共查询到20条相似文献,搜索用时 31 毫秒
1.
Ibrar Ahmed Peter J. Matthews Patrick J. Biggs Muhammad Naeem Patricia A. McLenachan Peter J. Lockhart 《Molecular ecology resources》2013,13(5):929-937
Recently, we reported the chloroplast genome‐wide association of oligonucleotide repeats, indels and nucleotide substitutions in aroid chloroplast genomes. We hypothesized that the distribution of oligonucleotide repeat sequences in a single representative genome can be used to identify mutational hotspots and loci suitable for population genetic, phylogenetic and phylogeographic studies. Using information on the location of oligonucleotide repeats in the chloroplast genome of taro (Colocasia esculenta), we designed 30 primer pairs to amplify and sequence polymorphic loci. The primers have been tested in a range of intra‐specific to intergeneric comparisons, including ten taro samples (Colocasia esculenta) from diverse geographical locations, four other Colocasia species (C. affinis, C. fallax, C. formosana, C. gigantea) and three other aroid genera (represented by Remusatia vivipara, Alocasia brisbanensis and Amorphophallus konjac). Multiple sequence alignments for the intra‐specific comparison revealed nucleotide substitutions (point mutations) at all 30 loci and microsatellite polymorphisms at 14 loci. The primer pairs reported here reveal levels of genetic variation suitable for high‐resolution phylogeographic and evolutionary studies of taro and other closely related aroids. Our results confirm that information on repeat distribution can be used to identify loci suitable for such studies, and we expect that this approach can be used in other plant groups. 相似文献
2.
JESS W. JONES MELANIE CULVER VICTOR DAVID JENNIFER STRUTHERS NATHAN A. JOHNSON RICHARD J. NEVES STEPHEN J. O'BRIEN ERIC M. HALLERMAN 《Molecular ecology resources》2004,4(4):649-652
Primers for 10 polymorphic microsatellite loci were developed and characterized for the endangered oyster mussel Epioblasma capsaeformis from the Clinch River, Tennessee. Microsatellite loci also were tested in four other populations or species. Amplification was successful for most loci in these closely related endangered species or populations; therefore, a high level of flanking sequence similarity was inferred for this group of species and populations. Allelic diversity ranged from nine to 20 alleles/locus, and averaged 13.6/locus. This study demonstrated the feasibility of using polymerase chain reaction (PCR) primers to amplify microsatellite loci across freshwater mussel species to conduct population genetics studies. 相似文献
3.
Francis E. Hinds Robert L. Close Mary T. Campbell Peter B. S. Spencer 《Molecular ecology resources》2002,2(1):42-44
The water rat (Hydromys chrysogaster) is well adapted to a semiaquatic life and is endemic to dispersed regions of Australia and New Guinea. To analyse the genetic diversity of water rat populations, polymorphic microsatellite markers were developed. A partial genomic library was screened for microsatellite sequences. Following isolation of the microsatellite sequences, primers were designed to amplify seven loci and of these loci, five were polymorphic. The sample tested for polymorphisms came from areas across Australia and New Guinea. Between three and 13 alleles were detected for each locus. In addition the primers amplified two loci in Mus musculus and Rattus rattus. 相似文献
4.
5.
EST derived SSR markers for comparative mapping in wheat and rice 总被引:18,自引:0,他引:18
Structural and functional relationships between the genomes of hexaploid wheat (Triticum aestivum L.) (2n=6x=42) and rice (Oryza sativa L.) (2n=2x=24) were evaluated using linkage maps supplemented with simple sequence repeat (SSR) loci obtained from publicly available expressed sequence tags (ESTs). EST-SSR markers were developed using two main strategies to design primers for each gene: (1) primer design for multiple species based on supercluster analysis, and (2) species-specific primer design. Amplification was more consistent using the species-specific primer design for each gene. Forty-four percent of the primers designed specifically for wheat sequences were successful in amplifying DNA from both species. Existing genetic linkage maps were enhanced for the wheat and rice genomes using orthologous loci amplified with 58 EST-SSR markers obtained from both wheat and rice ESTs. The PCR-based anchor loci identified by these EST-SSR markers support previous patterns of conservation between wheat and rice genomes; however, there was a high frequency of interrupted colinearity. In addition, multiple loci amplified by these primers made the comparative analysis more difficult. Enhanced comparative maps of wheat and rice provide a useful tool for interpreting and transferring molecular, genetic, and breeding information between these two important species. These EST-SSR markers are particularly useful for constructing comparative framework maps for different species, because they amplify closely related genes to provide anchor points across species.Communicated by R. Hagemann 相似文献
6.
Madhusudan Choudhary Joan E. Strassmann Carlos R. Solís David C. Queller 《Biochemical genetics》1993,31(1-2):87-96
We undertook a study to explore the potential of microsatellite loci as genetic markers for investigating kinship patterns
in a social waspParachartergus colobopterus. A plasmid library with small inserts was screened for several oligonucleotide repeat motifs. Positive clones were sequenced
and several were selected for further work. PCR primers were constructed that would amplify the tandem repeat region and a
number of female wasps were scored for variation in the number of tandem repeats at these loci. The five amplified loci were
far more variable than allozymes, with an average heterozygosity of 0.35.
This work was supported by NSF Grants BSR-9021514 and IBN-9210051. 相似文献
7.
Eleven microsatellite loci were identified and characterized in blackcurrant (Ribes nigrum L.) and related species. An enriched library was constructed and screened with simple sequence repeat (SSR) oligonucleotides. Positive clones were sequenced and primers were designed flanking the repeat motifs. These 11 microsatellites produce amplification products polymorphic across a range of Ribes germplasm, predominantly from the Eucoreosma section of the genus. The number of alleles varied from 2 to 18 with levels of diversity ranging from 0.18 to 0.91. 相似文献
8.
Lohse K Sharanowski B Blaxter M Nicholls JA Stone GN 《Molecular ecology resources》2011,11(3):521-529
Increasing numbers of phylogeographic studies make comparative inferences about the histories of co-distributed species. Although the aims of such studies are best achieved by jointly analysing sequences from multiple loci in a model-based framework, such data currently exist for few nonmodel systems. We used existing genomic data and expressed sequence tags (ESTs) for Hymenoptera and other insects to design intron-crossing primers for 40 loci, mainly ribosomal proteins, for chalcidoid parasitoids. Amplification success was scored on a range of taxa associated with two natural communities; oak galls and figs. Taxa were chosen at increasing distance from Nasonia, which was used for primer design, (i) within Pteromalids, (ii) within Chalcidoidea (Eupelmidae, Eulophidae, Eurytomidae, Ormyridae, Torymidae) and (iii) for a selection of distantly related gall and fig wasps (Cynipidae, Agaonidae). To assess the utility of these loci for phylogeographic and population genetic studies, we compared genetic diversity between Western Palaearctic refugia for two species. Our results show that it is feasible to design a large number of exon-primed-intron-crossing (EPIC) loci that may be informative about phylogeographic history within species but amplify across a large taxonomic range. 相似文献
9.
? Premise of the study: Microsatellite primers were developed for the endemic tree Litsea hypophaea (Lauraceae) in Taiwan to investigate its genetic diversity and population genetic structure and to investigate species delimitation within Litsea. ? Methods and Results: Fifteen new simple sequence repeat markers were developed from L. hypophaea with a magnetic bead enrichment method. Most loci were also amplified from three closely related species, L. coreana, L. lii, and L. acutivena. The number of alleles and observed and expected heterozygosities across loci varied with a range of 1-25, 0.000-1.000, and 0.000-0.956, respectively. ? Conclusions: The application of these microsatellite markers of L. hypophaea provides a tool for understanding genetic diversity and population differentiation. In addition, interspecific amplification suggests that these markers will also be useful for species identification of related taxa within Litsea in Taiwan. 相似文献
10.
Universal (consensus) primers are those primers that have the ability to amplify the targeted region of DNA across a broad
range of individuals in a certain group of organisms. In plants, such universal primers have been designed to target regions
in the nuclear, mitochondrial or chloroplast genome. Among these three genomes, the chloroplast genome is the most suited
for the design of consensus primers due to the lower rate of evolution and hence conservation of gene order and sequence of
the genome among the different plant species compared to the other two genomes. Several molecular studies in plants have developed
and used chloroplast-specific universal primers. In this review, I present some examples of the nuclear DNA-specific universal
primers and discuss the features of the chloroplast DNA that make it the most suited for the design of such primers. I then
refer to all chloroplast-specific primers developed so far and provide some examples of molecular studies and applications
that made use of them. 相似文献
11.
BHUMIKA SHOKEEN NIROJ K. SETHY SHALU CHOUDHARY SABHYATA BHATIA 《Molecular ecology resources》2005,5(4):818-820
We report the isolation and characterization of the first set of sequence‐tagged microsatellites sites (STMS) markers in Catharanthus roseus, a plant with a vast range of medicinal uses. The microsatellite loci were cloned from an enriched library constructed using degenerate primers. Based on the microsatellite motifs, seven STMS primer pairs were designed. They were used to amplify 32 accessions of C. roseus and one accession of Catharanthus trichophyllus. The primers amplified an average of 3.86 alleles per locus. The observed heterozygosity ranged from 0.2903 to 0.9688 with an average of 0.7511. The STMS markers of C. roseus also amplified corresponding loci in a related species (C. trichophyllus) suggesting conservation of the loci across the genus. These markers will prove useful for genetic diversity analysis and linkage map construction in C. roseus. 相似文献
12.
Eurytoma brunniventris is a parasitic wasp with a wide range of host species. We have developed primers for nine polymorphic microsatellite loci to allow examination of intraspecific population subdivision associated with two aspects of the biology of their hosts: host species (oak gallwasps) and the tree on which the gallwasp develops (different oak species). All nine loci amplified well across individuals collected from a range of gallwasp species and across two oak taxa. These microsatellite loci are potentially of value in the study of closely related economic pests such as seed predators of almonds (E. amygdali) and pistachios (E. plotnikovi). 相似文献
13.
Bressan Ede A Scotton DC Ferreira RR Jorge EC Sebbenn AM Gerald LT Figueira A 《American journal of botany》2012,99(6):e237-e239
? Premise of the study: Microsatellite primers were developed for Jatropha curcas (Euphorbiaceae), a tree species with large potential for biofuel production, to investigate its natural genetic diversity and mating system to facilitate the establishment of tree improvement and conservation programs. ? Methods and Results: Using a protocol for genomic library enrichment, 104 clones containing 195 repeat motifs were identified. Primer pairs were developed for 40 microsatellite loci and validated in 41 accessions of J. curcas from six provenances. Nine loci were polymorphic revealing from two to eight alleles per locus, and six primers were able to amplify alleles in the congeners J. podagrica, J. pohliana, and J. gossypifolia, but not in other Euphorbiaceae species, such as Hevea brasiliensis, Manihot esculenta, or Ricinus communis. ? Conclusions: The primers developed here revealed polymorphic loci that are suitable for genetic diversity and structure, mating system, and gene flow studies in J. curcas, and some congeners. 相似文献
14.
T. L. Maguire K. J. Edwards P. Saenger R. Henry 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(1-2):279-285
An enriched microsatellite library of the mangrove species Avicennia marina was constructed, in which 85.8% of the clones contained microsatellite sequences. Of the microsatellite repeat sequences
isolated, 55.0% were di-nucleotides, 34.2% were tri-nucleotides, 50.0% were perfect, 24.2% were imperfect, and 15.0% were
compound. Four different di-nucleotide repeats were isolated with repeat lengths ranging from 5 to 33; ten different tri-nucleotide
repeats were isolated with repeat lengths ranging from 3 to 25. The most common di-nucleotide was the AC/TG repeat; the most
common tri-nucleotide was the CCG/GGC repeat. Sixteen microsatellite sequences were selected for primer design, and 6 primers
were selected to investigate the polymorphism detected among 15 individuals of A. marina from three natural populations in Australia. A total of 40 alleles were detected at 6 microsatellite loci. The number of
alleles per microsatellite locus ranged from 5 to 13. On average, 7 alleles were detected per locus. All microsatellite loci
showed high levels of gene diversity (heterozygosity), with values ranging from 0.53 to 0.88; the mean value of gene diversity
was 0.70. Microsatellite loci were also tested for conservation across Avicennia species. There was a decline in amplification success with increasing divergence between Avicennia species. The results indicate that microsatellites are abundant in the Avicennia genome and can be valuable genetic markers for assessing the effects of deforestation and forest fragmentation in mangrove
communities, which is an important issue for mangrove conservation and afforestation schemes.
Received: 8 June 1999 / Accepted: 21 September 1999 相似文献
15.
Andrew A. Crowl Evgeny Mavrodiev Guilhem Mansion Rosemarie Haberle Annalaura Pistarino Georgia Kamari Dimitrios Phitos Thomas Borsch Nico Cellinese 《PloS one》2014,9(4)
Background
The Campanuloideae (Campanulaceae) are a highly diverse clade of angiosperms found mostly in the Northern Hemisphere, with the highest diversity in temperate areas of the Old World. Chloroplast markers have greatly improved our understanding of this clade but many relationships remain unclear primarily due to low levels of molecular evolution and recent and rapid divergence. Furthermore, focusing solely on maternally inherited markers such as those from the chloroplast genome may obscure processes such as hybridization. In this study we explore the phylogenetic utility of two low-copy nuclear loci from the pentatricopeptide repeat gene family (PPR). Rapidly evolving nuclear loci may provide increased phylogenetic resolution in clades containing recently diverged or closely related taxa. We present results based on both chloroplast and low-copy nuclear loci and discuss the utility of such markers to resolve evolutionary relationships and infer hybridization events within the Campanuloideae clade.Results
The inclusion of low-copy nuclear genes into the analyses provides increased phylogenetic resolution in two species-rich clades containing recently diverged taxa. We also obtain support for the placement of two early diverging lineages (Jasione and Musschia-Gadellia clades) that have previously been unresolved. Furthermore, phylogenetic analyses of PPR loci revealed potential hybridization events for a number of taxa (e.g., Campanula pelviformis and Legousia species). These loci offer greater overall topological support than obtained with plastid DNA alone.Conclusion
This study represents the first inclusion of low-copy nuclear genes for phylogenetic reconstruction in Campanuloideae. The two PPR loci were easy to sequence, required no cloning, and the sequence alignments were straightforward across the entire Campanuloideae clade. Although potentially complicated by incomplete lineage sorting, these markers proved useful for understanding the processes of reticulate evolution and resolving relationships at a wide range of phylogenetic levels. Our results stress the importance of including multiple, independent loci in phylogenetic analyses. 相似文献16.
Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species 总被引:14,自引:0,他引:14
T. Ishii N. Mori Y. Ogihara 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,103(6-7):896-904
Twenty four chloroplast microsatellite loci having more than ten mononucleotide repeats were identified from the entire chloroplast
DNA sequence of common wheat, Triticum aestivum cv Chinese Spring. For each microsatellite, a pair of primers were designed to produce specific PCR products in the range
of 100– 200 bp. The allelic diversity at the microsatellite loci was evaluated using 43 accessions from 11 Triticum and Aegilops species involved in wheat polyploid evolution. Polymorphic banding patterns were obtained at 21 out of 24 chloroplast microsatellite
loci. The three monomorphic microsatellites were found to be located in coding regions. For the polymorphic microsatellites,
the number of alleles per microsatellite ranged from 2 to 7 with an average of 4.33, and the diversity values (H) ranged from
0.05 to 0.72 with an average of 0.47. Significant correlations (P<0.01) were observed between the number of repeats and the number of alleles, and between the number of repeats and diversity
value, respectively. The genetic diversity explained by chloroplast microsatellites and nuclear RFLP markers were compared
using 22 tetraploid accessions. Although the number of alleles for nuclear RFLP markers was found to be higher than that for
chloroplast microsatellites, similar diversity values were observed for both types of markers. Among common wheat and its
ancestral species, the percentages of common chloroplast microsatellite alleles were calculated to examine their phylogenetic
relationships. As a result, Timopheevi wheat species were clearly distinguished from other species, and Emmer and common wheat
species were divided into two main groups, each consisting of a series of wild and cultivated species from tetraploid to hexaploid.
This indicates that the two types of chloroplast genomes of common wheat might have independently originated from the corresponding
types of wild and cultivated Emmer wheat species.
Received: 6 October 2000 / Accepted: 13 March 2001 相似文献
17.
Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding 总被引:2,自引:0,他引:2
Background
At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences. Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species.Methodology/Principal Findings
We scanned the entire chloroplast genomes of 12 genera to search for highly variable regions. The sequence data of 9 genera were from GenBank and 3 genera were of our own. We identified nearly 5% of the most variable loci from all variable loci in the chloroplast genomes of each genus, and then selected 23 loci that were present in at least three genera. The 23 loci included 4 coding regions, 2 introns, and 17 intergenic spacers. Of the 23 loci, the most variable (in order from highest variability to lowest) were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnSUGA-trnGUCC, petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnSUGA-trnGUCC, trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity per site (π values) across three genera. Other loci may have strong potential for resolving phylogenetic and species identification problems at the species level. The loci accD-psaI, rbcL-accD, rpl32-trnL, rps16-trnQ, and ycf1 are absent from some genera. To amplify and sequence the highly variable loci identified in this study, we designed primers from their conserved flanking regions. We tested the applicability of the primers to amplify target sequences in eight species representing basal angiosperms, monocots, eudicots, rosids, and asterids, and confirmed that the primers amplified the desired sequences of these species.Significance/Conclusions
Chloroplast genome sequences contain regions that are highly variable. Such regions are the first consideration when screening the suitable loci to resolve closely related species or genera in phylogenetic analyses, and for DNA barcoding. 相似文献18.
V. Mohindra L. Narain P. Punia A. Gopalakrishnan A. Mandal D. Kapoor A. G. Ponniah K. K. Lal 《Zeitschrift fur angewandte Ichthyologie》2005,21(6):478-482
Fifty‐four primers published for six cyprinid fishes were tested to amplify homologous microsatellite loci in Labeo dyocheilus. Fifteen primers yielded successful amplification and seven were polymorphic with 3–9 alleles. To evaluate utility of the identified loci in population genetic study, 84 samples were analysed. The samples were collected from four rivers viz. Beas, Satluj, Yamuna and Jiabharali. The four sample sets displayed different diversity levels, with observed heterozygosity from 0.34 to 0.53. Significant genotype heterogeneity (P < 0.001) over all loci indicated that the samples are not drawn from the same genepool. The identified microsatellite loci are promising for use in fine‐scale population structure analysis of L. dyocheilus. 相似文献
19.
Mariateresa de Cesare Trevor R. Hodkinson Susanne Barth 《Molecular breeding : new strategies in plant improvement》2010,26(3):539-544
Miscanthus and Saccharum are closely related perennial C4 grasses. Miscanthus has recently attracted interest as a non-food crop for energy and fibre production. However, molecular genetic tools for
the selection of new Miscanthus genotypes and study of its genetic resources are limited. We have identified six chloroplast (plastid) marker loci,containing
both microsatellites (cpSSRs) and single nucleotide polymorphisms (SNPs) and developed primers to amplify and sequence these
regions. The primers were designed using the complete chloroplast genome sequence of sugarcane and were tested on a collection
of 164 Miscanthus genotypes and 14 related species of the subfamily Panicoideae. The cpSSR markers were highly polymorphic, with the number
of alleles ranging from 10 to 16 per locus. Within the six cpSSR marker loci, the hybrid M. ×giganteus exhibits virtually no cpDNA variation compared with its putative parents M. sinensis and M. sacchariflorus. These SNP markers enable the differentiation of most Miscanthus species and detect infraspecific variation suitable for defining cytoplasmic genepools of Miscanthus for breeding purposes. 相似文献
20.
Universal primers for fluorescent labelling of PCR fragments--an efficient and cost-effective approach to genotyping by fluorescence 总被引:2,自引:0,他引:2
Directly labelling locus‐specific primers for microsatellite analysis is expensive and a common limitation to small‐budget molecular ecology projects. More cost‐effective end‐labelling of PCR products can be achieved through a three primer PCR approach, involving a fluorescently labelled universal primer in combination with modified locus‐specific primers with 5′ universal primer sequence tails. This technique has been widely used but has been limited largely due to a lack of available universal primers suitable for co‐amplifying large numbers of size overlapping loci and without requiring locus‐specific PCR conditions to be modified. In this study, we report a suite of four high‐performance universal primers that can be employed in a three primer PCR approach for efficient and cost‐effective fluorescent end‐labelling of PCR fragments. Amplification efficiency is maximized owing to high universal primer Tm values (approximately 60+ °C) that enhance primer versatility and enable higher annealing temperatures to be employed compared with commonly used universal primers such as M13. We demonstrate that these universal primers can be combined with multiple fluorophores to co‐amplify multiple loci efficiently via multiplex PCR. This method provides a level of multiplexing and PCR efficiency similar to microsatellite fluorescent detection assays using directly labelled primers while dramatically reducing project costs. Primer performance is tested using several alternative PCR strategies that involve both single and multiple fluorophores in single and multiplex PCR across a wide range of taxa. 相似文献