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Han C, Yang G, Zhang H, Peng H, Yang J, Zhu P, Zou J, Wang P. Development and validation of genome-wide SSR molecular markers of Tapes dorsatus. Mol Biol Rep 2024; 51:73. [PMID: 38175290 DOI: 10.1007/s11033-023-08949-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/24/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Tapes dorsatus is an economically important benthic animal in the Beibu Gulf of China. However, the deficiency of microsatellite markers has hindered the study of its genetics. The development of microsatellite markers will provide useful tools for genetic improvement, variety identification, phylogenetic analysis and resource conservation. METHODS AND RESULTS Within the genome sequence, 145,008 simple sequence repeats (SSRs) were identified, and 29,691 primer pairs were designed successfully. A total of 100 primer pairs were randomly synthesized for testing, and 93 primers yielded products. Sixty highly polymorphic primers were used to reveal the genetic diversity of 50 T. dorsatus individuals. The average number of alleles (Na) of the population was 10.40; the average number of effective alleles was 6.16, the average expected heterozygosity (He) was 0.82, and the average polymorphic information content was 0.80. The genetic structure of the population was detected, by which the population could be divided into three subpopulations. CONCLUSION We identified 145,008 SSRs in the genome of T. dorsatus and designed 29,691 primer pairs in this study. Of 100 synthesized primers, 60 were highly polymorphic and used to reveal the genetic diversity and structure of the population. The SSR markers identified here will provide useful tools and a foundation for genetic diversity, linkage mapping and molecular marker-aided breeding in T. dorsatus.
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Affiliation(s)
- Chunli Han
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China.
| | - Guohao Yang
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Huiling Zhang
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Huijing Peng
- Guangxi Institute of Oceanology, Beihai, 536000, China
| | - Jialin Yang
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Peng Zhu
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Jie Zou
- Guangxi Institute of Oceanology, Beihai, 536000, China.
| | - Pengliang Wang
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China.
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Sun X, Wang G, Yang J, Yu W, Xu J, Tang B, Ding G, Zhang D. Whole genome evaluation analysis and preliminary Assembly of Oratosquilla oratoria (Stomatopoda: Squillidae). Mol Biol Rep 2023; 50:4165-4173. [PMID: 36894769 DOI: 10.1007/s11033-023-08356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind. METHODS AND RESULTS A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria. CONCLUSION This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria.
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Affiliation(s)
- Xiaoli Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jie Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Wei Yu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jiayue Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Ge Ding
- Chemical and Biological Engineering College, Yancheng Institute of Technology, Yancheng, 224003, China
| | - Daizhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.
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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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Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis. Int J Mol Sci 2021; 22:ijms22041614. [PMID: 33562667 PMCID: PMC7915175 DOI: 10.3390/ijms22041614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/21/2021] [Accepted: 01/29/2021] [Indexed: 12/18/2022] Open
Abstract
Cytogenomics, the integration of cytogenetic and genomic data, has been used here to reconstruct the evolution of chromosomes 2 and 4 of Solea senegalensis. S. senegalensis is a flat fish with a karyotype comprising 2n = 42 chromosomes: 6 metacentric + 4 submetacentric + 8 subtelocentric + 24 telocentric. The Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (FISH-BAC) technique was applied to locate BACs in these chromosomes (11 and 10 BACs in chromosomes 2 and 4, respectively) and to generate integrated maps. Synteny analysis, taking eight reference fish species (Cynoglossus semilaevis, Scophthalmus maximus, Sparus aurata, Gasterosteus aculeatus, Xiphophorus maculatus, Oryzias latipes, Danio rerio, and Lepisosteus oculatus) for comparison, showed that the BACs of these two chromosomes of S. senegalensis were mainly distributed in two principal chromosomes in the reference species. Transposable Elements (TE) analysis showed significant differences between the two chromosomes, in terms of number of loci per Mb and coverage, and the class of TE (I or II) present. Analysis of TE divergence in chromosomes 2 and 4 compared to their syntenic regions in four reference fish species (C. semilaevis, S. maximus, O. latipes, and D. rerio) revealed differences in their age of activity compared with those species but less notable differences between the two chromosomes. Differences were also observed in peaks of divergence and coverage of TE families for all reference species even in those close to S. senegalensis, like S. maximus and C. semilaevis. Considered together, chromosomes 2 and 4 have evolved by Robertsonian fusions, pericentric inversions, and other chromosomal rearrangements mediated by TEs.
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Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution. Genes (Basel) 2020; 11:genes11080945. [PMID: 32824315 PMCID: PMC7464534 DOI: 10.3390/genes11080945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 01/02/2023] Open
Abstract
Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes.
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Restrepo-Escobar N, Márquez EJ. Microsatellite loci development for three catfish species from northwestern South America. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2019-0079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT The Neotropical catfish species Ageneiosus pardalis, Pimelodus grosskopfii, and Sorubim cuspicaudus are important fishery resources in Colombia that show historical declines in their capture. This study used next-generation sequencing with 454 FLX technology (Roche Applied Science) and bioinformatics analysis to develop between 18 and 24 microsatellite loci for these species. The novel microsatellite loci showed high values of polymorphic information content -PIC (A. pardalis: 0.601-0.903, P. grosskopfii: 0.748-0.946 and S. cuspicaudus: 0.383-0.876), and the average number of alleles/locus ranged from 7-15 for A. pardalis, 9-30 for P. grosskopfii and 5-14 for S. cuspicaudus. The average observed and expected heterozygosities were respectively, 0.757 ± 0.035 and 0.834 ± 0.015 for A. pardalis; 0.596 ± 0.040 and 0.881 ± 0.009 for P. grosskopfii; and 0.747 ± 0.031 and 0.757 ± 0.025 for S. cuspicaudus. For future studies, these loci can be useful to estimate the genetic diversity and population structure in these three Neotropical catfishes.
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García E, Cross I, Portela-Bens S, Rodríguez ME, García-Angulo A, Molina B, Cuadrado A, Liehr T, Rebordinos L. Integrative genetic map of repetitive DNA in the sole Solea senegalensis genome shows a Rex transposon located in a proto-sex chromosome. Sci Rep 2019; 9:17146. [PMID: 31748593 PMCID: PMC6868151 DOI: 10.1038/s41598-019-53673-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 11/05/2019] [Indexed: 01/07/2023] Open
Abstract
Repetitive sequences play an essential role in the structural and functional evolution of the genome, particularly in the sexual chromosomes. The Senegalese sole (Solea senegalensis) is a valuable flatfish in aquaculture albeit few studies have addressed the mapping and characterization of repetitive DNA families. Here we analyzed the Simple Sequence Repeats (SSRs) and Transposable elements (TEs) content from fifty-seven BAC clones (spanning 7.9 Mb) of this species, located in chromosomes by multiple fluorescence in situ hybridization (m-BAC-FISH) technique. The SSR analysis revealed an average density of 675.1 loci per Mb and a high abundance (59.69%) of dinucleotide coverage was observed, being ‘AC’ the most abundant. An SSR-FISH analysis using eleven probes was also carried out and seven of the 11 probes yielded positive signals. ‘AC’ probes were present as large clusters in almost all chromosomes, supporting the bioinformatic analysis. Regarding TEs, DNA transposons (Class II) were the most abundant. In Class I, LINE elements were the most abundant and the hAT family was the most represented in Class II. Rex/Babar subfamily, observed in two BAC clones mapping to chromosome pair 1, showed the longest match. This chromosome pair has been recently reported as a putative sexual proto-chromosome in this species, highlighting the possible role of the Rex element in the evolution of this chromosome. In the Rex1 phylogenetic tree, the Senegalese sole Rex1 retrotransposon could be associated with one of the four major ancient lineages in fish genomes, in which it is included O. latipes.
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Affiliation(s)
- Emilio García
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - María E Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Aglaya García-Angulo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Belén Molina
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Angeles Cuadrado
- Department of Biomedicine and Biotechnology, University of Alcala, 28871, Alcalá de Henares (Madrid), Spain
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510, Cádiz, Spain.
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Lin Q, Luo W, Wan S, Gao Z. De Novo Transcriptome Analysis of Two Seahorse Species (Hippocampus erectus and H. mohnikei) and the Development of Molecular Markers for Population Genetics. PLoS One 2016; 11:e0154096. [PMID: 27128031 PMCID: PMC4851356 DOI: 10.1371/journal.pone.0154096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 04/08/2016] [Indexed: 12/24/2022] Open
Abstract
Seahorse conservation has been performed utilizing various strategies for many decades, and the deeper understanding of genomic information is necessary to more efficiently protect the germplasm resources of seahorse species. However, little genetic information about seahorses currently exists in the public databases. In this study, high-throughput RNA sequencing for two seahorse species, Hippocampus erectus and H. mohnikei, was carried out, and de novo assembly generated 37,506 unigenes for H. erectus and 36,113 unigenes for H. mohnikei. Among them, 17,338 (46.23%) unigenes for H. erectus and 17,900 (49.57%) for H. mohnikei were successfully annotated based on the information available from the public databases. Through comparing the unigenes of two seahorse species, 7,802 candidate orthologous genes were identified and 5,268 genes among them could be annotated. In addition, gene ontology analysis of two species was similarly performed on biological processes, cellular components, and molecular functions. Twenty-four and twenty-one unigenes in H. erectus and H. mohnikei were annotated in the biosynthesis of unsaturated fatty acids pathways, and both seahorses lacked the Δ12 and Δ15 desaturases. Total of 8,992 and 9,116 SSR loci were obtained from H. erectus and H. mohnikei unigenes, respectively. Dozens of SSR were developed and then applied to assess the population genetic diversity, as well as cross-amplified in a related species, H. trimaculatus. The HO and HE values of the tested populations for H. erectus, H. mohnikei, and H. trimaculatus were medium. These resources would facilitate the conservation of the species through a better understanding of the genomics and comparative genome analysis within the Hippocampus genus.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, 510275, China
| | - Wei Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, 510275, China
| | - Shiming Wan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab. of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China
| | - Zexia Gao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab. of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China
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Adams RH, Blackmon H, Reyes-Velasco J, Schield DR, Card DC, Andrew AL, Waynewood N, Castoe TA. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Genome 2016; 59:295-310. [PMID: 27064176 DOI: 10.1139/gen-2015-0124] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.
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Affiliation(s)
- Richard H Adams
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Heath Blackmon
- b Department of Ecology, Evolution & Behavior, 1987 Upper Buford Cir., University of Minnesota, Saint Paul, MN 55108-6097, USA
| | - Jacobo Reyes-Velasco
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Drew R Schield
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Daren C Card
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Audra L Andrew
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Nyimah Waynewood
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Todd A Castoe
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
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Guo YS, Wang XY, Wang ZD, Zhao XX, Wang QH, Deng YW, Du XD. Highly efficient identification of thousands of microsatellite loci in the pearl oyster (Pinctada martensii) from RNA-Seq. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Biswas G, Kinoshita S, Kono T, Hikima JI, Sakai M. Evolutionary evidence of tumor necrosis factor super family members in the Japanese pufferfish (Takifugu rubripes): Comprehensive genomic identification and expression analysis. Mar Genomics 2015; 22:25-36. [PMID: 25792259 DOI: 10.1016/j.margen.2015.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/05/2015] [Accepted: 03/05/2015] [Indexed: 12/12/2022]
Abstract
Tumor necrosis factor (TNF) and its superfamily (TNFSF) members are important inflammatory cytokines. Although fish have fourteen TNFSF genes, their genomic location and existence are yet to be described and confirmed in the Japanese pufferfish (Fugu) (Takifugu rubripes). Therefore, we conducted in silico identification, synteny analysis of TNFSF genes from Fugu with that of zebrafish and human TNFSF loci and their expression analysis in various tissues. We identified ten novel TNFSF genes, viz. TNFSF5 (CD40L), TNFSF6 (FasL), three TNFSF10 (TRAIL) (-1, 2 and 3), TNFSF11 (RANKlg), TNFSF12 (TWEAK), two TNFSF13B (BAFF) (1 and 2) and TNFSF14 (LIGHT) belonging to seven TNFSFs in Fugu. Several features such as existence of TNF family signature, conservation of genes in TNF loci with human and zebrafish chromosomes and phylogenetic clustering with other teleost TNFSF orthologs confirmed their identity. Fugu TNFSF genes were constitutively expressed in all eight different tissues with most of them expressed highly in liver. Fugu TNFSF10 gene has three homologs present on chromosomes 10 (TNFSF10-1), 8 (TNFSF10-2) and 2 (TNFSF10-3). Moreover, a phylogenetic analysis containing all available vertebrate (mammals, birds, reptiles, amphibians and fish) TNFSF10 orthologs showed that Fugu TNFSF10-1 and 10-3 are present in all vertebrates, whereas TNFSF10-2 was not related to any mammalian and avian orthologs. Viral double-stranded RNA mimic poly (I:C) caused an elevated expression of three Fugu TNFSF10 genes in head kidney cells at 4h indicating probable role of these genes to induce apoptosis in virus-infected cells. In conclusion, Fugu possesses genes belonging to nine TNFSFs including the newly identified seven and previously reported two, TNFSF New (TNF-N) and TNFSF2 (TNF-α). Our findings would add up information to TNFSF evolution among vertebrates.
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Affiliation(s)
- Gouranga Biswas
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Shunsuke Kinoshita
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Tomoya Kono
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Jun-ichi Hikima
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Masahiro Sakai
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.
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Villanova GV, Vera M, Díaz J, Martinez P, Calcaterra NB, Arranz SE. Isolation and characterization of 20 polymorphic microsatellite loci in the migratory freshwater fish Leporinus obtusidens (Characiformes: Anostomidae) using 454 shotgun pyrosequencing. JOURNAL OF FISH BIOLOGY 2015; 86:1209-1217. [PMID: 25683648 DOI: 10.1111/jfb.12632] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 12/18/2014] [Indexed: 06/04/2023]
Abstract
Twenty polymorphic microsatellite markers were developed for the Neotropical fish Leporinus obtusidens using a next generation sequencing approach and tested in two other characifomes species, Schizodon platae and Prochilodus lineatus. Microsatellite loci alleles in L. obtusidens ranged between 2 and 20 alleles per locus (mean = 5·7), with expected heterozygosity values ranging from 0·097 to 0·956 (mean = 0·578) and observed heterozygosity values ranging from 0·000 to 0·800 (mean = 0·400) in a sample of 20 specimens from the lower Paraná River (Argentina). Most of these markers will be a valuable tool for captive breeding and stocking programmes, as well as for analyses of population connectivity and genetic structure in this broadly distributed Neotropical migratory fish.
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Affiliation(s)
- G V Villanova
- Instituto de Biología Molecular y Celular de Rosario (IBR) - CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda sede CCT, 2000 Rosario, Argentina; Area Biología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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Sahu B, Sahoo L, Joshi C, Mohanty P, Sundaray J, Jayasankar P, Das P. Isolation and characterization of polymorphic microsatellite loci in Indian major carp, Catla catla using next-generation sequencing platform. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Kavakiotis I, Triantafyllidis A, Samaras P, Voulgaridis A, Karaiskou N, Konstantinidis E, Vlahavas I. Pattern discovery for microsatellite genome analysis. Comput Biol Med 2014; 46:71-8. [DOI: 10.1016/j.compbiomed.2014.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/06/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
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Lü Z, Li H, Liu L, Cui W, Hu X, Wang C. Rapid development of microsatellite markers from the large yellow croaker (Pseudosciaena crocea) using next generation DNA sequencing technology. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Characterization of the heart transcriptome of the white shark (Carcharodon carcharias). BMC Genomics 2013; 14:697. [PMID: 24112713 PMCID: PMC3832898 DOI: 10.1186/1471-2164-14-697] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The white shark (Carcharodon carcharias) is a globally distributed, apex predator possessing physical, physiological, and behavioral traits that have garnered it significant public attention. In addition to interest in the genetic basis of its form and function, as a representative of the oldest extant jawed vertebrate lineage, white sharks are also of conservation concern due to their small population size and threat from overfishing. Despite this, surprisingly little is known about the biology of white sharks, and genomic resources are unavailable. To address this deficit, we combined Roche-454 and Illumina sequencing technologies to characterize the first transciptome of any tissue for this species. RESULTS From white shark heart cDNA we generated 665,399 Roche 454 reads (median length 387-bp) that were assembled into 141,626 contigs (mean length 503-bp). We also generated 78,566,588 Illumina reads, which we aligned to the 454 contigs producing 105,014 454/Illumina consensus sequences. To these, we added 3,432 non-singleton 454 contigs. By comparing these sequences to the UniProtKB/Swiss-Prot database we were able to annotate 21,019 translated open reading frames (ORFs) of ≥ 20 amino acids. Of these, 19,277 were additionally assigned Gene Ontology (GO) functional annotations. While acknowledging the limitations of our single tissue transcriptome, Fisher tests showed the white shark transcriptome to be significantly enriched for numerous metabolic GO terms compared to the zebra fish and human transcriptomes, with white shark showing more similarity to human than to zebra fish (i.e. fewer terms were significantly different). We also compared the transcriptome to other available elasmobranch sequences, for signatures of positive selection and identified several genes of putative adaptive significance on the white shark lineage. The white shark transcriptome also contained 8,404 microsatellites (dinucleotide, trinucleotide, or tetranucleotide motifs ≥ five perfect repeats). Detailed characterization of these microsatellites showed that ORFs with trinucleotide repeats, were significantly enriched for transcription regulatory roles and that trinucleotide frequency within ORFs was lower than for a wide range of taxonomic groups including other vertebrates. CONCLUSION The white shark heart transcriptome represents a valuable resource for future elasmobranch functional and comparative genomic studies, as well as for population and other biological studies vital for effective conservation of this globally vulnerable species.
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Zhou K, Aertsen A, Michiels CW. The role of variable DNA tandem repeats in bacterial adaptation. FEMS Microbiol Rev 2013; 38:119-41. [PMID: 23927439 DOI: 10.1111/1574-6976.12036] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/13/2013] [Accepted: 07/26/2013] [Indexed: 01/05/2023] Open
Abstract
DNA tandem repeats (TRs), also designated as satellite DNA, are inter- or intragenic nucleotide sequences that are repeated two or more times in a head-to-tail manner. Because TR tracts are prone to strand-slippage replication and recombination events that cause the TR copy number to increase or decrease, loci containing TRs are hypermutable. An increasing number of examples illustrate that bacteria can exploit this instability of TRs to reversibly shut down or modulate the function of specific genes, allowing them to adapt to changing environments on short evolutionary time scales without an increased overall mutation rate. In this review, we discuss the prevalence and distribution of inter- and intragenic TRs in bacteria and the mechanisms of their instability. In addition, we review evidence demonstrating a role of TR variations in bacterial adaptation strategies, ranging from immune evasion and tissue tropism to the modulation of environmental stress tolerance. Nevertheless, while bioinformatic analysis reveals that most bacterial genomes contain a few up to several dozens of intra- and intergenic TRs, only a small fraction of these have been functionally studied to date.
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Affiliation(s)
- Kai Zhou
- Department of Microbial and Molecular Systems (M²S), Faculty of Bioscience Engineering, Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
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Xiong LW, Wang Q, Qiu GF. Large-scale isolation of microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey. Int J Mol Sci 2012. [PMID: 23208373 PMCID: PMC3546693 DOI: 10.3390/ijms131216333] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Microsatellites are simple sequence repeats with a high degree of polymorphism in the genome; they are used as DNA markers in many molecular genetic studies. Using traditional methods such as the magnetic beads enrichment method, only a few microsatellite markers have been isolated from the Chinese mitten crab Eriocheir sinensis, as the crab genome sequence information is unavailable. Here, we have identified a large number of microsatellites from the Chinese mitten crab by taking advantage of Solexa genomic surveying. A total of 141,737 SSR (simple sequence repeats) motifs were identified via analysis of 883 Mb of the crab genomic DNA information, including mono-, di-, tri-, tetra-, penta- and hexa-nucleotide repeat motifs. The number of di-nucleotide repeat motifs was 82,979, making this the most abundant type of repeat motif (58.54%); the second most abundant were the tri-nucleotide repeats (42,657, 30.11%). Among di-nucleotide repeats, the most frequent repeats were AC motifs, accounting for 67.55% of the total number. AGG motifs were the most frequent (59.32%) of the tri-nucleotide motifs. A total of 15,125 microsatellite loci had a flanking sequence suitable for setting the primer of a polymerase chain reaction (PCR). To verify the identified SSRs, a subset of 100 primer pairs was randomly selected for PCR. Eighty two primer sets (82%) produced strong PCR products matching expected sizes, and 78% were polymorphic. In an analysis of 30 wild individuals from the Yangtze River with 20 primer sets, the number of alleles per locus ranged from 2–14 and the mean allelic richness was 7.4. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in four of the 20 microsatellite loci after sequential Bonferroni corrections. This method is cost- and time-effective in comparison to traditional approaches for the isolation of microsatellites.
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Affiliation(s)
- Liang-Wei Xiong
- Key laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China; E-Mail:
- Jiangsu Animal Husbandry & Veterinary College, Jiangsu 225300, China
| | - Qun Wang
- College of Life Science, East China Normal University, Shanghai 200062, China; E-Mail:
| | - Gao-Feng Qiu
- Key laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +86-21-6190-0436
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Rapid development of microsatellite markers for the endangered fish Schizothorax biddulphi (Günther) using next generation sequencing and cross-species amplification. Int J Mol Sci 2012. [PMID: 23203104 PMCID: PMC3509620 DOI: 10.3390/ijms131114946] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The Ho ranged from 0.15 to 0.83, and He ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers for non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis.
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Wang H, Huan P, Lu X, Liu B. Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome. Genes Genet Syst 2012; 86:197-205. [PMID: 21952209 DOI: 10.1266/ggs.86.197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A total of 2,970 EST-SSRs (2.38%) were identified by transcriptome sequencing of clam Meretrix meretrix (751,970 reads, ~310.82 Mbp), using 454 Genome Sequencer FLX next-generation sequencing platform. Dinucleotide SSR was the dominant repeat type (40.2%), followed by trinucleotide (37.8%), tetranuleotide (12.0%) and pentanucleotide (2.0%) SSR. The dominant repeat motif was AT (71.3%) in the dinucleotide SSR type and AAC (45.6%) in the trinucleotide SSR type. Nearly 79% of all microsatellites had flanking sequences suitable for PCR primer design. Half of PAL were found to be polymorphic in a subset of 40 primer pairs randomly selected. Specifically, the density of dinucleotide, trinucleotide and tetranucleotide repeats showed significant variation among four development stages (trochophore, D-veliger, pediveliger and postlarva). The results suggested that dinucleotide, trinucleotide and tetranucleotide SSRs may play an important role in contributing to the different expression profiles in larval stages.
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Affiliation(s)
- Hongxia Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Quingdao, China
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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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Kaneko G, Furukawa S, Kurosu Y, Yamada T, Takeshima H, Nishida M, Mitsuboshi T, Otaka T, Shirasu K, Koda T, Takemasa Y, Aki S, Mochizuki T, Fukushima H, Fukuda Y, Kinoshita S, Asakawa S, Watabe S. Correlation with larval body size of mRNA levels of growth hormone, growth hormone receptor I and insulin-like growth factor I in larval torafugu Takifugu rubripes. JOURNAL OF FISH BIOLOGY 2011; 79:854-874. [PMID: 21967578 DOI: 10.1111/j.1095-8649.2011.03037.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The full-length of insulin-like growth factor (IGF) complementary (c)DNAs encoded by igf-I and igf-II from torafugu pufferfish Takifugu rubripes were cloned in the present study. The deduced amino acid sequences of the two genes showed c. 80% identity each with those of Igf-I and Igf-II from other teleosts, respectively. Two growth hormone (GH) receptors, ghr1 and ghr2, were also cloned in silico using the T. rubripes Fugu genome database. The transcripts of T. rubripes igf-I were detected in slow muscle, heart, skin, gill, liver and intestine but not in fast muscle, spleen and testis of adult fish, whereas those of igf-II were found in all tissues examined. Subsequently, the accumulated messenger (m)RNA levels of igf-I and igf-II were investigated in an F(2) population derived from a male of an apparent fast-growing T. rubripes strain and a wild female T. rubripes together with those of other growth-related genes encoding Gh, Ghr1 and Ghr2, and with those of prolactin (Prl) and leptin (Lep) previously reported. The accumulated mRNA levels of igf-I, gh and ghr1 were significantly correlated to growth rate at larval stages in the population, but not for those of igf-II, prl, ghr2 and lep. Although it is unclear whether or not this phenotype is directly related to the heredity of the fast-growing strain, the findings suggest that the expression of igf-I, gh and ghr1 is involved in the regulation of growth rate at larval stages in T. rubripes.
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Affiliation(s)
- G Kaneko
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon. BMC Genomics 2011; 12:242. [PMID: 21575266 PMCID: PMC3124438 DOI: 10.1186/1471-2164-12-242] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/17/2011] [Indexed: 11/28/2022] Open
Abstract
Background The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses. Results We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome. Conclusions The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.
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Tan JC, Tan A, Checkley L, Honsa CM, Ferdig MT. Variable numbers of tandem repeats in Plasmodium falciparum genes. J Mol Evol 2010; 71:268-78. [PMID: 20730584 DOI: 10.1007/s00239-010-9381-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 08/09/2010] [Indexed: 11/29/2022]
Abstract
Genome variation studies in Plasmodium falciparum have focused on SNPs and, more recently, large-scale copy number polymorphisms and ectopic rearrangements. Here, we examine another source of variation: variable number tandem repeats (VNTRs). Interspersed low complexity features, including the well-studied P. falciparum microsatellite sequences, are commonly classified as VNTRs; however, this study is focused on longer coding VNTR polymorphisms, a small class of copy number variations. Selection against frameshift mutation is a main constraint on tandem repeats (TRs) in coding regions, while limited propagation of TRs longer than 975 nt total length is a minor restriction in coding regions. Comparative analysis of three P. falciparum genomes reveals that more than 9% of all P. falciparum ORFs harbor VNTRs, much more than has been reported for any other species. Moreover, genotyping of VNTR loci in a drug-selected line, progeny of a genetic cross, and 334 field isolates demonstrates broad variability in these sequences. Functional enrichment analysis of ORFs harboring VNTRs identifies stress and DNA damage responses along with chromatin modification activities, suggesting an influence on genome mutability and functional variation. Analysis of the repeat units and their flanking regions in both P. falciparum and Plasmodium reichenowi sequences implicates a replication slippage mechanism in the generation of TRs from an initially unrepeated sequence. VNTRs can contribute to rapid adaptation by localized sequence duplication. They also can confound SNP-typing microarrays or mapping short-sequence reads and therefore must be accounted for in such analyses.
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Affiliation(s)
- John C Tan
- The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
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25
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Kaluzhny D, Shchyolkina A, Livshits M, Lysov Y, Borisova O. A novel intramolecular G-quartet-containing fold of single-stranded d(GT)(8) and d(GT)(16) oligonucleotides. Biophys Chem 2009; 143:161-5. [PMID: 19493608 DOI: 10.1016/j.bpc.2009.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 05/08/2009] [Accepted: 05/14/2009] [Indexed: 11/24/2022]
Abstract
Human genome is shown to be enriched with (GT)(n) stretches of lengths from 8 to 20 dinucleotides. Low temperature (T< or =10 degrees C) conformations of d(GT)(n) oligonucleotides (n=7, 8, 12, 16, 20) were studied by means of circular dichroism (CD), thermal melting, ethidium bromide (EtBr) probing and single nucleotide substitutions. Rotational relaxation times for EtBr:d(GT)(n) complexes confirmed a monomolecular state of the oligonucleotides. CD spectra indicated involvement of all guanines of d(GT)(8) and d(GT)(16) in G-quartets, while dT(GT)(7), d(GT)(12) and d(GT)(20) were shown to be only partially ordered. The schemes of the d(GT)(8) and d(GT)(16) folds are suggested.
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Affiliation(s)
- Dmitry Kaluzhny
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia.
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Burridge CP, England PR. Tri- and tetranucleotide microsatellites in dhufish Glaucosoma hebracium (Perciformes). Mol Ecol Resour 2009; 9:948-51. [PMID: 21564801 DOI: 10.1111/j.1755-0998.2008.02508.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thirteen polymorphic tri- and tetranucleotide microsatellite markers are reported for the exploited marine dhufish (Glaucosoma hebracium) from southwestern Australia. Variation was assessed among 48 individuals collected from a single locality. Most loci had 2-5 alleles, although one had more than 20 alleles, with corresponding observed heterozygosities of 0.02-0.81. These loci were also polymorphic in congeneric species.
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Affiliation(s)
- Christopher P Burridge
- CSIRO Marine & Atmospheric Research, Private Bag 5, Wembley, WA 6913, Australia CSIRO Marine & Atmospheric Research, GPO Box 1538, Hobart, Tas. 7001, Australia
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Reichwald K, Lauber C, Nanda I, Kirschner J, Hartmann N, Schories S, Gausmann U, Taudien S, Schilhabel MB, Szafranski K, Glöckner G, Schmid M, Cellerino A, Schartl M, Englert C, Platzer M. High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research. Genome Biol 2009; 10:R16. [PMID: 19210790 PMCID: PMC2688266 DOI: 10.1186/gb-2009-10-2-r16] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 01/26/2009] [Accepted: 02/11/2009] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research. RESULTS To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred. CONCLUSIONS Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri.
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Affiliation(s)
- Kathrin Reichwald
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr,, 07745 Jena, Germany.
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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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Xu Z, Gutierrez L, Hitchens M, Scherer S, Sater AK, Wells DE. Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis. Bioinform Biol Insights 2008; 2:157-69. [PMID: 19812773 PMCID: PMC2735965 DOI: 10.4137/bbi.s561] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.
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Affiliation(s)
- Zhenkang Xu
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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30
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Kim TS, Booth JG, Gauch HG, Sun Q, Park J, Lee YH, Lee K. Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference. BMC Genomics 2008; 9:31. [PMID: 18215294 PMCID: PMC2257937 DOI: 10.1186/1471-2164-9-31] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 01/23/2008] [Indexed: 11/10/2022] Open
Abstract
Background Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism Neurospora crassa is an excellent system to study evolution and biological function of SSRs. Results We identified and characterized 2749 SSRs of 963 SSR types in the genome of N. crassa. The distribution of tri-nucleotide (nt) SSRs, the most common SSRs in N. crassa, was significantly biased in exons. We further characterized the distribution of 19 abundant SSR types (AST), which account for 71% of total SSRs in the N. crassa genome, using a Poisson log-linear model. We also characterized the size variation of SSRs among natural accessions using Polymorphic Index Content (PIC) and ANOVA analyses and found that there are genome-wide, chromosome-dependent and local-specific variations. Using polymorphic SSRs, we have built linkage maps from three line-cross populations. Conclusion Taking our computational, statistical and experimental data together, we conclude that 1) the distributions of the SSRs in the sequenced N. crassa genome differ systematically between chromosomes as well as between SSR types, 2) the size variation of tri-nt SSRs in exons might be an important mechanism in generating functional variation of proteins in N. crassa, 3) there are different levels of evolutionary forces in variation of amino acid repeats, and 4) SSRs are stable molecular markers for genetic studies in N. crassa.
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Affiliation(s)
- Tae-Sung Kim
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853 USA.
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31
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Zhang L, Chen C, Cheng J, Wang S, Hu X, Hu J, Bao Z. Initial analysis of tandemly repetitive sequences in the genome of Zhikong scallop (Chlamys farreri Jones et Preston). DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 2007; 19:195-205. [PMID: 17852361 DOI: 10.1080/10425170701462316] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Tandemly repetitive sequences are widespread in all eukaryotic genomes, but data on tandem repeats are limited in Zhikong scallop (Chlamys farreri). In the present study, paired-end sequencing of 2016 individual fosmid clones resulted in 3646 sequences. A total of 2,286,986 bp of genomic sequences were generated, representing approximately 1.84 per thousand of the Zhikong scallop genome. Using tandem repeats finder (TRF) software, a total of 2500 tandem repeats were found, including 313 satellites, 1816 minisatellites and 371 microsatellites. The cumulative length of tandem repeats was 552,558 bp, accounting for 24.16% of total length. Specifically, the length of microsatellites, minisatellites and satellites was 9425, 336,001 and 207,132 bp, accounting for 1.71, 60.81 and 37.49% of the length of tandem repeats, and 0.41, 14.69 and 9.06% of total length, respectively. The detailed information on the characteristic of all repeat units was also represented, which will provide a useful resource for physical mapping and better utilization of the existing genomic information in Zhikong scallop.
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Affiliation(s)
- Lingling Zhang
- Division of Life Science and Technology, Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, People's Republic of China.
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32
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Meglécz E, Anderson SJ, Bourguet D, Butcher R, Caldas A, Cassel-Lundhagen A, d'Acier AC, Dawson DA, Faure N, Fauvelot C, Franck P, Harper G, Keyghobadi N, Kluetsch C, Muthulakshmi M, Nagaraju J, Patt A, Péténian F, Silvain JF, Wilcock HR. Microsatellite flanking region similarities among different loci within insect species. INSECT MOLECULAR BIOLOGY 2007; 16:175-85. [PMID: 17298557 DOI: 10.1111/j.1365-2583.2006.00713.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements - or their remnants - than unique microsatellite sequences.
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Affiliation(s)
- E Meglécz
- Evolution Génome et Environnement, CASE 36, Université de Provence, Marseille, France.
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33
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Bai SL, Zhong X, Ma L, Zheng W, Fan LM, Wei N, Deng XW. A simple and reliable assay for detecting specific nucleotide sequences in plants using optical thin-film biosensor chips. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:354-66. [PMID: 17156412 DOI: 10.1111/j.1365-313x.2006.02951.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here we report the adaptation and optimization of an efficient, accurate and inexpensive assay that employs custom-designed silicon-based optical thin-film biosensor chips to detect unique transgenes in genetically modified (GM) crops and SNP markers in model plant genomes. Briefly, aldehyde-attached sequence-specific single-stranded oligonucleotide probes are arrayed and covalently attached to a hydrazine-derivatized biosensor chip surface. Unique DNA sequences (or genes) are detected by hybridizing biotinylated PCR amplicons of the DNA sequences to probes on the chip surface. In the SNP assay, target sequences (PCR amplicons) are hybridized in the presence of a mixture of biotinylated detector probes and a thermostable DNA ligase. Only perfect matches between the probe and target sequences, but not those with even a single nucleotide mismatch, can be covalently fixed on the chip surface. In both cases, the presence of specific target sequences is signified by a color change on the chip surface (gold to blue/purple) after brief incubation with an anti-biotin IgG horseradish peroxidase (HRP) to generate a precipitable product from an HRP substrate. Highly sensitive and accurate identification of PCR targets can be completed within 30 min. This assay is extremely robust, exhibits high sensitivity and specificity, and is flexible from low to high throughput and very economical. This technology can be customized for any nucleotide sequence-based identification assay and widely applied in crop breeding, trait mapping, and other work requiring positive detection of specific nucleotide sequences.
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Affiliation(s)
- Su-Lan Bai
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, and The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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34
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Sun B, Chang M, Chen D, Nie P. Gene structure and transcription of IRF-2 in the mandarin fish Siniperca chuatsi with the finding of alternative transcripts and microsatellite in the coding region. Immunogenetics 2006; 58:774-84. [PMID: 16871414 DOI: 10.1007/s00251-006-0129-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 05/04/2006] [Indexed: 10/24/2022]
Abstract
The gene of interferon regulatory factor-2 (IRF-2) has been cloned from the mandarin fish (Siniperca chuatsi). The IRF-2 gene has 6,418 nucleotides (nt) and contains eight exons and seven introns, encoding two mRNAs. The two IRF-2 mRNAs each contained an open reading frame of 873 nt, which both translate into the same 291 amino acids but differed in their 5' untranslated region: one mRNA was transcribed initially from the exon 1 bypassing exon 2, while the other was transcribed from the exon 2. The microsatellites (CA repeats) could be found in the carboxyl terminal region of mandarin fish IRF-2, which result in the truncated form molecules. The microsatellites' polymorphism was investigated, and eight alleles were found in 16 individuals. The microsatellites were also examined in IRF-2 of several freshwater perciform fishes. The transcription of the IRF-2 in different tissues with or without poly inosine-cytidine stimulation was analyzed by real-time PCR, and the constitutive transcription of both molecules could be detected in all the tissues examined.
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Affiliation(s)
- Baojian Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, People's Republic of China
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35
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Gao H, Kong J. The microsatellites and minisatellites in the genome of Fenneropenaeus chinensis. ACTA ACUST UNITED AC 2006; 16:426-36. [PMID: 16287622 DOI: 10.1080/10425170500354359] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Through two-time sequencing randomly in Fenneropenaeus chinensis, 2,597,000 bp cumulative length random genomic sequences about occupying 1.23 per thousand of the entire genome are obtained, in which the length of the first time sequencing is 884,000 bp, by cutting the genome DNA with Sau3AI enzyme, and the second is 1,713,000 bp by breaking the genome DNA with the physical method, ultrasonic. Using tandem repeat finder (TRF) soft to analyze the sequences, 4,588 tandem repeats are found, in which the number of microsatellites (1-6 bp) is 3,888, and 700 for minisatellites ( >or= 7 bp). The cumulative length of repeats is 305,555 bp, accounting for 11.72% of total cumulative sequence length, in which the cumulative length of microsatellites is 232,979 bp, accounting for 8.97% of total sequence length, and greater than those of other organisms, such as human and mosquito, etc. The dinucleotide repeat type is dominant in which the dominant repeat class is AT. The second abundant repeat type is trinucleotide, of which the dominant repeat class is AAT. Interestingly, of all of repeat types, the repeat numbers and repeat classes of primer number repeat types, such as pentanucleotide, heptanucleotide, elevennucleotide, etc. are less than those of repeat types beside them. The phenomena may involve the genesis and the evolution of microsatellites and minisatellites.
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Affiliation(s)
- Huan Gao
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR of China
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36
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Somorjai IML, Danzmann RG, Ferguson MM. Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies in rainbow trout (Oncorhynchus mykiss). Genetics 2004; 165:1443-56. [PMID: 14668393 PMCID: PMC1462839 DOI: 10.1093/genetics/165.3.1443] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We searched for quantitative trait loci (QTL) affecting upper temperature tolerance (UTT) in crosses between the Nauyuk Lake and Fraser River strains of Arctic charr (Salvelinus alpinus) using survival analysis. Two QTL were detected by using two microsatellite markers after correcting for experiment-wide error. A comparative mapping approach localized these two QTL to homologous linkage groups containing UTT QTL in rainbow trout (Oncorhynchus mykiss). Additional marginal associations were detected in several families in regions homologous to those with QTL in rainbow trout. Thus, the genes underlying UTT QTL may antedate the divergence of these two species, which occurred by approximately 16 MYA. The data also indicate that one pair of homeologs (ancestrally duplicated chromosomal segments) have contained QTL in Arctic charr since the evolution of salmonids from a tetraploid ancestor 25-100 MYA. This study represents one of the first examples of comparative QTL mapping in an animal polyploid group and illustrates the fate of QTL after genome duplication and reorganization.
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Affiliation(s)
- Ildiko M L Somorjai
- Department of Zoology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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37
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Li YC, Korol AB, Fahima T, Beiles A, Nevo E. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 2002; 11:2453-65. [PMID: 12453231 DOI: 10.1046/j.1365-294x.2002.01643.x] [Citation(s) in RCA: 601] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Microsatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation.
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Affiliation(s)
- You-Chun Li
- Institute of Evolution, University of Haifa, Haifa 31905, Israel
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38
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Affiliation(s)
- Greg Elgar
- United Kingdom Human Genome Mapping Project Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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39
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Bogani P, Simoni A, Lio' P, Germinario A, Buiatti M. Molecular variation in plant cell populations evolving in vitro in different physiological contexts. Genome 2001. [DOI: 10.1139/g01-033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous work has shown the fixation of context-specific random amplified polymorphic DNA (RAPD) patterns in tomato cell cultures grown for 2 years in different hormonal contexts. In this work, RAPD sequences were characterised and RAPD-derived molecular markers used for a further study of variation between and within auto- and auxo-trophic tomato cultures grown in different hormonal equilibria. Results were then compared with those obtained using microsatellite markers located in noncoding regions of differentiation- and hormone-related genes and with those obtained with the external transcribed spacer (ETS) from tomato rDNA. Hybridisation of RAPDs on a tomato genomic DNA bank, or on total DNA after enzymatic digestion, suggested that the markers were repetitive in nature. Sequence analysis, however, showed that the homology between different fragments was due mainly to the presence of homo-AT nucleotide stretches. Moreover, a series of computational methods, such as an information-theory algorithm coupled with ΔG estimates, suggested that the RAPD fragments isolated in our experiments are noncoding. The amplification of SSR-containing RAPD-derived markers, and of other SSRs located in noncoding regions of tomato functional genes, consistently showed polymorphism between auxo- and auto-trophic somaclones (the latter being either habituated or transgenic for Agrobacterium tumefaciens oncogenes) but not within these same clones. Differences were also found between auxotrophic clones and the differentiated tissue. These findings were confirmed by restriction fragment length polymorphism (RFLP) analysis with the REII repetitive element of the ETS from tomato rDNA, which was isolated during this study. The results obtained suggest a possible role for physiological context in the selection of RAPD patterns during the evolution of tomato cells with different endogenous hormonal equilibria. The results are discussed in terms of a possible role for variation in noncoding regions of hormone-related genes in the adaptation to different physiological contexts.Key words: Lycopersicon esculentum, RAPD, SSR, genetic variation, noncoding DNA, hormone control.
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40
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Amemiya CT, Amores A, Ota T, Mueller G, Garrity D, Postlethwait JH, Litman GW. Generation of a P1 artificial chromosome library of the Southern pufferfish. Gene 2001; 272:283-9. [PMID: 11470535 DOI: 10.1016/s0378-1119(01)00525-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We describe the generation of a P1 artificial chromosome genomic library from the Southern pufferfish, Spheroides nephelus. The arrayed library consists of approximately 30,000 clones and has an average insert size of 125-150 kb. The coverage is estimated to encompass seven to eight genome equivalents. The library has been used for isolating numerous genomic clones and for establishing contigs of several multigene families. Analysis of several of the clones from this library suggests a preponderance of CA repeat tracts relative to their abundance in humans. The library and high-density filters have been made available to the scientific public through genomics distribution companies.
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Affiliation(s)
- C T Amemiya
- Center for Human Genetics, Boston University School of Medicine, 715 Albany Street W408, Boston, MA, USA.
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41
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Shanti K, Kanungo MS. Interaction of nuclear proteins with repeat sequences in the 5' flanking region of mouse muscle creatine kinase gene during aging. Biochem Biophys Res Commun 2001; 283:260-4. [PMID: 11322798 DOI: 10.1006/bbrc.2001.4745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 5' flanking region of the mouse muscle creatine kinase (MCK) gene contains two repeat sequences-a mononucleotide repeat, (A)(22) (-2694 to -2673), and a tetranucleotide repeat, (GTTT)(8) (-2962 to -2931). We show here that these repeats in the mouse MCK gene bind to specific nuclear protein factors. Some of the factors interacting with these sequences are tissue-specific and show age-related decrease in the binding activity. Nonspecific competitor and heterologous DNA probes failed to compete out the complexes showing that the interaction is specific to the repeat sequences. These proteins may have a role in the expression of the gene during aging.
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Affiliation(s)
- K Shanti
- Molecular Biology Laboratory, Banaras Hindu University, Varanasi, 221005, India
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42
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Gerhard GS, Kauffman EJ, Grundy MA. Molecular cloning and sequence analysis of the Danio rerio catalase gene. Comp Biochem Physiol B Biochem Mol Biol 2000; 127:447-57. [PMID: 11281262 DOI: 10.1016/s0305-0491(00)00285-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Catalase is an antioxidant enzyme that plays a central role in the protection against oxidative stress through the metabolism of hydrogen peroxide. Catalase has been well studied in plants, bacteria, and mammals, but little work has been done in other vertebrate species. We have cloned the zebrafish (Danio rerio) catalase cDNA containing the complete coding region and analyzed expression by both reverse transcription polymerase chain reaction and western blot. The deduced amino acid sequence predicts a protein of 526 amino acids with both the primary DNA and amino acid sequences highly conserved among vertebrate species. The major protein-heme contact points in the catalase enzyme complex are also well conserved, although several amino acids associated with the second and third levels of the major substrate channel are not, suggesting potential differences in substrate access or specificity. The 3' flanking region of the cDNA contains a dinucleotide repeat near the termination codon consisting of a near perfect CA array that is polymorphic. The rat and mouse catalase genes also contain a CA repeat sequence in the 3' untranslated region, which, along with an adjacent 5' stem-loop structure, has previously been shown to be a site for mRNA protein binding (Clerch, 1995, Arch. Biochem. Biophys. 317 (1995) 267-274). A stem-loop structure is also predicted adjacent to the zebrafish CA repeat, suggesting a similar role in catalase gene regulation.
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Affiliation(s)
- G S Gerhard
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Abstract
Comparative genomics is a powerful approach to inference of the dynamics of genome evolution. Most information about the evolution of microsatellites in the genus Drosophila has been obtained from Drosophila melanogaster. For comparison, we collected microsatellite data for the distantly related species Drosophila virilis. Screening about 0.5 Mb of nonredundant genomic sequence from GenBank, we identified 239 dinucleotide microsatellites. On average, D. virilis dinucleotides were significantly longer than D. melanogaster microsatellites (7.69 repeats vs. 6.75 repeats). Similarly, direct cloning of microsatellites resulted in a higher mean repeat number in D. virilis than in D. melanogaster (12.7 repeats vs. 12.2 repeats). Characterization of 11 microsatellite loci mapping to division 40-49 on the fourth chromosome of D. virilis indicated that D. virilis microsatellites are more variable than those of D. melanogaster.
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Affiliation(s)
- C Schlötterer
- Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien, Vienna, Austria.
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44
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Roest Crollius H, Jaillon O, Dasilva C, Ozouf-Costaz C, Fizames C, Fischer C, Bouneau L, Billault A, Quetier F, Saurin W, Bernot A, Weissenbach J. Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. Genome Res 2000; 10:939-49. [PMID: 10899143 PMCID: PMC310905 DOI: 10.1101/gr.10.7.939] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tetraodon nigroviridis is a freshwater pufferfish 20-30 million years distant from Fugu rubripes. The genome of both tetraodontiforms is compact, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. The previously uncharacterized Tetraodon genome is described here together with a detailed analysis of its repeat content and organization. We report the sequencing of 46 megabases of bacterial artificial chromosome (BAC) end sequences, which represents a random DNA sample equivalent to 13% of the genome. The sequence and location of rRNA gene clusters, centromeric and subtelocentric satellite sequences have been determined. Minisatellites and microsatellites have been cataloged and notable differences were observed in comparison with microsatellites from Fugu. The genome contains homologies to all known families of transposable elements, including Ty3-gypsy, Ty1-copia, Line retrotransposons, DNA transposons, and retroviruses, although their overall abundance is <1%. This structural analysis is an important prerequisite to sequencing the Tetraodon genome.
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45
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Grützner F, Lütjens G, Rovira C, Barnes DW, Ropers HH, Haaf T. Classical and molecular cytogenetics of the pufferfish Tetraodon nigroviridis. Chromosome Res 2000; 7:655-62. [PMID: 10628667 DOI: 10.1023/a:1009292220760] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Because of its highly compact genome, the pufferfish has become an important animal model in genome research. Although the small chromosome size renders chromosome analysis difficult, we have established both classical and molecular cytogenetics in the freshwater pufferfish Tetraodon nigroviridis (TNI). The karyotype of T. nigroviridis consists of 2n = 42 biarmed chromosomes, in contrast to the known 2n = 44 chromosomes of the Japanese pufferfish Fugu rubripes (FRU). RBA banding can identify homologous chromosomes in both species. TNI 1 corresponds to two smaller FRU chromosomes, explaining the difference in chromosome number. TNI 2 is homologous to FRU 1. Fluorescence in-situ hybridization (FISH) allows one to map single-copy sequences, i.e. the Huntingtin gene, on chromosomes of the species of origin and also on chromosomes of the heterologous pufferfish species. Hybridization of total genomic DNA shows large blocks of (species-specific) repetitive sequences in the pericentromeric region of all TNI and FRU chromosomes. Hybridization with cloned human rDNA and classical silver staining reveal two large and actively transcribed rRNA gene clusters. Similar to the situation in mammals, the highly compact pufferfish genome is endowed with considerable amounts of localized repeat DNAs.
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Affiliation(s)
- F Grützner
- Max-Planck-Institute of Molecular Genetics, Berlin, Germany
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46
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Elgar G, Clark MS, Meek S, Smith S, Warner S, Edwards YJ, Bouchireb N, Cottage A, Yeo GS, Umrania Y, Williams G, Brenner S. Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res 1999; 9:960-71. [PMID: 10523524 PMCID: PMC310822 DOI: 10.1101/gr.9.10.960] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have generated and analyzed >50,000 shotgun clones from 1059 Fugu cosmid clones. All sequences have been minimally edited and searched against protein and DNA databases. These data are all displayed on a searchable, publicly available web site at. With an average of 50 reads per cosmid, this is virtually nonredundant sequence skimming, covering 30%-50% of each clone. This essentially random data set covers nearly 25 Mb (>6%) of the Fugu genome and forms the basis of a series of whole genome analyses which address questions regarding gene density and distribution in the Fugu genome and the similarity between Fugu and mammalian genes. The Fugu genome, with eight times less DNA but a similar gene repertoire, is ideally suited to this type of study because most cosmids contain more than one identifiable gene. General features of the genome are also discussed. We have made some estimation of the syntenic relationship between mammals and Fugu and looked at the efficacy of ORF prediction from short, unedited Fugu genomic sequences. Comparative DNA sequence analyses are an essential tool in the functional interpretation of complex vertebrate genomes. This project highlights the utility of using the Fugu genome in this kind of study.
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Affiliation(s)
- G Elgar
- UK Human Genome Mapping Project (HGMP) Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK.
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47
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Liu Z, Tan G, Li P, Dunham RA. Transcribed dinucleotide microsatellites and their associated genes from channel catfish Ictalurus punctatus. Biochem Biophys Res Commun 1999; 259:190-4. [PMID: 10334938 DOI: 10.1006/bbrc.1999.0751] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The presence of trinucleotide microsatellites within genes is a well-known cause for a number of genetic diseases. However, the precise distribution of dinucleotide microsatellites within genes is less well documented. Here we report 15 unique cDNAs containing dinucleotide repeats from the channel catfish Ictalurus punctatus. Gene identities of nine of the 15 cDNAs were determined, of which three encode structural genes, and six encode regulatory proteins. Five cDNAs harbored dinucleotide repeats in the 5' untranslated region (5'-NTR), nine in the 3'-NTR, and one in the coding region. The presence of these transcribed dinucleotide repeats and their potential expansion in size within coding regions could lead to disruption of the original protein and/or formation of new genes by frame shift. The low number of dinucleotide repeats within coding regions suggests that they were strongly selected against. All the transcribed microsatellite loci examined were polymorphic making them useful for gene mapping in catfish.
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Affiliation(s)
- Z Liu
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, 36849, USA.
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48
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Poulter R, Butler M, Ormandy J. A LINE element from the pufferfish (fugu) Fugu rubripes which shows similarity to the CR1 family of non-LTR retrotransposons. Gene 1999; 227:169-79. [PMID: 10023050 DOI: 10.1016/s0378-1119(98)00600-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study describes the consensus sequence of a full-length (4585bp) non-LTR retrotransposon from the fugu fish, Fugu rubripes. The retrotransposon, termed Maui, is represented by a group of very similar LINE elements found as multiple copies within the fish genome. Two long open reading frames (ORFs) are predicted from the sequence. The first ORF has a domain resembling a novel zinc finger motif recently found in both a turtle and a chicken (CR1) non-LTR retrotransposon. The second ORF includes sequences homologous to the endonuclease, reverse transcriptase and carboxy-terminal domains found in other non-LTR retrotransposons. Sequence comparisons of the predicted translation products of the two ORFs indicate that Maui is most closely related to a class of non-LTR retrotransposons represented by the CR1-like elements (chicken repeat 1 elements) that are present in several avian species and have recently been described in the turtle Platemys spixii. The sequence of the 3' untranslated region also supports this relationship since Maui resembles the CR1 like elements in not having a poly-A tail.
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Affiliation(s)
- R Poulter
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand.
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