EST-SSRs exhibited a lower level of genetic variability with the number of alleles of averaging only 2.6 alleles per locus. Cross-species utility indicated that three of the genomic-SSRs and eight of the EST-SSRs successfully cross-amplified in a related species, the walleye (Sander vitreus).
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Affiliation(s)
- Aibin Zhan
- Aquaculture Genetics and Breeding Laboratory, Ohio State University Aquaculture Research and Development Integration Program, 1864 Shyville Road, Piketon, Ohio 45661, USA. E-Mail:
| | - Yao Wang
- Department of Chemical & Biomolecular Engineering, Ohio State University, 140 West 19th Ave., Columbus, Ohio 43210, USA. E-Mail:
| | - Bonnie Brown
- Ecological Genetics Laboratory, Virginia Commonwealth University, Richmond, Virginia 23284, USA. E-Mail:
| | - Han-Ping Wang
- Aquaculture Genetics and Breeding Laboratory, Ohio State University Aquaculture Research and Development Integration Program, 1864 Shyville Road, Piketon, Ohio 45661, USA. E-Mail:
- *Author to whom correspondence should be addressed; E-Mail:
; Tel. +1-740-289-2071; Fax: +1-740-289-7491
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Wang S, Zhang L, Matz M. Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia). J Hered 2008; 100:329-37. [PMID: 19043068 DOI: 10.1093/jhered/esn100] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mining for microsatellites (also called simple sequence repeats [SSRs]) in public sequence databases of a common Indo-Pacific coral Acropora millepora identified 191 SSRs from 10 258 expressed sequence tag (EST) and 618 SSRs from 14 625 whole-genome shotgun (WGS) sequences. In contrast to other animals, trinucleotide repeats, rather than dinucleotide repeats, are dominant in the WGS-SSRs, and AAT is the most frequent trinucleotide motif in EST-SSRs. We successfully developed 40 polymorphic markers from EST-SSRs and WGS-SSRs. Both EST- and WGS-SSRs show high levels of polymorphism within corals from the same reef patch. Interestingly, markers WGS079 and WGS227 revealed SSR duplications in a few individuals, suggesting recent duplication events. Genotypic linkage disequilibrium was identified in 5 pairs of SSR markers, which will be invaluable for high-resolution studies of genetic admixture in natural populations of A. millepora. Transferability analysis showed that 25 of these markers can be successfully amplified in one of the most ubiquitous Indo-Pacific corals Acropora hyacinthus. The marker collection reported here is the largest ever developed for any reef-building coral. It holds great potential for addressing coral reef connectivity across the Indo-Pacific with an unprecedented precision, especially taking into account the cross-species transferability of a substantial number of markers.
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Affiliation(s)
- Shi Wang
- University of Texas at Austin, 78712, USA.
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Wang S, Sha Z, Sonstegard TS, Liu H, Xu P, Somridhivej B, Peatman E, Kucuktas H, Liu Z. Quality assessment parameters for EST-derived SNPs from catfish. BMC Genomics 2008; 9:450. [PMID: 18826589 PMCID: PMC2570692 DOI: 10.1186/1471-2164-9-450] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 09/30/2008] [Indexed: 12/15/2022] Open
Abstract
Background SNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to comparative genome analysis. However, discovery of SNPs requires genome sequencing efforts through whole genome sequencing or deep sequencing of reduced representation libraries. Such genome resources are not yet available for many species including catfish. A large resource of ESTs is to become available in catfish allowing identification of large number of SNPs, but reliability of EST-derived SNPs are relatively low because of sequencing errors. This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs. Results wo factors were found to be most significant for validation of EST-derived SNPs: the contig size (number of sequences in the contig) and the minor allele sequence frequency. The larger the contigs were, the greater the validation rate although the validation rate was reasonably high when the contigs contain four or more EST sequences with the minor allele sequence being represented at least twice in the contigs. Sequence quality surrounding the SNP under test is also crucially important. PCR extension appeared to be limited to a very short distance, prohibiting successful genotyping when an intron was present, a surprising finding. Conclusion Stringent quality assessment measures should be used when working with EST-derived SNPs. In particular, contigs containing four or more ESTs should be used and the minor allele sequence should be represented at least twice. Genotyping primers should be designed from a single exon, completely avoiding introns. Application of such quality assessment measures, along with large resources of ESTs, should provide effective means for SNP identification in species where genome sequence resources are lacking.
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Affiliation(s)
- Shaolin Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA.
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Pardo BG, Fernández C, Millán A, Bouza C, Vázquez-López A, Vera M, Alvarez-Dios JA, Calaza M, Gómez-Tato A, Vázquez M, Cabaleiro S, Magariños B, Lemos ML, Leiro JM, Martínez P. Expressed sequence tags (ESTs) from immune tissues of turbot (Scophthalmus maximus) challenged with pathogens. BMC Vet Res 2008; 4:37. [PMID: 18817567 PMCID: PMC2569028 DOI: 10.1186/1746-6148-4-37] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 09/25/2008] [Indexed: 11/30/2022] Open
Abstract
Background The turbot (Scophthalmus maximus; Scophthalmidae; Pleuronectiformes) is a flatfish species of great relevance for marine aquaculture in Europe. In contrast to other cultured flatfish, very few genomic resources are available in this species. Aeromonas salmonicida and Philasterides dicentrarchi are two pathogens that affect turbot culture causing serious economic losses to the turbot industry. Little is known about the molecular mechanisms for disease resistance and host-pathogen interactions in this species. In this work, thousands of ESTs for functional genomic studies and potential markers linked to ESTs for mapping (microsatellites and single nucleotide polymorphisms (SNPs)) are provided. This information enabled us to obtain a preliminary view of regulated genes in response to these pathogens and it constitutes the basis for subsequent and more accurate microarray analysis. Results A total of 12584 cDNAs partially sequenced from three different cDNA libraries of turbot (Scophthalmus maximus) infected with Aeromonas salmonicida, Philasterides dicentrarchi and from healthy fish were analyzed. Three immune-relevant tissues (liver, spleen and head kidney) were sampled at several time points in the infection process for library construction. The sequences were processed into 9256 high-quality sequences, which constituted the source for the turbot EST database. Clustering and assembly of these sequences, revealed 3482 different putative transcripts, 1073 contigs and 2409 singletons. BLAST searches with public databases detected significant similarity (e-value ≤ 1e-5) in 1766 (50.7%) sequences and 816 of them (23.4%) could be functionally annotated. Two hundred three of these genes (24.9%), encoding for defence/immune-related proteins, were mostly identified for the first time in turbot. Some ESTs showed significant differences in the number of transcripts when comparing the three libraries, suggesting regulation in response to these pathogens. A total of 191 microsatellites, with 104 having sufficient flanking sequences for primer design, and 1158 putative SNPs were identified from these EST resources in turbot. Conclusion A collection of 9256 high-quality ESTs was generated representing 3482 unique turbot sequences. A large proportion of defence/immune-related genes were identified, many of them regulated in response to specific pathogens. Putative microsatellites and SNPs were identified. These genome resources constitute the basis to develop a microarray for functional genomics studies and marker validation for genetic linkage and QTL analysis in turbot.
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Affiliation(s)
- Belén G Pardo
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
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Bouza C, Hermida M, Millán A, Vilas R, Vera M, Fernández C, Calaza M, Pardo BG, Martínez P. Characterization of EST-derived microsatellites for gene mapping and evolutionary genomics in turbot. Anim Genet 2008; 39:666-70. [PMID: 18786152 DOI: 10.1111/j.1365-2052.2008.01784.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The detection of microsatellite sequences within expressed sequence tags (ESTs) connects potential markers with specific genes, generating type I markers. We have developed and mapped by linkage analysis a set of EST-derived microsatellites in the turbot, Scophthalmus maximus. One hundred and ninety-one microsatellites were identified from 9256 turbot ESTs. Primer design was possible with 98 microsatellites. After genotyping 25 wild turbot and the parents of two reference families for linkage analysis, 43 EST-derived microsatellites were selected because they met technical and polymorphism criteria. A final set of 31 EST-derived microsatellites could be mapped to 17 linkage groups of the turbot consensus map based on 242 anonymous microsatellites. Twenty-four microsatellite-containing ESTs were functionally annotated, confirming them as type I markers. Nineteen were mapped in the turbot consensus map. These EST-derived microsatellites constitute useful tools for genome scanning of turbot populations, marker-assisted selection programmes and comparative mapping.
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Affiliation(s)
- C Bouza
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
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Rasmussen RS, Morrissey MT. DNA-Based Methods for the Identification of Commercial Fish and Seafood Species. Compr Rev Food Sci Food Saf 2008; 7:280-295. [PMID: 33467804 DOI: 10.1111/j.1541-4337.2008.00046.x] [Citation(s) in RCA: 230] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The detection of species substitution has become an important topic within the food industry and there is a growing need for rapid, reliable, and reproducible tests to verify species in commercial fish and seafood products. Increases in international trade and global seafood consumption, along with fluctuations in the supply and demand of different fish and seafood species, have resulted in intentional product mislabeling. The effects of species substitution are far-reaching and include economic fraud, health hazards, and illegal trade of protected species. To improve detection of commercial seafood fraud, a variety of DNA-based techniques have been developed, including Multiplex PCR, FINS, PCR-RFLP, PCR-RAPD, PCR-AFLP, and PCR-SSCP, which are all based on polymorphisms in the genetic codes of different species. These techniques have been applied in the differentiation of many types of fish and seafood species, such as gadoids, salmonids, scombroids, and bivalves. Some emerging technologies in this field include the use of real-time PCR, lab-on-a-chip, and DNA microarray chips. In this review article, the major DNA-based methods currently employed in the authentication of commercial fish and seafood species are discussed and future trends are highlighted. Examples of commercial applications and the use of online database resources are also considered.
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Affiliation(s)
- Rosalee S Rasmussen
- Author Rasmussen is with Dept. of Food Science and Technology, OSU Seafood Laboratory, Oregon State Univ., 2001 Marine Dr., Room 253, Astoria, OR 97103, U.S.A. Author Morrissey is with Oregon State University Food Innovation Center, 1207 NW Naito Parkway, Portland, OR 97209, U.S.A. Direct inquiries to author Morrissey (E-mail: )
| | - Michael T Morrissey
- Author Rasmussen is with Dept. of Food Science and Technology, OSU Seafood Laboratory, Oregon State Univ., 2001 Marine Dr., Room 253, Astoria, OR 97103, U.S.A. Author Morrissey is with Oregon State University Food Innovation Center, 1207 NW Naito Parkway, Portland, OR 97209, U.S.A. Direct inquiries to author Morrissey (E-mail: )
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Identification of microsatellites in cattle unigenes. J Genet Genomics 2008; 35:261-6. [DOI: 10.1016/s1673-8527(08)60037-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 02/18/2008] [Accepted: 02/19/2008] [Indexed: 11/20/2022]
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Wang Y, Ren R, Yu Z. Bioinformatic mining of EST-SSR loci in the Pacific oyster, Crassostrea gigas. Anim Genet 2008; 39:287-9. [PMID: 18307582 DOI: 10.1111/j.1365-2052.2008.01701.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A set of expressed sequence tag-simple sequence repeat (EST-SSR) markers of the Pacific oyster, Crassostrea gigas, was developed through bioinformatic mining of the GenBank public database. As of June 30, 2007, a total of 5132 EST sequences from GenBank were downloaded and screened for di-, tri- and tetra-nucleotide repeats, with criteria set at a minimum of 5, 4 and 4 repeats for the three categories of SSRs respectively. Seventeen polymorphic microsatellite markers were characterized. Allele numbers ranged from 3 to 10, and the observed and expected heterozygosity values varied from 0.125 to 0.770 and from 0.113 to 0.732 respectively. Eleven loci were at Hardy-Weinberg equilibrium (HWE); the other six loci showed significant departure from HWE (P < 0.01), suggesting possible presence of null alleles. Pairwise check of linkage disequilibrium (LD) indicated that 11 of 136 pairs of loci showed significant LD (P < 0.01), likely due to HWE present in single markers. Cross-species amplification was examined for five other Crassostrea species and reasonable results were obtained, promising usefulness of these markers in oyster genetics.
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Affiliation(s)
- Y Wang
- Laboratory of Marine Bio-resource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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Yu H, Li Q. Exploiting EST Databases for the Development and Characterization of EST–SSRs in the Pacific Oyster (Crassostrea gigas). J Hered 2008; 99:208-14. [DOI: 10.1093/jhered/esm124] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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