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Coleman JL, Wyffels JT, Penfold LM, Richardson D, Maddox JD. Development of genetic markers for reproductive management of toucans. Zoo Biol 2023; 42:825-833. [PMID: 37338091 DOI: 10.1002/zoo.21792] [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: 05/07/2022] [Revised: 04/26/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.
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Affiliation(s)
- Jeffrey L Coleman
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Jennifer T Wyffels
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, Delaware, USA
- Ripley's Aquariums, Orlando, Florida, USA
| | - Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - J Dylan Maddox
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
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2
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Takki O, Komissarov A, Kulak M, Galkina S. Identification of Centromere-Specific Repeats in the Zebra Finch Genome. Cytogenet Genome Res 2022; 162:55-63. [DOI: 10.1159/000521716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/25/2021] [Indexed: 11/19/2022] Open
Abstract
Tandem repetitive sequences represent a significant part of many genomes but remain poorly characterized due to various methodological difficulties. Here, we describe the tandem repeat composition in the genome of zebra finch, <i>Taeniopygia guttata</i>, a species that has long served as an animal model, primarily in neurobiology and comparative genomics. Using available genome sequencing raw read datasets, we bioinformatically reconstructed consensus sequences of several tandem repeats and proved that the most abundant ones, <i>Tgut191A</i> and <i>Tgut716A</i>, are centromere-associated in chromosomes. Each centromeric region can have a different number of copies of each repeat, with <i>Tgut716A</i> enrichment in almost all microchromosomes and sex chromosomes. Sequences similar to <i>Tgut191A</i> and <i>Tgut716A</i> found in other Estrildidae and Viduidae species can be considered as candidate centromeric sequences, but this requires further cytogenetic verification.
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3
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Krietsch J, Cragnolini M, Kuhn S, Lanctot RB, Saalfeld ST, Valcu M, Kempenaers B. Extrapair paternity in a sequentially polyandrous shorebird: limited evidence for the sperm storage hypothesis. Anim Behav 2022. [DOI: 10.1016/j.anbehav.2021.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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4
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Booth Jones KA, Nicoll MAC, Raisin C, Dawson DA, Hipperson H, Horsburgh GJ, Groombridge JJ, Ismar SMH, Sweet P, Jones CG, Tatayah V, Ruhomaun K, Norris K. Widespread gene flow between oceans in a pelagic seabird species complex. Mol Ecol 2017; 26:5716-5728. [PMID: 28833786 DOI: 10.1111/mec.14330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/02/2017] [Accepted: 08/07/2017] [Indexed: 12/15/2022]
Abstract
Global-scale gene flow is an important concern in conservation biology as it has the potential to either increase or decrease genetic diversity in species and populations. Although many studies focus on the gene flow between different populations of a single species, the potential for gene flow and introgression between species is understudied, particularly in seabirds. The only well-studied example of a mixed-species, hybridizing population of petrels exists on Round Island, in the Indian Ocean. Previous research assumed that Round Island represents a point of secondary contact between Atlantic (Pterodroma arminjoniana) and Pacific species (Pterodroma neglecta and Pterodroma heraldica). This study uses microsatellite genotyping and tracking data to address the possibility of between-species hybridization occurring outside the Indian Ocean. Dispersal and gene flow spanning three oceans were demonstrated between the species in this complex. Analysis of migration rates estimated using bayesass revealed unidirectional movement of petrels from the Atlantic and Pacific into the Indian Ocean. Conversely, structure analysis revealed gene flow between species of the Atlantic and Pacific oceans, with potential three-way hybrids occurring outside the Indian Ocean. Additionally, geolocation tracking of Round Island petrels revealed two individuals travelling to the Atlantic and Pacific. These results suggest that interspecific hybrids in Pterodroma petrels are more common than was previously assumed. This study is the first of its kind to investigate gene flow between populations of closely related Procellariiform species on a global scale, demonstrating the need for consideration of widespread migration and hybridization in the conservation of threatened seabirds.
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Affiliation(s)
- Katherine A Booth Jones
- Institute of Zoology, Zoological Society London, London, UK.,Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK
| | | | - Claire Raisin
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK.,Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK
| | - Deborah A Dawson
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK
| | - Helen Hipperson
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK
| | - Gavin J Horsburgh
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK
| | - Jim J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK
| | - Stefanie M H Ismar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul Sweet
- Division of Vertebrate Zoology - Ornithology, American Museum of Natural History, New York, NY, USA
| | - Carl G Jones
- Mauritian Wildlife Foundation, Vacoas, Mauritius.,Durrell Wildlife Conservation Trust, Channel Islands, UK
| | | | - Kevin Ruhomaun
- National Parks and Conservation Service (Government of Mauritius), Reduit, Mauritius
| | - Ken Norris
- Institute of Zoology, Zoological Society London, London, UK
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5
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Botero-Delgadillo E, Quirici V, Poblete Y, Cuevas É, Kuhn S, Girg A, Teltscher K, Poulin E, Kempenaers B, Vásquez RA. Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird. Ecol Evol 2017; 7:8363-8378. [PMID: 29075455 PMCID: PMC5648682 DOI: 10.1002/ece3.3342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/23/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022] Open
Abstract
The distribution of suitable habitat influences natal and breeding dispersal at small spatial scales, resulting in strong microgeographic genetic structure. Although environmental variation can promote interpopulation differences in dispersal behavior and local spatial patterns, the effects of distinct ecological conditions on within‐species variation in dispersal strategies and in fine‐scale genetic structure remain poorly understood. We studied local dispersal and fine‐scale genetic structure in the thorn‐tailed rayadito (Aphrastura spinicauda), a South American bird that breeds along a wide latitudinal gradient. We combine capture‐mark‐recapture data from eight breeding seasons and molecular genetics to compare two peripheral populations with contrasting environments in Chile: Navarino Island, a continuous and low density habitat, and Fray Jorge National Park, a fragmented, densely populated and more stressful environment. Natal dispersal showed no sex bias in Navarino but was female‐biased in the more dense population in Fray Jorge. In the latter, male movements were restricted, and some birds seemed to skip breeding in their first year, suggesting habitat saturation. Breeding dispersal was limited in both populations, with males being more philopatric than females. Spatial genetic autocorrelation analyzes using 13 polymorphic microsatellite loci confirmed the observed dispersal patterns: a fine‐scale genetic structure was only detectable for males in Fray Jorge for distances up to 450 m. Furthermore, two‐dimensional autocorrelation analyzes and estimates of genetic relatedness indicated that related males tended to be spatially clustered in this population. Our study shows evidence for context‐dependent variation in natal dispersal and corresponding local genetic structure in peripheral populations of this bird. It seems likely that the costs of dispersal are higher in the fragmented and higher density environment in Fray Jorge, particularly for males. The observed differences in microgeographic genetic structure for rayaditos might reflect the genetic consequences of population‐specific responses to contrasting environmental pressures near the range limits of its distribution.
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Affiliation(s)
- Esteban Botero-Delgadillo
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile.,SELVA: Research for conservation in the Neotropics Bogotá Colombia
| | - Verónica Quirici
- Departamento de Ecología y Biodiversidad Facultad de Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile.,Centro de Investigación Para la Sustentabilidad Universidad Andrés Bello Santiago Chile
| | - Yanina Poblete
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile.,Instituto de Ciencias Naturales Universidad de las Américas Santiago Chile
| | - Élfego Cuevas
- Doctorado en Medicina de la Conservación Facultad de Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile
| | - Sylvia Kuhn
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Alexander Girg
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Kim Teltscher
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Rodrigo A Vásquez
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
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6
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Moura RF, Dawson DA, Nogueira DM. The use of microsatellite markers in Neotropical studies of wild birds: a literature review. AN ACAD BRAS CIENC 2017; 89:145-154. [PMID: 28177053 DOI: 10.1590/0001-3765201620160378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022] Open
Abstract
Despite extensive habitat fragmentation, the Neotropical region possesses 30% of the world´s bird species. Microsatellites have remained one of the most popular genetic markers and have been used in ecological and conservation studies since the 1990's. We conducted a literature review comparing the number of papers published from January 1990 to July 2015 that used microsatellite markers for studies of wild birds in the Neotropical region, USA and some European countries. We assigned the articles to three categories of studies: population genetics, animal behavior/kinship analysis and the development of species-specific bird microsatellite markers. We also compared the studies in the Neotropics that used heterologous versus species-specific markers and provide a list of heterologous markers of utility in multiple birds. Despite the rich bird fauna in the Neotropics, the number of articles published represents only 5.6% of that published by the USA and selected European countries. Within the Neotropical region, Brazil possessed 60.5% of the total papers published, with the remaining 39.5% shared between five countries. We conclude that the lack of specialized laboratories and resources still represents a limit to microsatellite-based genetic studies of birds within the Neotropical region. To overcome these limitations, we suggest the use of heterologous microsatellite markers as a cost-effective and time-effective tool to assist ecological studies of wild birds.
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Affiliation(s)
- Renan F Moura
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, BR 465, Km 07, 23890-000 Seropédica, RJ, Brazil
| | - Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - Denise M Nogueira
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro/UFRRJ, BR 465 Km 07, 23890-000 Seropédica, RJ, Brazil
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7
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Bi G, dos Remedios N, Dawson DA, Kingma SA, Schroeder J, Dugdale HL. A multiplex set for microsatellite typing and sexing of the European bee-eater (Merops apiaster). EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-1012-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Kleven O, Aarvak T, Jacobsen KO, Solheim R, Øien IJ. Cross-species amplification of microsatellite loci for non-invasive genetic monitoring of the snowy owl (Bubo scandiacus). EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-0986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Sahu J, Das Talukdar A, Devi K, Choudhury MD, Barooah M, Modi MK, Sen P. E-Microsatellite Markers for Centella asiatica (Gotu Kola) Genome: Validation and Cross-Transferability in Apiaceae Family for Plant Omics Research and Development. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:52-65. [DOI: 10.1089/omi.2014.0113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jagajjit Sahu
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
- Department of Life Science and Bioinformatics, Assam University, Assam, India
| | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Assam, India
| | - Kamalakshi Devi
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | | | - Madhumita Barooah
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | - Mahendra Kumar Modi
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | - Priyabrata Sen
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
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10
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Abalaka J, Hudin NS, Ottosson U, Bloomer P, Hansson B. Genetic diversity and population structure of the range restricted rock firefinch Lagonosticta sanguinodorsalis. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0667-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Ferrer ES, García-Navas V, Sanz JJ, Ortego J. Individual genetic diversity and probability of infection by avian malaria parasites in blue tits (Cyanistes caeruleus). J Evol Biol 2014; 27:2468-82. [PMID: 25264126 DOI: 10.1111/jeb.12489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/01/2014] [Indexed: 11/30/2022]
Abstract
Understanding the importance of host genetic diversity for coping with parasites and infectious diseases is a long-standing goal in evolutionary biology. Here, we study the association between probability of infection by avian malaria (Plasmodium relictum) and individual genetic diversity in three blue tit (Cyanistes caeruleus) populations that strongly differ in prevalence of this parasite. For this purpose, we screened avian malaria infections and genotyped 789 blue tits across 26 microsatellite markers. We used two different arrays of markers: 14 loci classified as neutral and 12 loci classified as putatively functional. We found a significant relationship between probability of infection and host genetic diversity estimated at the subset of neutral markers that was not explained by strong local effects and did not differ among the studied populations. This relationship was not linear, and probability of infection increased up to values of homozygosity by locus (HL) around 0.15, reached a plateau at values of HL from 0.15 to 0.40 and finally declined among a small proportion of highly homozygous individuals (HL > 0.4). We did not find evidence for significant identity disequilibrium, which may have resulted from a low variance of inbreeding in the study populations and/or the small power of our set of markers to detect it. A combination of subtle positive and negative local effects and/or a saturation threshold in the association between probability of infection and host genetic diversity in combination with increased resistance to parasites in highly homozygous individuals may explain the observed negative quadratic relationship. Overall, our study highlights that parasites play an important role in shaping host genetic variation and suggests that the use of large sets of neutral markers may be more appropriate for the study of heterozygosity-fitness correlations.
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Affiliation(s)
- E S Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ciudad Real, Spain; Departamento de Ciencias Ambientales, Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
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12
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Martín-Gálvez D, Molina-Morales M, Dawson DA, Parejo D, Martínez JG, Avilés JM. Characterization of 28 microsatellite loci in the European roller Coracias garrulus (Coracidae, AVES). EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0851-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Hosseinpour B, Bakhtiarizadeh MR, Mirabbassi SM, Ebrahimie E. Comparison of hematopoietic cancer stem cells with normal stem cells leads to discovery of novel differentially expressed SSRs. Gene 2014; 550:10-7. [PMID: 25084127 DOI: 10.1016/j.gene.2014.07.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 07/02/2014] [Accepted: 07/29/2014] [Indexed: 11/19/2022]
Abstract
Tandem repeat expansion in the transcriptomics level has been considered as one of the underlying causes of different cancers. Cancer stem cells are a small portion of cancer cells within the main neoplasm and can remain alive during chemotherapy and re-induce tumor growth. The EST-SSR background of cancer stem cells and possible roles of expressed SSRs in altering normal stem cells to cancer ones have not been investigated yet. Here, SSR distributions in hematopoietic normal and cancer stem cells were compared based on the expressed EST-SSR. One hundred eighty nine and 223 EST-SSRs were identified in cancer and normal stem cells, respectively. The EST-SSR expression pattern was significantly different between normal and cancer stem cells. The frequencies of AC/GT and TA/TA EST-SSRs were about 10% higher in cancer than normal stem cells. Remarkably, the number of triplets in cancer stem cells was 1.5 times higher than that in normal stem cells. GAT EST-SSR was frequent in cancer stem cells, but, conversely, normal stem cells did not express GAT EST-SSR. We suggest this EST-SSR as a novel triplet in cancer stem cell induction. Translating EST-SSRs to amino acids demonstrated that Asp and Ile were more abundant in cancer stem cells compared to normal stem cells. Finally, Gene Ontology (GO) enrichment analysis was carried out on genes containing triplet SSRs and showed that SSRs intentionally visit some specific GO classes. Interestingly, a NF-kappa (nuclear factor-kB) binding transcription factor was significantly hit by SSR instability which is a hallmark for leukemia stem cells. NF-kappa is an over represented transcription factor during cancer progression. It seems that there is a crosstalk between the NF-kB transcription factor and expressed GAT tandem repeat which negatively regulate apoptosis. In addition to better understanding of tumorigenesis, the findings of this study offer new DNA markers for diagnostic purposes and identifying at risk populations. In addition, a new approach for gene discovery in cancer by target analysis of differentially expressed EST-SSRs between cancer and normal stem cells is presented here.
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Affiliation(s)
| | | | | | - Esmaeil Ebrahimie
- Institute of Biotechnology, Shiraz University, Shiraz, Iran; School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia.
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14
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Voegeli B, Saladin V, Wegmann M, Richner H. Heterozygosity is linked to the costs of immunity in nestling great tits (Parus major). Ecol Evol 2013; 3:4815-27. [PMID: 24363906 PMCID: PMC3867913 DOI: 10.1002/ece3.854] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 12/02/2022] Open
Abstract
There is growing evidence that heterozygosity–fitness correlations (HFCs) are more pronounced under harsh conditions. Empirical evidence suggests a mediating effect of parasite infestation on the occurrence of HFCs. Parasites have the potential to mediate HFCs not only by generally causing high stress levels but also by inducing resource allocation tradeoffs between the necessary investments in immunity and other costly functions. To investigate the relative importance of these two mechanisms, we manipulated growth conditions of great tit nestlings by brood size manipulation, which modifies nestling competition, and simultaneously infested broods with ectoparasites. We investigated under which treatment conditions HFCs arise and, second, whether heterozygosity is linked to tradeoff decisions between immunity and growth. We classified microsatellites as neutral or presumed functional and analyzed these effects separately. Neutral heterozygosity was positively related to the immune response to a novel antigen in parasite-free nests, but not in infested nests. For nestlings with lower heterozygosity levels, the investments in immunity under parasite pressure came at the expenses of reduced feather growth, survival, and female body condition. Functional heterozygosity was negatively related to nestling immune response regardless of the growth conditions. These contrasting effects of functional and neutral markers might indicate different underlying mechanisms causing the HFCs. Our results confirm the importance of considering marker functionality in HFC studies and indicate that parasites mediate HFCs by influencing the costs of immune defense rather than by a general increase in environmental harshness levels.
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Affiliation(s)
- Beatrice Voegeli
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Verena Saladin
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Michèle Wegmann
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Heinz Richner
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern Baltzerstrasse 6, 3012, Bern, Switzerland
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15
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Cardoso SD, Gonçalves D, Robalo JI, Almada VC, Canário AVM, Oliveira RF. Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats. Mar Genomics 2013; 11:11-6. [PMID: 23665344 DOI: 10.1016/j.margen.2013.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 12/12/2022]
Abstract
Transcriptome data are a good resource to develop microsatellites due to their potential in targeting candidate genes. However, developing microsatellites can be a time-consuming enterprise due to the numerous primer pairs to be tested. Therefore, the use of methodologies that make it efficient to identify polymorphic microsatellites is desirable. Here we used a 62,038 contigs transcriptome assembly, obtained from pyrosequencing a peacock blenny (Salaria pavo) multi-tissue cDNA library, to mine for microsatellites and in silico evaluation of their polymorphism. A total of 4190 microsatellites were identified in 3670 unique unigenes, and from these microsatellites, in silico polymorphism was detected in 733. We selected microsatellites based either on their in silico polymorphism and annotation results or based only on their number of repeats. Using these two approaches, 28 microsatellites were successfully amplified in twenty-six individuals, and all but 2 were found to be polymorphic, being the first genetic markers for this species. Our results showed that the strategy of selection based on number of repeats is more efficient in obtaining polymorphic microsatellites than the strategy of in silico polymorphism (allelic richness was 8.2±3.85 and 4.56±2.45 respectively). This study demonstrates that combining the knowledge of number of repeats with other predictors of variability, for example in silico microsatellite polymorphism, improves the rates of polymorphism, yielding microsatellites with higher allelic richness, and decreases the number of monomorphic microsatellites obtained.
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Affiliation(s)
- Sara D Cardoso
- Unidade de Investigação em Eco-Etologia, Instituto Superior de Psicologia Aplicada - Instituto Universitário, Rua Jardim do Tabaco, 34, 1149-041 Lisboa, Portugal.
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16
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Inbreeding causes early death in a passerine bird. Nat Commun 2012; 3:863. [PMID: 22643890 DOI: 10.1038/ncomms1870] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/25/2012] [Indexed: 01/19/2023] Open
Abstract
Inbreeding typically reduces fitness. Related partners may fail to reproduce and any inbred offspring may die early or fail to reproduce themselves. Here we show that inbreeding causes early death in the zebra finch Taeniopygia guttata, and among inbred individuals of the same inbreeding coefficient (F), those that die early are more homozygous (estimated from single nucleotide polymorphisms) than those that survive to adulthood. Therefore, we identify two ways by which inbreeding depression may be underestimated in studies of inbreeding. First, a failure to study early life history could mean that the magnitude of inbreeding depression is routinely underestimated. Second, the observation that the most homozygous individuals of the same pedigree F were the least likely to survive to sexual maturity provides evidence that realized inbreeding, estimated from a high density of markers spread throughout the genome, explains variation in survival above and beyond what pedigree-based measures of inbreeding can explain.
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17
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Dawson DA, Horsburgh GJ, Krupa AP, Stewart IRK, Skjelseth S, Jensen H, Ball AD, Spurgin LG, Mannarelli ME, Nakagawa S, Schroeder J, Vangestel C, Hinten GN, Burke T. Microsatellite resources for Passeridae species: a predicted microsatellite map of the house sparrow Passer domesticus. Mol Ecol Resour 2012; 12:501-23. [PMID: 22321340 DOI: 10.1111/j.1755-0998.2012.03115.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We identified microsatellite sequences of potential utility in the house sparrow (Passer domesticus) and assigned their predicted genome locations. These sequences included newly isolated house sparrow loci, which we fully characterized. Many of the newly isolated loci were polymorphic in two other species of Passeridae: Berthelot's pipit Anthus berthelotii and zebra finch Taeniopygia guttata. In total, we identified 179 microsatellite markers that were either isolated directly from, or are of known utility in, the house sparrow. Sixty-seven of these markers were designed from unique sequences that we isolated from a house sparrow genomic library. These new markers were combined with 36 house sparrow markers isolated by other studies and 76 markers isolated from other passerine species but known to be polymorphic in the house sparrow. We utilized sequence homology to assign chromosomal locations for these loci in the assembled zebra finch genome. One hundred and thirty-four loci were assigned to 25 different autosomes and eight loci to the Z chromosome. Examination of the genotypes of known-sex house sparrows for 37 of the new loci revealed a W-linked locus and an additional Z-linked locus. Locus Pdoμ2, previously reported as autosomal, was found to be Z-linked. These loci enable the creation of powerful and cost-effective house sparrow multiplex primer sets for population and parentage studies. They can be used to create a house sparrow linkage map and will aid the identification of quantitative trait loci in passerine species.
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Affiliation(s)
- Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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18
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Lesser MR, Parchman TL, Buerkle CA. Cross-species transferability of SSR loci developed from transciptome sequencing in lodgepole pine. Mol Ecol Resour 2011; 12:448-55. [PMID: 22171820 DOI: 10.1111/j.1755-0998.2011.03102.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the advent of next generation sequencing technologies, transcriptome level sequence collections are arising as prominent resources for the discovery of gene-based molecular markers. In a previous study more than 15,000 simple sequence repeats (SSRs) in expressed sequence tag (EST) sequences resulting from 454 pyrosequencing of Pinus contorta cDNA were identified. From these we developed PCR primers for approximately 4000 candidate SSRs. Here, we tested 184 of these SSRs for successful amplification across P. contorta and eight other pine species and examined patterns of polymorphism and allelic variability for a subset of these SSRs. Cross-species transferability was high, with high percentages of loci producing PCR products in all species tested. In addition, 50% of the loci we screened across panels of individuals from three of these species were polymorphic and allelically diverse. We examined levels of diversity in a subset of these SSRs by collecting genotypic data across several populations of Pinus ponderosa in northern Wyoming. Our results indicate the utility of mining pyrosequenced EST collections for gene-based SSRs and provide a source of molecular markers that should bolster evolutionary genetic investigations across the genus Pinus.
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Affiliation(s)
- Mark R Lesser
- Program in Ecology, University of Wyoming, Laramie, WY 82071, USA.
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19
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Bakhtiarizadeh MR, Ebrahimi M, Ebrahimie E. Discovery of EST-SSRs in lung cancer: tagged ESTs with SSRs lead to differential amino acid and protein expression patterns in cancerous tissues. PLoS One 2011; 6:e27118. [PMID: 22073269 PMCID: PMC3208562 DOI: 10.1371/journal.pone.0027118] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 10/11/2011] [Indexed: 11/18/2022] Open
Abstract
Tandem repeats are found in both coding and non-coding sequences of higher organisms. These sequences can be used in cancer genetics and diagnosis to unravel the genetic basis of tumor formation and progression. In this study, a possible relationship between SSR distributions and lung cancer was studied by comparative analysis of EST-SSRs in normal and lung cancerous tissues. While the EST-SSR distribution was similar between tumorous tissues, this distribution was different between normal and tumorous tissues. Trinucleotides tandem repeats were highly different; the number of trinucleotides in ESTs of lung cancer was 3 times higher than normal tissue. Significant negative correlation between normal and cancerous tissue showed that cancerous tissue generates different types of trinucleotides. GGC and CGC were the more frequent expressed trinucleotides in cancerous tissue, but these SSRs were not expressed in normal tissue. Similar to the EST level, the expression pattern of EST-SSRs-derived amino acids was significantly different between normal and cancerous tissues. Arg, Pro, Ser, Gly, and Lys were the most abundant amino acids in cancerous tissues, and Leu, Cys, Phe, and His were significantly more abundant in normal tissues than in cancerous tissues. Next, the putative functions of triplet SSR-containing genes were analyzed. In cancerous tissue, EST-SSRs produce different types of proteins. Chromodomain helicase DNA binding proteins were one of the major protein products of EST-SSRs in the cancerous library, while these proteins were not produced from EST-SSRs in normal tissue. For the first time, the findings of this study confirmed that EST-SSRs in normal lung tissues are different than in unhealthy tissues, and tagged ESTs with SSRs cause remarkable differences in amino acid and protein expression patterns in cancerous tissue. We suggest that EST-SSRs and EST-SSRs differentially expressed in cancerous tissue may be suitable candidate markers for lung cancer diagnosis and prediction.
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Affiliation(s)
| | - Mansour Ebrahimi
- Department of Biology & Bioinformatics Research Group, University of Qom, Qom, Iran
| | - Esmaeil Ebrahimie
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia
- * E-mail:
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20
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Vogiatzi E, Lagnel J, Pakaki V, Louro B, Canario AVM, Reinhardt R, Kotoulas G, Magoulas A, Tsigenopoulos CS. In silico mining and characterization of simple sequence repeats from gilthead sea bream (Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays. Mar Genomics 2011; 4:83-91. [PMID: 21620329 DOI: 10.1016/j.margen.2011.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/09/2011] [Accepted: 01/12/2011] [Indexed: 12/30/2022]
Abstract
We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95 kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number. EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs.
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Affiliation(s)
- Emmanouella Vogiatzi
- Institute of Marine Biology and Genetics (IMBG), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
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21
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WORDLEY CLAIRE, SLATE JON, STAPLEY JESSICA. Mining online genomic resources in
Anolis carolinensis
facilitates rapid and inexpensive development of cross‐species microsatellite markers for the
Anolis
lizard genus. Mol Ecol Resour 2010; 11:126-33. [DOI: 10.1111/j.1755-0998.2010.02863.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- CLAIRE WORDLEY
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - JON SLATE
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - JESSICA STAPLEY
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
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22
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Birkhead TR, Hemmings N, Spottiswoode CN, Mikulica O, Moskát C, Bán M, Schulze-Hagen K. Internal incubation and early hatching in brood parasitic birds. Proc Biol Sci 2010; 278:1019-24. [PMID: 20880882 DOI: 10.1098/rspb.2010.1504] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The offspring of brood parasitic birds benefit from hatching earlier than host young. A proposed but little-known strategy to achieve this is 'internal incubation', by retaining the egg in the oviduct for an additional 24 h. To test this, we quantified the stage of embryo development at laying in four brood parasitic birds (European cuckoo, Cuculus canorus; African cuckoo, Cuculus gularis; greater honeyguide, Indicator indicator; and the cuckoo finch, Anomalospiza imberbis). For the two cuckoos and the honeyguide, all of which lay at 48 h intervals, embryos were at a relatively advanced stage at laying; but for the cuckoo finch (laying interval: 24 h) embryo stage was similar to all other passerines laying at 24 h intervals. The stage of embryo development in the two cuckoos and honeyguide was similar to that of a non-parasitic species that lay at an interval of 44-46 h, but also to the eggs of the zebra finch Taeniopygia guttata incubated artificially at body temperature immediately after laying, for a further 24 h. Comparison with the zebra finch shows that internal incubation in the two cuckoos and honeyguide advances hatching by 31 h, a figure consistent with the difference between the expected and the observed duration of incubation in the European cuckoo predicted from egg mass. Rather than being a specific adaptation to brood parasitism, internal incubation is a direct consequence of a protracted interval between ovulation (and fertilization) and laying, but because it results in early hatching may have predisposed certain species to become brood parasitic.
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Affiliation(s)
- T R Birkhead
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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23
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Xia JH, Yue GH. Identification and analysis of immune-related transcriptome in Asian seabass Lates calcarifer. BMC Genomics 2010; 11:356. [PMID: 20525308 PMCID: PMC2893601 DOI: 10.1186/1471-2164-11-356] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 06/04/2010] [Indexed: 01/21/2023] Open
Abstract
Background Fish diseases caused by pathogens are limiting their production and trade, affecting the economy generated by aquaculture. Innate immunity system is the first line of host defense in opposing pathogenic organisms or any other foreign material. For identification of immune-related genes in Asian seabass Lates calcarifer, an important marine foodfish species, we injected bacterial lipopolysaccharide (LPS), a commonly used elicitor of innate immune responses to eight individuals at the age of 35 days post-hatch and applied the suppression subtractive hybridization (SSH) technique to selectively amplify spleen cDNA of differentially expressed genes. Results Sequencing and bioinformatic analysis of 3351 ESTs from two SSH libraries yielded 1692 unique transcripts. Of which, 618 transcripts were unknown/novel genes and the remaining 1074 were similar to 743 known genes and 105 unannotated mRNA sequences available in public databases. A total of 161 transcripts were classified to the category "response to stimulus" and 115 to "immune system process". We identified 25 significantly up-regulated genes (including 2 unknown transcripts) and 4 down-regulated genes associated with immune-related processes upon challenge with LPS. Quantitative real-time PCR confirmed the differential expression of these genes after LPS challenge. Conclusions The present study identified 1692 unique transcripts upon LPS challenge for the first time in Asian seabass by using SSH, sequencing and bioinformatic analysis. Some of the identified transcripts are vertebrate homologues and others are hitherto unreported putative defence proteins. The obtained immune-related genes may allow for a better understanding of immunity in Asian seabass, carrying out detailed functional analysis of these genes and developing strategies for efficient immune protection against infections in Asian seabass.
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Affiliation(s)
- Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, 117604 Republic of Singapore
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24
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Linking genetic mechanisms of heterozygosity-fitness correlations to footprints of selection at single loci. Evol Ecol 2010. [DOI: 10.1007/s10682-010-9377-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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DAWSON DEBORAHA, HORSBURGH GAVINJ, KÜPPER CLEMENS, STEWART IANRK, BALL ALEXANDERD, DURRANT KATEL, HANSSON BENGT, BACON IDA, BIRD SUSANNAH, KLEIN ÁKOS, KRUPA ANDREWP, LEE JIN, MARTÍN‐GÁLVEZ DAVID, SIMEONI MICHELLE, SMITH GEMMA, SPURGIN LEWISG, BURKE TERRY. New methods to identify conserved microsatellite loci and develop primer sets of high cross‐species utility – as demonstrated for birds. Mol Ecol Resour 2010; 10:475-94. [DOI: 10.1111/j.1755-0998.2009.02775.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- DEBORAH A. DAWSON
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - GAVIN J. HORSBURGH
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - CLEMENS KÜPPER
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - IAN R. K. STEWART
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - ALEXANDER D. BALL
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - KATE L. DURRANT
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - BENGT HANSSON
- Department of Animal Ecology, Ecology Building, Lund University SE‐223 62 Lund, Sweden
| | - IDA BACON
- Institute of Evolutionary Biology, School of Biological Sciences, King’s Building, University of Edinburgh, Edinburgh, EH9 3JT, Scotland, UK
| | - SUSANNAH BIRD
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - ÁKOS KLEIN
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - ANDREW P. KRUPA
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - JIN‐WON LEE
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - DAVID MARTÍN‐GÁLVEZ
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - MICHELLE SIMEONI
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - GEMMA SMITH
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - LEWIS G. SPURGIN
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - TERRY BURKE
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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26
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Ball AD, Stapley J, Dawson DA, Birkhead TR, Burke T, Slate J. A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics 2010; 11:218. [PMID: 20359323 PMCID: PMC2864244 DOI: 10.1186/1471-2164-11-218] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 04/01/2010] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence. RESULTS We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy. CONCLUSIONS When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable.
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Affiliation(s)
- Alexander D Ball
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jessica Stapley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Tim R Birkhead
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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Mossman JA, Slate J, Birkhead TR. Mitochondrial haplotype does not affect sperm velocity in the zebra finch Taeniopygia guttata. J Evol Biol 2009; 23:422-32. [PMID: 20040001 DOI: 10.1111/j.1420-9101.2009.01913.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondrial DNA (mtDNA) variation has been suggested as a possible cause of variation in male fertility because sperm activity is tightly coupled to mitochondrial oxidative phosphorylation and ATP production, both of which are sensitive to mtDNA mutations. Since male-specific phenotypes such as sperm have no fitness consequences for mitochondria due to maternal mitochondrial (and mtDNA) inheritance, mtDNA mutations that are deleterious in males but which have negligible or no fitness effect in females can persist in populations. How often such mutations arise and persist is virtually unknown. To test whether there were associations between mtDNA variation and sperm performance, we haplotyped 250 zebra finches Taeniopygia guttata from a large pedigreed-population and measured sperm velocity using computer-assisted sperm analysis. Using quantitative genetic 'animal' models, we found no effect of mtDNA haplotype on sperm velocity. Therefore, there is no evidence that in this system mitochondrial mutations have asymmetric fitness effects on males and females, leading to genetic variation in male fertility that is blind to natural selection.
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Affiliation(s)
- J A Mossman
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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Olano-Marin J, Dawson DA, Girg A, Hansson B, Ljungqvist M, Kempenaers B, Mueller JC. A genome-wide set of 106 microsatellite markers for the blue tit (Cyanistes caeruleus). Mol Ecol Resour 2009; 10:516-32. [PMID: 21565051 DOI: 10.1111/j.1755-0998.2009.02777.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have characterized a set of 106 microsatellite markers in 26-127 individual blue tits (Cyanistes caeruleus), and assigned their location on the zebra finch (Taeniopygia guttata) and on the chicken (Gallus gallus) genome on the basis of sequence homology. Thirty-one markers are newly designed from zebra finch EST (expressed sequence tags) sequences, 22 markers were developed by others from EST sequences using different methods and the remaining 53 loci were previously designed or modified passerine markers. The 106 microsatellite markers are distributed over 26 and 24 chromosomes in the zebra finch and in the chicken genome respectively and the number of alleles varies between 2 and 49. Eight loci deviate significantly from Hardy-Weinberg equilibrium and show a high frequency of null alleles, and three pairs of markers located in the same chromosome appear to be in linkage disequilibrium. With the exception of these few loci, the polymorphic microsatellite markers presented here provide a useful genome-wide resource for population and evolutionary genetic studies of the blue tit, in addition to their potential utility in other passerine birds.
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Affiliation(s)
- Juanita Olano-Marin
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Postfach 1564, D-82305 Starnberg (Seewiesen), Germany Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK Department of Animal Ecology, Ecology Building, Lund University, SE-223 62 Lund, Sweden
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MARTÍN‐GÁLVEZ DAVID, DAWSON DEBORAHA, HORSBURGH GAVINJ, BURKE TERRY. Isolation, characterization and chromosome locations of polymorphic black‐billed magpie
Pica pica
(Corvidae, AVES) microsatellite loci. Mol Ecol Resour 2009; 9:1506-12. [DOI: 10.1111/j.1755-0998.2009.02703.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- DAVID MARTÍN‐GÁLVEZ
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - DEBORAH A. DAWSON
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - GAVIN J. HORSBURGH
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - TERRY BURKE
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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30
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Shan X, Ray DA, Bunge JA, Peterson DG. A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization. BMC Genomics 2009; 10 Suppl 2:S9. [PMID: 19607660 PMCID: PMC2966330 DOI: 10.1186/1471-2164-10-s2-s9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian. Results The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. NotI digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7×) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole). Conclusion We have demonstrated the utility of the Crocodylus porosus BAC library as a tool in genomics research. The BAC library should expedite complete genome sequencing of C. porosus and facilitate detailed analysis of genome evolution within Crocodylia and between crocodilians and diverse amniote lineages including birds, mammals, and other non-avian reptiles.
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Affiliation(s)
- Xueyan Shan
- Mississippi Genome Exploration Laboratory, Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, USA.
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LEE JINWON, JANG BYOUNGSOON, DAWSON DEBORAHA, BURKE TERRY, HATCHWELL BENJ. Fine-scale genetic structure and its consequence in breeding aggregations of a passerine bird. Mol Ecol 2009; 18:2728-39. [DOI: 10.1111/j.1365-294x.2009.04228.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
Although the application of population and evolutionary genetic theory and methods to address issues of conservation relevance has a long history, the formalization of conservation genetics as a research field is still relatively recent. One of the periodic catalysts for increased research effort in the field has been advances in molecular technologies, leading to an increasingly wider variety of molecular markers for application in conservation genetic studies. To date, genetic methods have been applied in conservation biology primarily as selectively neutral molecular tools for resolving questions of conservation relevance. However, there has been renewed interest in complementing the analysis of neutral markers with the assessment of loci that may be directly involved in responses to processes such as environmental change, with a view to identifying the genes involved in them. These kinds of studies are now possible due to the increase in availability of genomic resources for nonmodel organisms, and there will likely be an even more rapid increase in the near future due to the advent of new ultrahigh throughput-sequencing technologies. This review considers the implications of the most recent developments in genomic technologies and their potential for contributing to the conservation of populations and species. Three "conservation genomics" case studies are presented (Atlantic salmon, Salmo sala; the butterfly, Melitaea cinxia; and the California condor, Gymnogyps californianus) in order to demonstrate the diversity of applications now possible. While it is clear that genomics approaches in conservation will not replace other tried-and-true methods, these recent developments open up an exciting new range of possibilities that will enable further diversification of the application of genomics in conservation biology.
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Affiliation(s)
- Craig R Primmer
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
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Simeoni M, Dawson DA, Gentle LK, Coiffait L, Wolff K, Evans KL, Gaston KJ, Hatchwell BJ. Characterization of 38 microsatellite loci in the European blackbird, Turdus merula (Turdidae, AVES). Mol Ecol Resour 2009; 9:1520-6. [PMID: 21564948 DOI: 10.1111/j.1755-0998.2009.02708.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We characterized 38 microsatellite loci in the European blackbird, Turdus merula. Thirty-seven loci were identified by testing 242 loci that had been originally isolated in other avian species. One additional locus was isolated from a European blackbird genomic library. All loci were characterized in 20-29 blackbirds from a population in the Czech Republic and displayed between two and 16 alleles, with observed heterozygosity ranging from 0.04 to 1.00. Thirty-seven loci could be assigned a chromosome location in the zebra finch (Taeniopygia guttata) genome based on sequence homology.
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Affiliation(s)
- Michelle Simeoni
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Yue GH, Zhu ZY, Wang CM, Xia JH. A simple and efficient method for isolating polymorphic microsatellites from cDNA. BMC Genomics 2009; 10:125. [PMID: 19320968 PMCID: PMC2667190 DOI: 10.1186/1471-2164-10-125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 03/25/2009] [Indexed: 11/21/2022] Open
Abstract
Background Microsatellites in cDNA are useful as molecular markers because they represent transcribed genes and can be used as anchor markers for linkage and comparative mapping, as well as for studying genome evolution. Microsatellites in cDNA can be detected in existing ESTs by data mining. However, in most fish species, no ESTs are available or the number of ESTs is limited, although fishes represent half of the vertebrates on the earth. We developed a simple and efficient method for isolation of microsatellites from cDNA in fish. Results The method included normalization of 150 ng cDNA using 0.5 U duplex-specific nuclease (DSN) at 65°C for 30 min, enrichment of microsatellites using biotinylated oligonucleotides and magnetic field, and directional cloning of cDNA into a vector. We tested this method to enrich CA- and GA-microsatellites from cDNA of Asian seabass, and demonstrated that enrichment of microsatellites from normalized cDNA could increased the efficiency of microsatellite isolation over 30 times as compared to direct sequencing of clones from cDNA libraries. One hundred and thirty-nine (36.2%) out of 384 clones from normalized cDNA contained microsatellites. Unique microsatellite sequences accounted for 23.6% (91/384) of sequenced clones. Sixty microsatellites isolated from cDNA were characterized, and 41 were polymorphic. The average allele number of the 41 microsatellites was 4.85 ± 0.54, while the expected heterozygosity was 0.56 ± 0.03. All the isolated microsatellites inherited in a Mendelian pattern. Conclusion Normalization of cDNA substantially increased the efficiency of enrichment of microsatellites from cDNA. The described method for isolation of microsatellites from cDNA has the potential to be applied to a wide range of fish species. The microsatellites isolated from cDNA could be useful for linkage and comparative mapping, as well as for studying genome evolution.
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Affiliation(s)
- Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Lab, 1 Research Link, National University of Singapore, 117604 Singapore.
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A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution. Genetics 2008; 179:651-67. [PMID: 18493078 DOI: 10.1534/genetics.107.086264] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Passeriformes are the largest order of birds and one of the most widely studied groups in evolutionary biology and ecology. Until recently genomic tools in passerines relied on chicken genomic resources. Here we report the construction and analysis of a whole-genome linkage map for the zebra finch (Taeniopygia guttata) using a 354-bird pedigree. The map contains 876 SNPs dispersed across 45 linkage groups and we found only a few instances of interchromosomal rearrangement between the zebra finch and the chicken genomes. Interestingly, there was a greater than expected degree of intrachromosomal rearrangements compared to the chicken, suggesting that gene order is not conserved within avian chromosomes. At 1068 cM the map is approximately only one quarter the length of the chicken linkage map, providing further evidence that the chicken has an unusually high recombination rate. Male and female linkage-map lengths were similar, suggesting no heterochiasmy in the zebra finch. This whole-genome map is the first for any passerine and a valuable tool for the zebra finch genome sequence project and for studies of quantitative trait loci.
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Tang J, Baldwin SJ, Jacobs JM, Linden CGVD, Voorrips RE, Leunissen JA, van Eck H, Vosman B. Large-scale identification of polymorphic microsatellites using an in silico approach. BMC Bioinformatics 2008; 9:374. [PMID: 18793407 PMCID: PMC2562394 DOI: 10.1186/1471-2105-9-374] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 09/15/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative SSR markers still is time consuming and expensive. In many species only a relatively small percentage of SSR markers turn out to be polymorphic. This is particularly true for markers derived from expressed sequence tags (ESTs). In EST databases a large redundancy of sequences is present, which may contain information on length-polymorphisms in the SSR they contain, and whether they have been derived from heterozygotes or from different genotypes. Up to now, although a number of programs have been developed to identify SSRs in EST sequences, no software can detect putatively polymorphic SSRs. RESULTS We have developed PolySSR, a new pipeline to identify polymorphic SSRs rather than just SSRs. Sequence information is obtained from public EST databases derived from heterozygous individuals and/or at least two different genotypes. The pipeline includes PCR-primer design for the putatively polymorphic SSR markers, taking into account Single Nucleotide Polymorphisms (SNPs) in the flanking regions, thereby improving the success rate of the potential markers. A large number of polymorphic SSRs were identified using publicly available EST sequences of potato, tomato, rice, Arabidopsis, Brassica and chicken.The SSRs obtained were divided into long and short based on the number of times the motif was repeated. Surprisingly, the frequency of polymorphic SSRs was much higher in the short SSRs. CONCLUSION PolySSR is a very effective tool to identify polymorphic SSRs. Using PolySSR, several hundred putative markers were developed and stored in a searchable database. Validation experiments showed that almost all markers that were indicated as putatively polymorphic by polySSR were indeed polymorphic. This greatly improves the efficiency of marker development, especially in species where there are low levels of polymorphism, like tomato. When combined with the new sequencing technologies PolySSR will have a big impact on the development of polymorphic SSRs in any species.PolySSR and the polymorphic SSR marker database are available from http://www.bioinformatics.nl/tools/polyssr/.
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Affiliation(s)
- Jifeng Tang
- Laboratory of Bioinformatics, Wageningen University, PO Box 8128, 6700 ET Wageningen, the Netherlands.
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Karaiskou N, Buggiotti L, Leder E, Primmer CR. High degree of transferability of 86 newly developed zebra finch EST-linked microsatellite markers in 8 bird species. ACTA ACUST UNITED AC 2008; 99:688-93. [PMID: 18583388 DOI: 10.1093/jhered/esn052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
High-resolution analysis for population genetic and functional studies requires the use of large numbers of polymorphic markers. The recent increase of available genetic tools is facilitated by the use of publicly available expressed sequence tag (EST) sequence databases that are a valuable resource for identifying gene-linked markers. In the present study, we applied bioinformatics analyses to identify microsatellite markers present in EST sequences from a zebra finch (Taeniopgia guttata) EST database and we explore the success of cross-species amplification of EST-linked microsatellite markers in 7 passerine and 1 nonpasserine species. Eighty-six zebra finch EST-linked microsatellite loci were screened for polymorphism revealing a high amplification success rate and adequate levels of polymorphism (33.3-51%) for relatively closely related species, whereas success decreased in the most distantly related species to zebra finch. EST-linked microsatellites appear to be more highly transferable between taxa than anonymous microsatellites as they revealed higher amplification and polymorphism success between different families indicating that they will be a useful source of gene-linked polymorphic markers in a broad range of avian species.
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Affiliation(s)
- Nikoletta Karaiskou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, PO Box 54 124, Thessaloniki, Macedonia, Greece
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Replogle K, Arnold AP, Ball GF, Band M, Bensch S, Brenowitz EA, Dong S, Drnevich J, Ferris M, George JM, Gong G, Hasselquist D, Hernandez AG, Kim R, Lewin HA, Liu L, Lovell PV, Mello CV, Naurin S, Rodriguez-Zas S, Thimmapuram J, Wade J, Clayton DF. The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution. BMC Genomics 2008; 9:131. [PMID: 18366674 PMCID: PMC2329646 DOI: 10.1186/1471-2164-9-131] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 03/18/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts. RESULTS We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500-15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing approximately 22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations. CONCLUSION Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.
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Affiliation(s)
- Kirstin Replogle
- Cell & Developmental Biology, Univ. of Illinois, Urbana, IL, USA
- Institute for Genomic Biology, Univ. of Illinois, Urbana, IL, USA
| | | | - Gregory F Ball
- Psychological & Brain Sci., Johns Hopkins Univ., Baltimore, MD, USA
| | - Mark Band
- W.M. Keck Center for Comparative & Functional Genomics, Univ. of Illinois, Urbana, IL, USA
| | | | - Eliot A Brenowitz
- Psychology, Biology, and Bloedel Hearing Research Center, Univ. of Washington, Seattle, WA, USA
| | - Shu Dong
- Cell & Developmental Biology, Univ. of Illinois, Urbana, IL, USA
| | - Jenny Drnevich
- W.M. Keck Center for Comparative & Functional Genomics, Univ. of Illinois, Urbana, IL, USA
| | | | - Julia M George
- Mol. & Integrative Physiology, Univ. of Illinois, Urbana, IL, USA
| | - George Gong
- W.M. Keck Center for Comparative & Functional Genomics, Univ. of Illinois, Urbana, IL, USA
| | | | - Alvaro G Hernandez
- W.M. Keck Center for Comparative & Functional Genomics, Univ. of Illinois, Urbana, IL, USA
| | - Ryan Kim
- W.M. Keck Center for Comparative & Functional Genomics, Univ. of Illinois, Urbana, IL, USA
| | - Harris A Lewin
- Institute for Genomic Biology, Univ. of Illinois, Urbana, IL, USA
- Animal Sciences, Univ. of Illinois, Urbana, IL, USA
| | - Lei Liu
- W.M. Keck Center for Comparative & Functional Genomics, Univ. of Illinois, Urbana, IL, USA
| | - Peter V Lovell
- Neurological Sci. Inst., Oregon Hlth. Sci. Univ., Beaverton, OR, USA
| | - Claudio V Mello
- Neurological Sci. Inst., Oregon Hlth. Sci. Univ., Beaverton, OR, USA
| | - Sara Naurin
- Animal Ecology, Lund University, S-223 62 Lund, Sweden
| | | | - Jyothi Thimmapuram
- W.M. Keck Center for Comparative & Functional Genomics, Univ. of Illinois, Urbana, IL, USA
| | - Juli Wade
- Psychology, Zoology & Neuroscience, Michigan State Univ., East Lansing, MI, USA
| | - David F Clayton
- Cell & Developmental Biology, Univ. of Illinois, Urbana, IL, USA
- Institute for Genomic Biology, Univ. of Illinois, Urbana, IL, USA
- Neuroscience Program, Univ. of Illinois, Urbana, IL, USA
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Kim KS, Ratcliffe ST, French BW, Liu L, Sappington TW. Utility of EST-Derived SSRs as Population Genetics Markers in a Beetle. J Hered 2008; 99:112-24. [DOI: 10.1093/jhered/esm104] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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