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1.
Isolation and characterization of microsatellite loci from the entomopathogenic fungus Beauveria bassiana (Ascomycota: Hypocreales) 总被引:1,自引:0,他引:1
Beauveria bassiana, an entomogenous fungus used for the biological control of pest insects, comprises a globally‐distributed species complex of regionally endemic lineages. In order to study the population genetics of B. bassiana, detail species boundaries, conduct ecological studies of natural populations and track fates of experimentally‐released strains, sensitive genetic markers are required. We describe the isolation and characterization of eight microsatellite loci that amplify successfully from strains representative of the phylogenetic diversity in the B. bassiana complex. 相似文献
2.
ELIZABETH A. SINCLAIR REBECCA SCHOLL ROBERT L. BEZY KEITH A. CRANDALL JACK W. SITES 《Molecular ecology resources》2006,6(1):233-236
We report the development of 17 di‐ and tetranucleotide microsatellite markers in the Yellow‐Spotted Night Lizard Lepidophyma flavimaculatum. Levels of heterozygosity ranged from 0 to 100%. Several loci also amplify in other Lepidophyma species and several species of the sister genus Xantusia. High levels of variation at some loci indicate that they will be useful for parentage assessment and population genetic studies, whereas the 15 loci that amplify across multiple Lepidophyma species suggest these will be useful in determining the origin of parthenogenetic populations. 相似文献
3.
Yasuda SP Nakayama AA Iwabuchi M Minato S Tsuchiya K Suzuki H 《Molecular ecology resources》2009,9(2):569-571
Eight microsatellite markers were developed for the Japanese dormouse (Glirulus japonicus), a natural monument and near‐threatened species in Japan. The markers amplify in individuals from all of the mitochondrial lineages detected in a previous study. Numerous polymorphisms were detected in specimens from a local population in central Honshu (11–21 alleles per locus; n = 31) and from the entire distribution range of the species (19–41 alleles per locus; n = 152). These microsatellites will be useful in conservation genetic studies of G. japonicus. 相似文献
4.
A set of 41 polymorphic microsatellite markers were developed using a CT/AG‐enriched genomic library of Fragaria vesca cv. Reine des Vallées. Thirty‐five of them were polymorphic in F. vesca and were tested in one accession each of six additional diploid Fragaria species and the octoploid Fragaria× ananassa. A mean of 5.3 alleles per locus and a low level of observed heterozygosity were generally detected in the 32 single‐locus simple sequence repeats of F. vesca. Most of these loci amplify in the other diploid species and in F. × ananassa. 相似文献
5.
C. Taylor K. Madsen S. Borg M. C. Møller B. Boelt P. H. Holm 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,103(4):648-658
Genetic analysis, particularly the development of genetic linkage maps in forage grass species, lags well behind other members
of the Poaceae. Comparative mapping within this family has revealed extensive conservation in gene and marker synteny among chromosomes
of diverse genera. Recently, the ability to transfer mapped STS markers between barley and wheat has been demonstrated. The
transfer of mapped STS markers between cereals and forage grasses could provide PCR-based markers for comparative mapping
in these species providing they amplify homologous sequences. In this study, primers derived from three barley genes of defined
function and a gene from Phalaris coerulescens were used to amplify homologous fragments in Lolium perenne. Primers derived from two barley and two oat cDNA clones were also tested along with eight barley and two Triticum tauchii STS markers. Twenty one primer pairs derived from 18 loci were tested. Eleven primer pairs (52%) amplified homologous sequences
in L. perenne from ten (55%) of the loci targetted. Thirteen new STS markers were generated in L. perenne, of which ten have been mapped in barley or rye and amplify homologous sequences in L. perenne.
Received: 20 October 2000 / Accepted: 13 January 2001 相似文献
6.
Six single‐locus, polymorphic microsatellite markers in a perennial herbaceous plant, Polygonum cuspidatum, were developed. Tests to amplify these six loci in another Polygonum species failed, suggesting that the six markers are specific to P. cuspidatum. 相似文献
7.
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
8.
B. J. Schemerhorn S. Greeman M. Banks J. Vulule N.‐F. Sagnon C. Costantini N. J. Besansky 《Molecular ecology resources》2003,3(4):505-507
A total of 39 dinucleotide microsatellite‐containing clones were sequenced from a principal African malaria vector, Anopheles funestus. Primers designed to amplify 20 loci were used to genotype A. funestus mosquitoes from Burkina Faso and Kenya. Of nine polymorphic loci that amplified reliably and could be scored unambiguously, the overall within‐sample gene diversity was similar between locales, 0.77 and 0.78, with an allelic richness per locus of five to 11. Both the high level of polymorphism and absence of significant heterozygote deficiency at any locus favour these markers for studies of population structure that are vital to controlling this medically important species. 相似文献
9.
A microsatellite‐enriched genomic library was obtained from black‐bellied angler Lophius budegassa and six polymorphic dinucleotide markers were successfully optimized. These markers showed levels of polymorphism ranging from 0.363 to 0.662 and allele numbers ranging from three to seven. These markers were also found to successfully amplify in the closely related Lophius piscatorius (angler) and thus appear to be useful for genetic stock structure analysis in both species. 相似文献
10.
Laurence J. Clarke Julien Soubrier Laura S. Weyrich Alan Cooper 《Molecular ecology resources》2014,14(6):1160-1170
Studies of insect assemblages are suited to the simultaneous DNA‐based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR‐amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR‐amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR‐amplified the blend using five primer sets, targeting either COI or 16S, with high‐throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers. 相似文献
11.
A novel method of caenophidian snake sex identification using molecular markers based on two gametologous genes
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Nararat Laopichienpong Panupong Tawichasri Lawan Chanhome Rattanin Phatcharakullawarawat Worapong Singchat Attachai Kantachumpoo Narongrit Muangmai Sunutcha Suntrarachun Kazumi Matsubara Surin Peyachoknagul Kornsorn Srikulnath 《Ecology and evolution》2017,7(13):4661-4669
Sex identification provides important information for ecological and evolutionary studies, as well as benefiting snake conservation management. Traditional methods such as cloacal probing or cloacal popping are counterproductive for sex identification concerning very small species, resulting in difficulties in the management of their breeding programs. In this study, the nucleotide sequences of gametologous genes (CTNNB1 and WAC genes) were used for the development of molecular sexing markers in caenophidian snakes. Two candidate markers were developed with the two primer sets, and successfully amplified by a single band on the agarose gel in male (ZZ) and two bands, differing in fragment sizes, in female (ZW) of 16 caenophidian snakes for CTNNB1 and 12 caenophidian snakes for WAC. Another candidate marker was developed with the primer set to amplify the specific sequence for CTNNB1W homolog, and the PCR products were successfully obtained in a female‐specific 250‐bp DNA bands. The three candidate PCR sexing markers provide a simple sex identification method based on the amplification of gametologous genes, and they can be used to facilitate effective caenophidian snake conservation and management programs. 相似文献
12.
CAROLYNE BARDELEBEN 《Molecular ecology resources》2004,4(4):698-700
Thirteen polymorphic microsatellite markers have been developed for the little greenbul, Andropadus virens. The number of alleles range from two to 15 per locus with the observed heterozygosity ranging from 0.15 to 0.92. Eight sets of primers also amplify in closely related species, Andropadus laterostris and Andropadus tephrolaemus. These markers will be useful for analysis of questions concerning population genetic structure and models of speciation. 相似文献
13.
FLAVIO GAROIA SILLA MARZOLA ILARIA GUARNIERO MASSIMO TRENTINI FAUSTO TINTI 《Molecular ecology resources》2006,6(1):144-146
A microsatellite‐enriched genomic library was obtained from the common sole, Solea vulgaris, and seven polymorphic dinucleotide markers were successfully optimized. These markers showed levels of expected heterozygosity ranging from 0.55 to 0.83 and allele number ranging from eight to 12. Three of these markers were also found to successfully amplify in the closely related Solea senegalensis and can be employed to define population genetic structure of the two Solea species and for inferring stock origins. 相似文献
14.
Identification of microsatellite DNA markers for population structure analysis in Indian major carp, Cirrhinus mrigala (Hamilton-Buchanan, 1882) 总被引:6,自引:0,他引:6
K. K. Lal T. Chauhan A. Mandal R. K. Singh L. Khulbe A. G. Ponniah V. Mohindra 《Zeitschrift fur angewandte Ichthyologie》2004,20(2):87-91
Forty‐four primer sequences available for four cyprinid fishes were tested to amplify microsatellite loci in Indian major carp, Cirrhinus mrigala. A total of 12 loci were successfully amplified with clear scorable patterns and five thereof were polymorphic. Suitability of the identified polymorphic loci in population structure analysis of C. mrigala was assessed. Genetic variation was examined in 76 specimens collected from five different rivers. The mean observed heterozygosity ranged from 0.247 to 0.333. Significant heterogeneity in allele frequencies was detected, indicating that the samples analysed did not belong to homogenous populations. The identified microsatellite markers are promising for the analysis of intraspecific divergence in C. mrigala across its distribution range. 相似文献
15.
C. F. Quiros J. Hu P. This A. M. Chevre M. Delseny 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1991,82(5):627-632
Summary This paper reports the application of the RAPD (random amplification of polymorphic DNA sequence) markers in Brassica genetics. Forty-seven arbitrary decamer oligonucletides were used as primers to amplify genomic DNA by polymerase chain reaction. Some of the amplified products were genome specific and could be found in both diploid and derived amphidiploid species. Of a total of 65 such markers, 16 were A genome, 37 B genome, and 12 C genome specific. Of the 37 B-genome-specific markers, 11 were mapped on four independent chromosomes of B. nigra with the aid of existing B. napus-nigra disomic alien addition lines. 相似文献
16.
Benjamin Bornet Elisabeth Antoine Sylvaine Franoise Claire Marcaillou‐Le Baut 《Journal of phycology》2005,41(3):704-711
Harmful algal blooms are a serious threat to shellfish farming and human health all over the world. The monitoring of harmful algae in coastal waters originally involved morphological identification through microscopic examinations, which was often difficult unless performed by specialists and even then often did not permit identification of toxic species. More recently, specific molecular markers have been used to identify specific phytoplankton species or strains. Here we report on the use of the intersimple sequence repeat (ISSR) technique to develop specific sequence characterized amplified region markers (SCAR) and to identify with these tools two toxic species in French coastal waters, the diatom Pseudo‐nitzschia pseudodelicatissima (Hasle) Hasle and the dinoflagellate Alexandrium catenella (Whedon and Kofoid 1936), Balech 1985. Six polymorphic ISSR regions were selected among amplified fingerprints of a representative sample of phytoplankton species. After cloning and sequencing the selected polymorphic ISSR regions, pairs of internal primers were designed to amplify a unique and specific sequence designed as a SCAR marker. Of the six selected SCAR markers, three were specific to P. pseudodelicatissima and one for A. catenella. The SCAR marker specificity was confirmed by using basic local alignment search tool comparison, by experimental assays on different strains from 11 countries, and by checking that the sequence amplified was the expected one. When tested on water samples collected along the French shores, the four specific SCAR markers proved to be efficient tools for fast and low‐cost detection of toxic phytoplankton species. 相似文献
17.
Schnurbusch T Collins NC Eastwood RF Sutton T Jefferies SP Langridge P 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,115(4):451-461
Toxicity due to high levels of soil boron (B) represents a significant limitation to cereal production in some regions, and
the Bo1 gene provides a major source of B toxicity tolerance in bread wheat (Triticum aestivum L.). A novel approach was used to develop primers to amplify and sequence gene fragments specifically from the Bo1 region of the hexaploid wheat genome. Single-nucleotide polymorphisms (SNPs) identified were then used to generate markers
close to Bo1 on the distal end of chromosome 7BL. In the 16 gene fragments totaling 19.6 kb, SNPs were observed between the two cultivars
Cranbrook and Halberd at a low frequency (one every 613 bp). Furthermore, SNPs were distributed unevenly, being limited to
only two genes. In contrast, RFLP provided a much greater number of genetic markers, with every tested gene identifying polymorphism.
Bo1 previously known only as a QTL was located as a discrete Mendelian locus. In total, 28 new RFLP, PCR and SSR markers were
added to the existing map. The 1.8 cM Bo1 interval of wheat corresponds to a 227 kb section of rice chromosome 6L encoding 21 predicted proteins with no homology to
any known B transporters. The co-dominant PCR marker AWW5L7 co-segregated with Bo1 and was highly predictive of B tolerance status within a set of 94 Australian bread wheat cultivars and breeding lines. The
markers and rice colinearity described here represent tools that will assist B tolerance breeding and the positional cloning
of Bo1.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
18.
19.
Tony Gamble 《Molecular ecology》2016,25(10):2114-2116
Next‐generation sequencing methods have initiated a revolution in molecular ecology and evolution (Tautz et al. 2010 ). Among the most impressive of these sequencing innovations is restriction site‐associated DNA sequencing or RAD‐seq (Baird et al. 2008 ; Andrews et al. 2016 ). RAD‐seq uses the Illumina sequencing platform to sequence fragments of DNA cut by a specific restriction enzyme and can generate tens of thousands of molecular genetic markers for analysis. One of the many uses of RAD‐seq data has been to identify sex‐specific genetic markers, markers found in one sex but not the other (Baxter et al. 2011 ; Gamble & Zarkower 2014 ). Sex‐specific markers are a powerful tool for biologists. At their most basic, they can be used to identify the sex of an individual via PCR. This is useful in cases where a species lacks obvious sexual dimorphism at some or all life history stages. For example, such tests have been important for studying sex differences in life history (Sheldon 1998 ; Mossman & Waser 1999 ), the management and breeding of endangered species (Taberlet et al. 1993 ; Griffiths & Tiwari 1995 ; Robertson et al. 2006 ) and sexing embryonic material (Hacker et al. 1995 ; Smith et al. 1999 ). Furthermore, sex‐specific markers allow recognition of the sex chromosome system in cases where standard cytogenetic methods fail (Charlesworth & Mank 2010 ; Gamble & Zarkower 2014 ). Thus, species with male‐specific markers have male heterogamety (XY) while species with female‐specific markers have female heterogamety (ZW). In this issue, Fowler & Buonaccorsi ( 2016 ) illustrate the ease by which RAD‐seq data can generate sex‐specific genetic markers in rockfish (Sebastes). Moreover, by examining RAD‐seq data from two closely related rockfish species, Sebastes chrysomelas and Sebastes carnatus (Fig. 1 ), Fowler & Buonaccorsi ( 2016 ) uncover shared sex‐specific markers and a conserved sex chromosome system. 相似文献
20.
Oyster (Crassostrea gigas) is widely distributed in coastal areas of world. We developed and evaluated simple sequence repeat (SSR) markers from expressed
sequence tags (ESTs) of C. gigas and to amplify EST-SSR in C. gigas. Characteristics of 11 EST-SSR loci were investigated using 45 C. gigas individuals. The number of alleles per locus ranged from two to thirteen. The observed heterozygosity (H
o) ranged from 0.0889 to 0.7333 and the expected heterozygosity (H
e) ranged from 0.0859 to 0.8981. Because of their high level of polymorphism, our 11 single-locus EST-SSR markers will be valuable
tools for research on mating system, population genetics and systemic evolution of oyster in the future. 相似文献