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Kumar C, Kumar R, Singh SK, Goswami AK, Nagaraja A, Paliwal R, Singh R. Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies. PLoS One 2020; 15:e0237538. [PMID: 32804981 PMCID: PMC7431106 DOI: 10.1371/journal.pone.0237538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Dearth of genomic resources particularly, microsatellite markers in nutritionally and commercially important fruit crop, guava necessitate the development of the novel genomic SSR markers through the library enrichment techniques. Three types of 3' -biotinylated oligonucleotide probes [(CT)14, (GT)12, and (AAC)8] were used to develop microsatellite enriched libraries. A total of 153 transformed colonies were screened of which 111 positive colonies were subjected for Sanger sequencing. The clones having more than five motif repeats were selected for primer designing and a total of 38 novel genomic simple sequence repeats could be identified. The g-SSRs had the motif groups ranging from monomer to pentamer out of which dimer group occurred the most (89.47%). Out of 38 g-SSRs markers developed, 26 were found polymorphic, which showed substantial genetic diversity among the guava genotypes including wild species. The average number of alleles per locus, major allele frequency, gene diversity, expected heterozygosity and polymorphic information content of 26 SSRs were 3.46, 0.56, 0.53, 0.29 and 0.46, respectively. The rate of cross-species transferability of the developed g-SSR loci varied from 38.46 to 80.77% among the studied wild Psidium species. Generation of N-J tree based on 26 SSRs grouped the 40 guava genotypes into six clades with two out-groups, the wild guava species showed genetic distinctness from cultivated genotypes. Furthermore, population structure analysis grouped the guava genotypes into three genetic groups, which were partly supported by PCoA and N-J tree. Further, AMOVA and PCoA deciphered high genetic diversity among the present set of guava genotypes including wild species. Thus, the developed novel g-SSRs were found efficient and informative for diversity and population structure analyses of the guava genotypes. These developed novel g-SSR loci would add to the new genomic resource in guava, which may be utilized in genomic-assisted guava breeding.
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Affiliation(s)
- Chavlesh Kumar
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ramesh Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Goswami
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - A. Nagaraja
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ritu Paliwal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Tian R, Zhang C, Huang Y, Guo X, Chen M. A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data. Genes (Basel) 2019; 10:E917. [PMID: 31717904 PMCID: PMC6895799 DOI: 10.3390/genes10110917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022] Open
Abstract
Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.
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Affiliation(s)
| | | | | | | | - Maohua Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, Yangling 712100, China; (R.T.); (C.Z.); (Y.H.); (X.G.)
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Wu JX, Zhang YN, Deng DD, Xu XX, Zhou ZZ. Analysis on Microsatellite Loci of Daphnia similoides sinensis and Rapid Development of Primer Based on Transcriptome Sequencing. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419060188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Development and characterization of polymorphic microsatellite markers in northern fulmar, Fulmarus glacialis (Procellariiformes), and cross-species amplification in eight other seabirds. Genes Genomics 2019; 41:1015-1026. [PMID: 31134591 DOI: 10.1007/s13258-019-00819-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 04/11/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND In the North Pacific, northern fulmar (Fulmarus glacialis) forms extensive colonies in few locales, which may lead to limited gene flow and locale-specific population threats. In the Atlantic, there are thousands of colonies of varying sizes and in Europe the species is considered threatened. Prior screens and classical microsatellite development in fulmar failed to provide a suite of markers adequate for population genetics studies. OBJECTIVES The objective of this study was to isolate a suite of polymorphic microsatellite loci with sufficient variability to quantify levels of gene flow, population affinity, and identify familial relationships in fulmar. We also performed a cross-species screening of these markers in eight other species. METHODS We used shotgun sequencing to isolate 26 novel microsatellite markers in fulmar to screen for variability using individuals from two distinct regions: the Pacific (Chagulak Island, Alaska) and the Atlantic (Hafnarey Island, Iceland). RESULTS Polymorphism was present in 24 loci in Chagulak and 23 in Hafnarey, while one locus failed to amplify in either colony. Polymorphic loci exhibited moderate levels of genetic diversity and this suite of loci uncovered genetic structuring between the regions. Among the other species screened, polymorphism was present in one to seven loci. CONCLUSION The loci yielded sufficient variability for use in population studies and estimation of familial relationships; as few as five loci provide resolution to determine individual identity. These markers will allow further insight into the global population dynamics and phylogeography of fulmars. We also demonstrated some markers are transferable to other species.
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Sun S, Fu P, Cheng Y, Zhou X, Han J. Characterization and transferability of microsatellites for Gentiana lawrencei var. farreri (Gentianaceae). APPLICATIONS IN PLANT SCIENCES 2018; 6:e1015. [PMID: 29732246 PMCID: PMC5828123 DOI: 10.1002/aps3.1015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/13/2017] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed for a medicinal herb, Gentiana lawrencei var. farreri (Gentianaceae), for the future assessment of population genetic structure and potential hybridization events with related taxa. METHODS AND RESULTS Using the 454 FLX+ sequencing platform, we obtained 81,717 clean reads with an average length of 291 bp. A total of 3031 primer pairs were designed, and 96 were selected for validation. A set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms in three G. lawrencei var. farreri populations and one G. veitchiorum population. Among the four populations, the average number of alleles per locus was 15.2. Finally, a set of 17 unlinked loci were determined to be in Hardy-Weinberg equilibrium after two linked loci were removed. CONCLUSIONS The identified simple sequence repeat markers will be useful for genetic diversity and evolution studies in G. lawrencei var. farreri and related taxa.
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Affiliation(s)
- Shan‐Shan Sun
- College of Life ScienceLuoyang Normal University6 Jiqing RoadLuoyangHennaPeople's Republic of China
| | - Peng‐Cheng Fu
- College of Life ScienceLuoyang Normal University6 Jiqing RoadLuoyangHennaPeople's Republic of China
| | - Yan‐Wei Cheng
- College of Life ScienceLuoyang Normal University6 Jiqing RoadLuoyangHennaPeople's Republic of China
| | - Xiao‐Jun Zhou
- College of Life ScienceLuoyang Normal University6 Jiqing RoadLuoyangHennaPeople's Republic of China
| | - Jian‐Min Han
- College of Life ScienceLuoyang Normal University6 Jiqing RoadLuoyangHennaPeople's Republic of China
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6
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Development and characterization of a new set of genomic microsatellite markers in rice bean (Vigna umbellata (Thunb.) Ohwi and Ohashi) and their utilization in genetic diversity analysis of collections from North East India. PLoS One 2017; 12:e0179801. [PMID: 28686712 PMCID: PMC5501436 DOI: 10.1371/journal.pone.0179801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/05/2017] [Indexed: 12/15/2022] Open
Abstract
Rice bean [Vigna umbellate (Thumb.) Ohwi and Ohashi] is an underutilized crop believed to be domesticated in the Myanmar-Thailand region of Asia. In India, rice bean is mainly cultivated in the North-Eastern Hills, which is a hotspot for biological diversity. A 5' anchored PCR was used to develop microsatellite markers in rice bean. Twenty-eight specific primer pairs were designed and employed to characterize sixty five ricebean accessions collected from North East India. A total of 179 alleles were amplified with an average of 6.393 alleles per locus. The gene diversity was high (mean 0.534) in the accessions collected from Darjeeling, Nagaland and Manipur, which are bordering areas with East Nepal and Myanmar, respectively. Exceptionally high outcrossing rate was observed in the entire population. Population structure analysis identified three distinct clusters in which accessions collected from areas bordering Myanmar and East Nepal grouped separately. Using a combination of STRUCTURE and Principal Coordinate Analysis, relative affinity of the intermediate accessions could be established. However, differences in allelic counts among populations were non-significant. The results showed that there is a high level of genetic diversity within the accessions, with high outcrossing rate.
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Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA. Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration. Nucleic Acids Res 2017; 45:1553-1565. [PMID: 28007941 PMCID: PMC5388403 DOI: 10.1093/nar/gkw1226] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 11/22/2016] [Indexed: 11/14/2022] Open
Abstract
Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated.
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Affiliation(s)
- Lauren B A Woodruff
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas E Gorochowski
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas Roehner
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Tarjei S Mikkelsen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Douglas Densmore
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - D Benjamin Gordon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Nicol
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Christopher A Voigt
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Glenn TC, Faircloth BC. Capturing Darwin's dream. Mol Ecol Resour 2016; 16:1051-8. [PMID: 27454358 PMCID: PMC5318190 DOI: 10.1111/1755-0998.12574] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 01/28/2023]
Abstract
Evolutionary biologists from Darwin forward have dreamed of having data that would elucidate our understanding of evolutionary history and the diversity of life. Sequence capture is a relatively old DNA technology, but its use is growing rapidly due to advances in (i) massively parallel DNA sequencing approaches and instruments, (ii) massively parallel bait construction, (iii) methods to identify target regions and (iv) sample preparation. We give a little historical context to these developments, summarize some of the important advances reported in this special issue and point to further advances that can be made to help fulfill Darwin's dream.
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Affiliation(s)
- Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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Saeed AF, Wang R, Wang S. Microsatellites in Pursuit of Microbial Genome Evolution. Front Microbiol 2016; 6:1462. [PMID: 26779133 PMCID: PMC4700210 DOI: 10.3389/fmicb.2015.01462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022] Open
Abstract
Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.
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Affiliation(s)
- Abdullah F. Saeed
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
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Isolation and characterization of 14 polymorphic microsatellite loci in the big-headed turtle (Platysternon megacephalum). Biochem Genet 2014; 52:203-8. [PMID: 24449181 DOI: 10.1007/s10528-014-9640-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
Abstract
The big-headed turtle (Platysternon megacephalum) is critically endangered because of overharvesting, illegal trade, and habitat destruction. Assessment of genetic variability in existing populations becomes very important to the taxonomy and conservation of this species. Here we describe 14 microsatellite loci isolated from an enriched genomic library of the big-headed turtle, and the polymorphisms of these loci were assessed in 28 individuals from Huizhou, Heyuan, Zhaoqing, and Shaoguan of Guangdong, China. The range of polymorphism information content is 0.305-0.738, and no evidence of significant linkage disequilibrium was found among any pairs of loci. These 14 new polymorphic microsatellite loci can be used in population genetics, taxonomy, phylogeography, behavior ecology, and conservation efforts of Platysternon megacephalum.
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Gao Z, Wu J, Liu Z, Wang L, Ren H, Shu Q. Rapid microsatellite development for tree peony and its implications. BMC Genomics 2013; 14:886. [PMID: 24341681 PMCID: PMC3878651 DOI: 10.1186/1471-2164-14-886] [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: 06/03/2013] [Accepted: 12/04/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microsatellites are ubiquitous in genomes of various organisms. With the realization that they play roles in developmental and physiological processes, rather than exist as 'junk' DNA, microsatellites are receiving increasing attention. Next-generation sequencing allows acquisition of large-scale microsatellite information, and is especially useful for plants without reference genome sequences. RESULTS In this study, enriched DNA libraries of tree peony, a well-known ornamental woody shrub, were used for high-throughput microsatellite development by 454 GS-FLX Titanium pyrosequencing. We obtained 675,221 reads with an average length of 356 bp. The total size of examined sequences was 240,672,018 bp, from which 237,134 SSRs were identified. Of these sequences, 164,043 contained SSRs, with 27% featuring more than one SSR. Interestingly, a high proportion of SSRs (43%) were present in compound formation. SSRs with repeat motifs of 1-4 bp (mono-, di-, tri-, and tetra-nucleotide repeats) accounted for 99.8% of SSRs. Di-nucleotide repeats were the most abundant. As in most plants, the predominant motif in tree peony was (A/T)n, with (G/C)n less common. The lengths of SSRs were classified into 11 groups. The shortest SSRs (10 bp) represented 1% of the total number, whereas SSRs 21-30 and 101-110 bp long accounted for 26% and 29%, respectively, of all SSRs. Many sequences (42,111) were mapped to CDS (coding domain sequence) regions using Arabidopsis as a reference. GO annotation analysis predicted that CDSs with SSRs performed various functions associated with cellular components, molecular functions, and biological processes. Of 100 validated primer pairs, 24 were selected for polymorphism analysis among 23 genotypes; cluster analysis of the resulting data grouped genotypes according to known relationships, confirming the usefulness of the developed SSR markers. CONCLUSIONS The results of our large-scale SSR marker development using tree peony are valuable for investigating plant genomic structural evolution and elucidating phenotypic variation in this species during its evolution and artificial selection. The newly identified SSRs should be useful for genetic linkage map construction, QTL mapping, gene location and cloning, and molecular marker-assisted breeding. In addition, the genome-wide marker resources generated in this study should aid genomic studies of tree peony and related species.
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Affiliation(s)
- Zhimin Gao
- Beijing Botanical Garden, Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, PR China.
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Cruse-Sanders JM, Parker KC, Friar EA, Huang DI, Mashayekhi S, Prince LM, Otero-Arnaiz A, Casas A. Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico. Ecol Evol 2013; 3:1340-55. [PMID: 23762520 PMCID: PMC3678488 DOI: 10.1002/ece3.524] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 12/16/2012] [Accepted: 12/18/2012] [Indexed: 11/12/2022] Open
Abstract
Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (H E = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear-cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species.
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Du FK, Xu F, Qu H, Feng S, Tang J, Wu R. Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR database. PLoS One 2013; 8:e61337. [PMID: 23593466 PMCID: PMC3623821 DOI: 10.1371/journal.pone.0061337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/08/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Microsatellite markers or Simple Sequence Repeats (SSRs) are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. METHODOLOGY/PRINCIPAL FINDINGS A total of 94,090 non-redundant Expressed Sequence Tags (ESTs) from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37%) and hexanucleotides (33%) repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs) and selected 673 of these pairs at random for further validation. 575 pairs (85%) gave successful amplification, of which, 464 (80.7%) were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html). CONCLUSIONS The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.
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Affiliation(s)
- Fang K. Du
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Fang Xu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hong Qu
- Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
| | - Sisi Feng
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jijun Tang
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, United States of America
| | - Rongling Wu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Smee MR, Pauchet Y, Wilkinson P, Wee B, Singer MC, ffrench-Constant RH, Hodgson DJ, Mikheyev AS. Microsatellites for the marsh fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers. PLoS One 2013; 8:e54721. [PMID: 23349956 PMCID: PMC3549983 DOI: 10.1371/journal.pone.0054721] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/14/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Until recently the isolation of microsatellite markers from Lepidoptera has proved troublesome, expensive and time-consuming. Following on from a previous study of Edith's checkerspot butterfly, Euphydryas editha, we developed novel microsatellite markers for the vulnerable marsh fritillary butterfly, E. aurinia. Our goal was to optimize the process in order to reduce both time and cost relative to prevailing techniques. This was accomplished by using a combination of previously developed techniques: in silico mining of a de novo assembled transcriptome sequence, and genotyping the microsatellites found there using an economic method of fluorescently labelling primers. PRINCIPAL FINDINGS In total, we screened nine polymorphic microsatellite markers, two of which were previously published, and seven that were isolated de novo. These markers were able to amplify across geographically isolated populations throughout Continental Europe and the UK. Significant deviations from Hardy-Weinberg equilibrium were evident in some populations, most likely due to the presence of null alleles. However, we used an F(st) outlier approach to show that these markers are likely selectively neutral. Furthermore, using a set of 128 individuals from 11 populations, we demonstrate consistency in population differentiation estimates with previously developed amplified fragment length polymorphism (AFLP) markers (r = 0.68, p<0.001). SIGNIFICANCE Rapid development of microsatellite markers for difficult taxa such as Lepidoptera, and concordant results with other putatively neutral molecular markers, demonstrate the potential of de novo transcriptional sequencing for future studies of population structure and gene flow that are desperately needed for declining species across fragmented landscapes.
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Affiliation(s)
- Melanie R Smee
- Department of Biology, University of York, York, United Kingdom.
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Di Maio A, De Castro O. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology. APPLICATIONS IN PLANT SCIENCES 2013; 1:apps1200158. [PMID: 25202476 PMCID: PMC4105349 DOI: 10.3732/apps.1200158] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 10/17/2012] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • METHODS AND RESULTS We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • CONCLUSIONS The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.
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Affiliation(s)
- Antonietta Di Maio
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Via Foria 223, 80139 Napoli, Italy
| | - Olga De Castro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Via Foria 223, 80139 Napoli, Italy
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Yang T, Bao SY, Ford R, Jia TJ, Guan JP, He YH, Sun XL, Jiang JY, Hao JJ, Zhang XY, Zong XX. High-throughput novel microsatellite marker of faba bean via next generation sequencing. BMC Genomics 2012; 13:602. [PMID: 23137291 PMCID: PMC3542174 DOI: 10.1186/1471-2164-13-602] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/04/2012] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Faba bean (Vicia faba L.) is an important food legume crop, grown for human consumption globally including in China, Turkey, Egypt and Ethiopia. Although genetic gain has been made through conventional selection and breeding efforts, this could be substantially improved through the application of molecular methods. For this, a set of reliable molecular markers representative of the entire genome is required. RESULTS A library with 125,559 putative SSR sequences was constructed and characterized for repeat type and length from a mixed genome of 247 spring and winter sown faba bean genotypes using 454 sequencing. A suit of 28,503 primer pair sequences were designed and 150 were randomly selected for validation. Of these, 94 produced reproducible amplicons that were polymorphic among 32 faba bean genotypes selected from diverse geographical locations. The number of alleles per locus ranged from 2 to 8, the expected heterozygocities ranged from 0.0000 to 1.0000, and the observed heterozygosities ranged from 0.0908 to 0.8410. The validation by UPGMA cluster analysis of 32 genotypes based on Nei's genetic distance, showed high quality and effectiveness of those novel SSR markers developed via next generation sequencing technology. CONCLUSIONS Large scale SSR marker development was successfully achieved using next generation sequencing of the V. faba genome. These novel markers are valuable for constructing genetic linkage maps, future QTL mapping, and marker-assisted trait selection in faba bean breeding efforts.
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Affiliation(s)
- Tao Yang
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Bei R, Chen J, Liu H, Huang J, Yu H, Wu Z. Isolation and characterization of 12 microsatellite loci in the Chinese crocodile lizard (Shinisaurus crocodilurus). CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9635-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Genetic population structure of the masked palm civet Paguma larvata, (Carnivora: Viverridae) in Japan, revealed from analysis of newly identified compound microsatellites. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0357-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zhang D, Ding G, Ge B, Zhang H, Tang B. Development and characterization of microsatellite loci of Oratosquilla oratoria (Crustacea: Squillidae). CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-011-9495-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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D'Andrea M, Roncarati A, Melotti P, Scarano MT, Pilla F. Development of 23 microsatellite markers for assessing genetic variability in the tub gurnard (Trigla lucerna L.). Anim Genet 2012; 43:650-1. [DOI: 10.1111/j.1365-2052.2012.02319.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2011] [Indexed: 11/26/2022]
Affiliation(s)
- M. D'Andrea
- Università degli Studi del Molise; 86100; Campobasso; Italy
| | - A. Roncarati
- Scuola di Scienze Mediche Veterinarie; Università di Camerino; 62024; Matelica; MC; Italy
| | - P. Melotti
- Scuola di Scienze Mediche Veterinarie; Università di Camerino; 62024; Matelica; MC; Italy
| | - M.-T. Scarano
- Consiglio Nazionale delle Ricerche; Istituto di Genetica Vegetale; 80055; Portici; NA; Italy
| | - F. Pilla
- Università degli Studi del Molise; 86100; Campobasso; Italy
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Rueda EC, Amavet P, Brancolini F, Sommer J, Ortí G. Isolation and characterization of eight polymorphic microsatellite markers for the migratory characiform fish, Salminus brasiliensis. JOURNAL OF FISH BIOLOGY 2011; 79:1370-1375. [PMID: 22026613 DOI: 10.1111/j.1095-8649.2011.03109.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Eight polymorphic microsatellite loci were isolated and characterized for the migratory freshwater fish Salminus brasiliensis (Characiformes) and tested on 67 individuals from nine geographically distant locations along the Paraná Basin. The number of alleles per locus ranged from four to 14, with observed heterozygosity estimates ranging from 0·15 to 0·79.
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Affiliation(s)
- E C Rueda
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, Ciudad Universitaria, 3000 Santa Fe, Argentina
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Yuan L, Xia J, Zhang L, Hu C. Development of 16 microsatellite loci of the tropical sea cucumber Stichopus horrens with cross-amplification in the congeneric species Stichopus monotuberculatus. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9530-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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[Enrichment and screening of the microsatellite markers in Microtus fortis and its preliminary application in genetic diversity research]. YI CHUAN = HEREDITAS 2011; 33:989-95. [PMID: 21951800 DOI: 10.3724/sp.j.1005.2011.00989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This study was to isolate microsatellite markers from Microtus fortis genome by magnetic beads enrichments. Through hybridization of biotin-labeled microsatellite oligonucleotide probes, which were captured by streptavidin-coated magnetic with the adaptor-ligated enzyme-digested genome fragments, single-stranded DNA fragments containing microsatellites were obtained. After PCR amplification, these fragments were then cloned into T vectors and were transformed into competent cells subsequently. Ninety-two microsatellite sequences were randomly isolated from 70 positive clones. Twenty-one out of 27 pairs of designed microsatellite primers were screened out from the microsatellite sequences, and 10 out of the 21 microsatellite loci were used to investigate the genetic diversity of three populations of M. fortis, Hunan (wild), Hunan (domesticated), and Ningxia (domesticated). All the 10 microsatellite loci used to analyze the genetic diversity exhibited a good level of polymorphism. The values of observed number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) were all the highest in the Hunan (wild) population, lower in the Hunan (domesticated) population, and the lowest in the Ningxia (domesticated) population.
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Cavagnaro PF, Chung SM, Manin S, Yildiz M, Ali A, Alessandro MS, Iorizzo M, Senalik DA, Simon PW. Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. BMC Genomics 2011; 12:386. [PMID: 21806822 PMCID: PMC3162538 DOI: 10.1186/1471-2164-12-386] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 08/01/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. RESULTS Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. CONCLUSIONS The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae.
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Affiliation(s)
- Pablo F Cavagnaro
- Dept. of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
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Casas F, Mougeot F, Sánchez-Barbudo I, Dávila JA, Viñuela J. Fitness consequences of anthropogenic hybridization in wild red-legged partridge (Alectoris rufa, Phasianidae) populations. Biol Invasions 2011. [DOI: 10.1007/s10530-011-0062-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sun D, Li H, Xu T, Wang R. Short Communication Development and characterization of microsatellite markers for the walking goby (Scartelaos viridis; Gobiidae). GENETICS AND MOLECULAR RESEARCH 2011; 10:203-7. [DOI: 10.4238/vol10-1gmr1015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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[Isolation of microsatellite markers from Paralichthys olivaceus and its application in genetic structure analysis]. YI CHUAN = HEREDITAS 2010; 32:1057-64. [PMID: 20943494 DOI: 10.3724/sp.j.1005.2010.01057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Magnetic bead enrich-method and plasmid detection-method were used to isolate microsatellite DNA from Paralichthys olivaceus genome. The microsatellite markers were applied to analyze natural population structure of four populations, which were collected from Dalian, Beidaihe, Dandong, and Qingdao. Two thousand eight hundred and five microsatellite sequence clones were isolated and 3120 microsatellite loci were obtained. From these sequences, 57.97% were perfect, 7.25% were imperfect and 34.78% were compound. This allowed to design 135 pairs of primers with the software Primer Premier 3.0. Seventy-eight pairs were synthesized and 30 pairs were polymorphic. The effective number of alleles ranged from 3.93 to 9.94 (6.95 in average) with observed and expected heterozygosities ranging from 0.532 to 0.895 (0.753 in average) and 0.635 to 0.902 (0.820 in average), respectively. Hardy-Weinberg equilibrium analysis in 30 microsatellite loci by genetic deviation index (d) ranged from -0.247 to 0.512, among which 7 loci had heterozygote excess (d>0) and the rest showed heterozygote deficit (damp;0). A dendrogram was constructed based on NJ methods using MEGA3.0 software package. Four populations were divided into two clusters. Dalian population and Dandong population were grouped in one cluster, while Beidaihe population and Qingdao population were classified into another cluster.
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Geng J, Li K, Zhang Y, Hu S. A modified enrichment method to construct microsatellite library from plateau pika genome (Ochotona curzoniae). GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 8:72-6. [PMID: 20451163 PMCID: PMC5054129 DOI: 10.1016/s1672-0229(10)60007-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A microsatellite-enriched library of plateau pika (Ochotona curzoniae) was constructed according to the strong affinity between biotin and streptavidin. Firstly, genomic DNA was fragmented by ultrasonication, which is a major improvement over traditional methods. Linker-ligated DNA fragments were hybridized with biotinylated microsatellite probes, and then were subjected to streptavidin-coated magnetic beads. PCR amplification was performed to obtain double-stranded DNA fragments containing microsatellites. Ligation and transformation were carried out by using the pGEM-T Vector System I and Escherichia coli DH10B competent cells. Sequencing results showed that 80.2% of clones contained microsatellite repeat motif. Several modifications make this protocol time-efficient and technically easier than the traditional ones; particularly, composition and relative abundance of microsatellite repeats in plateau pika genome were truly represented through the optimized PCR conditions. This method has also been successfully applied to construct microsatellite-enriched genomic libraries of Chinese hamster (Cricetulus griseus) and small abalone [Haliotis diversicolor (Reeve)] with high rates of positive clones, demonstrating its feasibility and stability.
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Affiliation(s)
- Jianing Geng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
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de Morgan A, Brodsky L, Ronin Y, Nevo E, Korol A, Kashi Y. Genome-wide analysis of DNA turnover and gene expression in stationary-phase Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2010; 156:1758-1771. [PMID: 20167621 DOI: 10.1099/mic.0.035519-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Exponential-phase yeast cells readily enter stationary phase when transferred to fresh, carbon-deficient medium, and can remain fully viable for up to several months. It is known that stationary-phase prokaryotic cells may still synthesize substantial amounts of DNA. Although the basis of this phenomenon remains unclear, this DNA synthesis may be the result of DNA maintenance and repair, recombination, and stress-induced transposition of mobile elements, which may occur in the absence of DNA replication. To the best of our knowledge, the existence of DNA turnover in stationary-phase unicellular eukaryotes remains largely unstudied. By performing cDNA-spotted (i.e. ORF) microarray analysis of stationary cultures of a haploid Saccharomyces cerevisiae strain, we demonstrated on a genomic scale the localization of a DNA-turnover marker [5-bromo-2'-deoxyuridine (BrdU); an analogue of thymidine], indicative of DNA synthesis in discrete, multiple sites across the genome. Exponential-phase cells on the other hand, exhibited a uniform, total genomic DNA synthesis pattern, possibly the result of DNA replication. Interestingly, BrdU-labelled sites exhibited a significant overlap with highly expressed features. We also found that the distribution among chromosomes of BrdU-labelled and expressed features deviates from random distribution; this was also observed for the overlapping set. Ty1 retrotransposon genes were also found to be labelled with BrdU, evidence for transposition during stationary phase; however, they were not significantly expressed. We discuss the relevance and possible connection of these results to DNA repair, mutation and related phenomena in higher eukaryotes.
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Affiliation(s)
- A de Morgan
- Institute of Evolution, Department of Evolutionary Biology and Ecology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - L Brodsky
- Institute of Evolution, Department of Evolutionary Biology and Ecology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Y Ronin
- Institute of Evolution, Department of Evolutionary Biology and Ecology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - E Nevo
- Institute of Evolution, Department of Evolutionary Biology and Ecology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - A Korol
- Institute of Evolution, Department of Evolutionary Biology and Ecology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Y Kashi
- Department of Biotechnology and Food Engineering, Technion, Israel Institute of Technology, Haifa 30200, Israel
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Isolation and characterization of 10 microsatellite markers in Helice tientsinensis (Brachyura: Varunidae). CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9074-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Characterization of 20 microsatellite markers in the plowshare tortoise, Astrochelys yniphora. CONSERV GENET 2009. [DOI: 10.1007/s10592-008-9715-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Nielsen JL, Graziano SL, Seitz AC. Fine-scale population genetic structure in Alaskan Pacific halibut (Hippoglossus stenolepis). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9943-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ascunce MS, Bouwma AM, Shoemaker D. Characterization of 24 microsatellite markers in 11 species of fire ants in the genus Solenopsis (Hymenoptera: Formicidae). Mol Ecol Resour 2009; 9:1475-9. [PMID: 21564937 DOI: 10.1111/j.1755-0998.2009.02688.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The social parasite ant Solenopsis daguerrei infests colonies of several mound-building fire ant species. Twenty-four microsatellite markers were isolated from a repeat-enriched genomic library of S. daguerrei. Eleven loci were polymorphic in this ant with two to six alleles per locus. Expected heterozygosity ranged from 0.0222 to 0.7940 among loci. Most microsatellites amplified successfully across the 11 Solenopsis species tested and will be useful for evolutionary genetic studies in this diverse ant group.
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Affiliation(s)
- Marina S Ascunce
- US Department of Agriculture, Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology (CMAVE), 1600 SW 23rd Drive, Gainesville, FL 32608, USA Department of Entomology, College of Agriculture, University of Kentucky, S-225 Agricultural Science Center North, Lexington, KY 40546, USA
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Characterization of 20 microsatellite marker loci in the Malagasy tree boa (Sanzinia madagascariensis madagascariensis). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9866-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Isolation and characterization of microsatellite markers for Temminck’s Tragopan (Tragopan temminckii). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9817-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Nance HA, Daly-Engel TS, Marko PB. New microsatellite loci for the endangered scalloped hammerhead shark, Sphyrna lewini. Mol Ecol Resour 2009; 9:955-7. [PMID: 21564803 DOI: 10.1111/j.1755-0998.2008.02510.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We isolated 15 microsatellite markers for the scalloped hammerhead shark, Sphyrna lewini. Loci were tested on 80 specimens of S. lewini from four Eastern Pacific samples. The number of alleles per locus ranged from 6 to 31 (mean = 14). Observed and expected levels of heterozygosity per locus ranged from 0.39 to 0.91 (mean = 0.70) and from 0.54 to 0.90 (mean = 0.76), respectively. No pairs of loci were in gametic disequilibrium after Bonferroni correction of α. One locus showed significantly lower heterozygosity than expected under Hardy-Weinberg proportions in two populations, possibly caused by null alleles.
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Affiliation(s)
- Holly A Nance
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, South Carolina 29634, USA Hawaii Institute of Marine Biology, PO Box 1346, Kaneohe, Hawaii 96744, USA
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IZUMI H, HASEGAWA O, HIGASHI S. Isolation of polymorphic microsatellite markers in the tree sparrow (Passer montanus). Mol Ecol Resour 2009; 9:245-7. [DOI: 10.1111/j.1755-0998.2008.02427.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Bhatia S, Shokeen B. Isolation of microsatellites from Catharanthus roseus (L.) G. Don using enriched libraries. Methods Mol Biol 2009; 547:289-302. [PMID: 19521853 DOI: 10.1007/978-1-60327-287-2_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Catharanthus roseus is an indispensable source of the anticancerous alkaloids-vincristine and vinblastine, even though they are produced in trace amounts in vivo. In order to increase the yield of alkaloids, in vitro tissue culture studies are carried out which result in a large number of lines/cultures. For identification and characterization of the in vitro cultures, microsatellites in the form of STMS (Sequenced Tagged Microsatellite Sites) markers are used for identification of genetic polymorphism. STMS markers are also used for assessment of genetic diversity within natural populations as well as for construction of genetic linkage maps. Isolation of microsatellites and development of STMS markers typically involves library construction and screening, DNA sequencing, polymerase chain reaction (PCR) primer design, and PCR optimization. This chapter details two approaches for the isolation of microsatellite loci. The first approach is based on PCR using microsatellite containing primers which also have degenerate bases at the 5 cent-end that act as anchors preventing the primers from slippage to the 3 cent-end and the subsequent loss of polymorphism. The multi-locus PCR amplified product is cloned and sequenced. Though this method generates a large number of microsatellites, the major drawback is the high redundancy observed in this method. The second approach described in this chapter is based on the construction of a microsatellite enriched library which involves preferential cloning of the microsatellite enriched fraction of genomic DNA. This method therefore necessitates the isolation of microsatellites through hybridization with biotin labeled oligoprobe followed by their capture with streptavidin-coated magnetic beads. In comparison to the first approach, this approach yields less redundant clones with high microsatellite enrichment. Moreover enriched libraries are 40-60 times more efficient than the conventional small insert genomic libraries.
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Affiliation(s)
- Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Ascunce MS, Scotty Yang CC, Geden C, Shoemaker D. Twenty-three new microsatellite loci in the stable fly, Stomoxys calcitrans (L.) (Diptera: Muscidae). Mol Ecol Resour 2009; 9:271-3. [PMID: 21564624 DOI: 10.1111/j.1755-0998.2008.02445.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stable fly, Stomoxys calcitrans (L.), is a significant pest of cattle. Twenty-three microsatellite markers were isolated from a repeat-enriched genomic library of S. calcitrans. We characterized variation at these markers and found that 17 loci were polymorphic in two fly populations from Florida. Two to nine alleles were observed among the variable microsatellite loci and expected heterozygosities ranged from 0.03704 to 0.85115. These markers will be useful for characterizing population genetic differentiation and for tracking the migration patterns of stable flies in the USA and worldwide.
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Affiliation(s)
- Marina S Ascunce
- US Department of Agriculture, Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology (CMAVE), 1600 SW 23rd Drive, Gainesville, FL 32608, USA, Department of Entomology, National Taiwan University, No. 1, Sec 4, Roosevelt Road, Taipei 106, Taiwan
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AZUMA N, MIRANDA RM, GOSHIMA S, ABE S. Polymorphic microsatellite markers isolated from the neptune whelkNeptunea arthritica. Mol Ecol Resour 2009; 9:120-1. [DOI: 10.1111/j.1755-0998.2008.02179.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Klug H, St. Mary CM, Clark A. Isolation and characterization of microsatellite DNA markers for the flagfish Jordanella floridae. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9522-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Characterization of 18 microsatellite marker loci in the white-collared lemur (Eulemur cinereiceps). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9760-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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43
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Vogler BR, Bailey CA, Shore GD, McGuire SM, Engberg SE, Fickel J, Louis EE, Brenneman RA. Characterization of 26 microsatellite marker loci in the fossa (Cryptoprocta ferox). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9758-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Han BY, Hua PY, Gu XM, Miller-Butterworth CM, Zhang SY. Isolation and characterization of microsatellite loci in the western long-fingered bat, Miniopterus magnater. Mol Ecol Resour 2008; 8:1445-7. [PMID: 21586071 PMCID: PMC7168459 DOI: 10.1111/j.1471-8286.2007.02008.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We isolated and characterized 10 microsatellite loci in the western long-fingered bat, Miniopterus magnater. These loci were tested on 48 individuals from Anhui Province of China, and all loci were highly polymorphic. The mean number of observed alleles per locus was 13.6 (range from six to 27). Observed and expected heterozygosity values ranged from 0.364 to 0.957, and from 0.676 to 0.951, respectively. After Bonferroni correction, four loci deviated significantly from Hardy-Weinberg equilibrium. No pairs of loci were in linkage disequilibrium. These polymorphic markers will be used to examine population structure and genetic diversity in this species.
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Affiliation(s)
- B Y Han
- School of Life Science, East China Normal University, Shanghai 200062, China, School of Geographical and Biological Sciences, Guizhou Normal University, Guiyang 550001, China, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
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Ramarokoto R, Lei R, Vincent J, Day S, Shore GD, Brenneman RA, Louis EE. Characterization of twenty-one microsatellites developed from Propithecus diadema. CONSERV GENET 2008. [DOI: 10.1007/s10592-007-9500-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Frommlet JC, Iglesias-Rodríguez MD. MICROSATELLITE GENOTYPING OF SINGLE CELLS OF THE DINOFLAGELLATE SPECIES LINGULODINIUM POLYEDRUM (DINOPHYCEAE): A NOVEL APPROACH FOR MARINE MICROBIAL POPULATION GENETIC STUDIES(1). JOURNAL OF PHYCOLOGY 2008; 44:1116-1125. [PMID: 27041708 DOI: 10.1111/j.1529-8817.2008.00566.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In recent years, two new approaches have been introduced in genetic studies of phytoplankton species. One is the application of highly polymorphic microsatellite markers, which allow detailed population genetic studies; the other is the development of methods that enable the direct genetic characterization of single cells as an alternative to clonal cultures. The aim of this study was to combine these two approaches in a method that would allow microsatellite genotyping of single phytoplankton cells, providing a novel tool for high-resolution population genetic studies. The dinoflagellate species Lingulodinium polyedrum (F. Stein) J. D. Dodge was selected as a model organism to develop this novel approach. The method we describe here is based on several key developments: (i) a simple and efficient DNA extraction method for single cells, (ii) the characterization of microsatellite markers for L. polyedrum, (iii) a protocol for the species identification of single cells through the analysis of partial rRNA gene sequences, and (iv) a two-step multiplex PCR protocol for the simultaneous amplification of microsatellite markers and partial rRNA gene sequences from single cells. Our protocol allowed the amplification of up to six microsatellite loci together with either the complete ITS1-5.8S-ITS2 region or a partial 18S region of the ribosomal gene of L. polyedrum from single motile cells and resting cysts. This article describes and evaluates the developed approach and discusses its significance for population genetic studies of L. polyedrum and other phytoplankton species.
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Affiliation(s)
- Jörg C Frommlet
- National Oceanography Centre, Southampton, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - M Débora Iglesias-Rodríguez
- National Oceanography Centre, Southampton, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
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Characterization of 21 microsatellite marker loci in the Milne-Edwards’ Sifaka (Propithecus edwardsi). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9702-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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48
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Characterization of 22 microsatellite marker loci in the Madagascar rousette (Rousettus madagascariensis). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9679-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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49
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Haas SE, Smith JV, Kimball RT, Clark AM. Isolation and characterization of polymorphic microsatellite markers for the brown-headed nuthatch (Sitta pusilla). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9703-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Characterization of 21 microsatellite marker loci in the silky sifaka (Propithecus candidus). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9668-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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