Showing papers in "Applications in Plant Sciences in 2013"
TL;DR: A targeted enrichment strategy to facilitate rapid and low-cost next-generation sequencing (NGS) of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms was explored and yielded nearly complete to complete plasts with exceptionally high coverage.
Abstract: Premise of the study: We explored a targeted enrichment strategy to facilitate rapid and low-cost next-generation sequencing (NGS) of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms. Methods and Results: A custom RNA probe set including the complete sequences of 22 previously sequenced eudicot plastomes was designed to facilitate hybridization-based targeted enrichment of eudicot plastid genomes. Using this probe set and an Agilent SureSelect targeted enrichment kit, we conducted an enrichment experiment including 24 angiosperms (22 eudicots, two monocots), which were subsequently sequenced on a single lane of the Illumina GAIIx with single-end, 100-bp reads. This approach yielded nearly complete to complete plastid genomes with exceptionally high coverage (mean coverage: 717×), even for the two monocots. Conclusions: Our enrichment experiment was highly successful even though many aspects of the capture process employed were suboptimal. Hence, significant improvement...
101 citations
TL;DR: The addition of TBT-PAR during routine PCR is an effective method to improve amplification of DNA extracted from herbarium specimens or plants that are known to contain PCR inhibitors.
Abstract: Premise of the study: PCR amplification of DNA extracted from plants is sometimes difficult due to the presence of inhibitory compounds. An effective method to overcome the inhibitory effect of compounds that contaminate DNA from difficult plant specimens is needed. Methods and Results: The effectiveness of a PCR additive reagent containing trehalose, bovine serum albumin (BSA), and polysorbate-20 (Tween-20) (TBT-PAR) was tested. PCR of DNA extracted from fresh, silica-dried, and herbarium leaf material of species of Achariaceae, Asteraceae, Lacistemataceae, and Samydaceae that failed using standard techniques were successful with the addition of TBT-PAR. Conclusions: The addition of TBT-PAR during routine PCR is an effective method to improve amplification of DNA extracted from herbarium specimens or plants that are known to contain PCR inhibitors.
85 citations
TL;DR: Vouchers are crucial in authenticating the taxonomy of an organism, as a tool for identifying localities of the taxon, and for additional taxonomic, genetic, ecological, and/or environmental research.
Abstract: What is a voucher and why is it important in research? As a preserved specimen of an identified taxon deposited in a permanent and accessible storage facility, the voucher serves as the supporting material for published studies of the taxon and ensures that the science is repeatable. Vouchers are crucial in authenticating the taxonomy of an organism, as a tool for identifying localities of the taxon, and for additional taxonomic, genetic, ecological, and/or environmental research.
66 citations
TL;DR: This technique was successfully used to develop microsatellite markers in several plant species by combining two techniques in the same PCR reaction: custom-labeling of primers by the investigator and multiplexing multiple primers together in thesame reaction.
Abstract: Premise of the study: Development of genetic markers can be costly and time-consuming, especially when multiple primer pairs are fluorescently labeled. This step was streamlined by combining two techniques in the same PCR reaction: (1) custom-labeling of primers by the investigator and (2) multiplexing multiple primers together in the same reaction. Methods and Results: This technique was successfully used to develop microsatellite markers in several plant species. Microsatellites amplified with this multiplexing process were identical to those generated from PCR using individual primer pairs and with traditional methods using a priori labeled fluorescent primers. Tests of PCR cycling programs revealed that conditions recommended for the commercial kit generated stronger fragment peaks than the previously recommended cycling protocol. Conclusions: This technique is an efficient and economical way to fluorescently label multiple microsatellite primers in the same reaction. It is also applicable to other ma...
57 citations
TL;DR: This protocol results in the extraction of high-quality RNA from a variety of plant tissues representing vascular and nonvascular plants, using quantitative PCR and semiquantitative reverse transcription PCR.
Abstract: Premise of the study: To study gene expression in plants, high-quality RNA must be extracted in quantities sufficient for subsequent cDNA library construction. Field-based collections are often limited in quantity and quality of tissue and are typically preserved in RNAlater. Obtaining sufficient and high-quality yield from variously preserved samples is essential to studies of comparative biology. We present a protocol for the extraction of high-quality RNA from even the most recalcitrant plant tissues. Methods and Results: Tissues from mosses, cycads, and angiosperm floral organs and leaves were preserved in RNAlater or frozen fresh at −80°C. Extractions were performed and quality was measured for yield and purity. Conclusions: This protocol results in the extraction of high-quality RNA from a variety of plant tissues representing vascular and nonvascular plants. RNA was used for cDNA synthesis to generate libraries for next-generation sequencing and for expression studies using quantitative PCR (qPCR) ...
47 citations
TL;DR: Visikol is as effective as chloral hydrate in providing clarity and resolution of all tissues examined, allowing observation of deeper layers of cells and making it effective in research, botanical and quality control, and for educational applications.
Abstract: Premise of the study: This study presents Visikol™, a new proprietary formulation that can be used as an efficient replacement for chloral hydrate as a clearing agent for microscopic examination. In the United States, chloral hydrate is regulated and therefore difficult to acquire. Methods and Results: Fresh and dry samples of the following plants: ginger (Zingiber officinale), mate (Ilex paraguariensis), lime basil (Ocimum americanum), oregano (Origanum vulgare), and mouse-ear cress (Arabidopsis thaliana), were cleared using Visikol or chloral hydrate solution and compared using a light microscope. Conclusions: This new method can be used successfully to clear specimens, allowing identification of diagnostic characteristics for the identification of plant materials. Visikol is as effective as chloral hydrate in providing clarity and resolution of all tissues examined. Tissues become transparent, allowing observation of deeper layers of cells and making it effective in research, botanical and quality cont...
37 citations
TL;DR: These loci will enable genetic diversity studies of P. alba and P. chilensis and contribute to fine-scale population structure, indirect estimation of relatedness among individuals, and marker-assisted selection.
Abstract: Premise of the study: As only six useful microsatellite loci that exhibit broad cross-amplification are so far available for Prosopis species, it is necessary to develop a larger number of codominant markers for population genetic studies. Simple sequence repeat (SSR) markers obtained for Prosopis species from a 454 pyrosequencing run were optimized and characterized for studies in P. alba and P. chilensis. Methods and Results: Twelve markers that were successfully amplified showed polymorphism in P. alba and P. chilensis. The number of alleles per locus ranged between two and seven and heterozygosity estimates ranged from 0.2 to 0.8. Most of these loci cross-amplify in P. ruscifolia, P. flexuosa, P. kuntzei, P. glandulosa, and P. pallida. Conclusions: These loci will enable genetic diversity studies of P. alba and P. chilensis and contribute to fine-scale population structure, indirect estimation of relatedness among individuals, and marker-assisted selection.
33 citations
TL;DR: This study shows that the extracted features from leaf images are invariant to scale and rotation because those features are close to positive correlation in terms of coefficient correlation.
Abstract: Premise of the study: Because plant identification demands extensive knowledge and complex terminologies, even professional botanists require significant time in the field for mastery of the subject. As plant leaves are normally regarded as possessing useful characteristics for species identification, leaf recognition through images can be considered an important research issue for plant recognition. Methods: This study proposes a feature extraction method for leaf contours, which describes the lines between the centroid and each contour point on an image. A length histogram is created to represent the distribution of distances in the leaf contour. Thereafter, a classifier is applied from a statistical model to calculate the matching score of the template and query leaf. Results: The experimental results show that the top value achieves 92.7% and the first two values can achieve 97.3%. In the scale invariance test, those 45 correlation coefficients fall between the minimal value of 0.98611 and the maximal...
33 citations
TL;DR: In this article, the authors report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA.
Abstract: Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs) and >20,000 simple sequence repeat (SSR) DNA sites. Conclusions: To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced re...
31 citations
TL;DR: This is the first paper on microCT integrated with 3D segmentation and computer animation applied to silicified seed cones, which resulted in excellent 2D serial sections and segmented 3D reconstructions, revealing features requisite to cone identification and understanding of strobilus construction.
Abstract: Premise of the study: As an alternative to conventional thin-sectioning, which destroys fossil material, high-resolution X-ray computed tomography (also called microtomography or microCT) integrated with scientific visualization, three-dimensional (3D) image segmentation, size analysis, and computer animation is explored as a nondestructive method of imaging the internal anatomy of 150-million-year-old conifer seed cones from the Late Jurassic Morrison Formation, USA, and of recent and other fossil cones. Methods: MicroCT was carried out on cones using a General Electric phoenix v|tome|x s 240D, and resulting projections were processed with visualization software to produce image stacks of serial single sections for two-dimensional (2D) visualization, 3D segmented reconstructions with targeted structures in color, and computer animations. Results: If preserved in differing densities, microCT produced images of internal fossil tissues that showed important characters such as seed phyllotaxy or number of se...
28 citations
TL;DR: This set of EST-SSR primer pairs will be valuable tools for future population genetic studies of E. gomphocephala and other eucalypts, particularly for studying gene-linked variation and informing seed-sourcing strategies for ecological restoration.
Abstract: Premise of the study: New microsatellite (simple sequence repeat [SSR]) primers were developed from Eucalyptus expressed sequence tags (ESTs) and optimized for genetic studies of the southwestern Australian tree E. gomphocephala, which is severely impacted by tree health decline and habitat fragmentation. Methods and Results: A total of 133 gene-homologous EST-SSR primer pairs were designed for Eucalyptus, and 44 were screened in E. gomphocephala. Of these, 17 produced reliable amplification products and 11 were polymorphic. Between two and 13 alleles were observed per locus, and observed heterozygosities ranged from 0.172 to 0.867. All 17 EST-SSRs that amplified E. gomphocephala cross-amplified to at least one of E. marginata, E. camaldulensis, and E. victrix. Conclusions: This set of EST-SSR primer pairs will be valuable tools for future population genetic studies of E. gomphocephala and other eucalypts, particularly for studying gene-linked variation and informing seed-sourcing strategies for ecologica...
TL;DR: Cross-amplification results indicated that 12 out of 15 loci amplified polymorphic loci in 23 species in the genus Tilia will be useful tools for investigating the phylogeography and hybridization of Tilia species.
Abstract: Premise of the study: Microsatellite markers in the genus Tilia were developed to investigate the genetic variation in T. platyphyllos and its relationship with T. cordata. Methods and Results: Fifteen microsatellite markers were developed using a microsatellite enrichment protocol. Most loci show a high level of polymorphism in two T. platyphyllos populations from France. The number of alleles ranged from one to 15, with a mean of 8.96. The mean observed and expected heterozygosities were 0.71 and 0.70, respectively. Cross-amplification results indicated that 12 out of 15 loci amplified polymorphic loci in 23 species in the genus. Conclusions: These markers will be useful tools for investigating the phylogeography and hybridization of Tilia species.
TL;DR: The microsatellite markers discovered in this study will be useful in genetic mapping, marker-assisted breeding, and characterization of germplasm.
Abstract: Premise of the study: We developed microsatellite markers in the legume Lens culinaris from publicly available databases to enrich the limited marker resource available for the crop. Methods and Results: Eighty-two primer sets were identified using expressed sequence sets of L. culinaris available in the National Center for Biotechnology Information (NCBI) database and were characterized in six species of Lens. Among them, 20 simple sequence repeat (SSR) primers produced no amplification product, 43 produced monomorphic products, and 19 were polymorphic. The primers amplified mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats with one to four alleles. These SSR loci successfully amplified in five related wild species, with a total of 61 primer pairs in L. nigricans and L. odemensis (98.39%), 59 in L. tomentosus (95.1 %), and 60 in L. ervoides and L. orientalis (96.7%), respectively. Conclusions: The microsatellite markers discovered in this study will be useful in genetic mapping, marker-assiste...
TL;DR: In this paper, single nucleotide polymorphism (SNP) markers based on Competitive Allele-Specific PCR (KASPar) were developed from sequences of three Citrus species.
Abstract: Premise of the study: Single nucleotide polymorphism (SNP) markers based on Competitive Allele-Specific PCR (KASPar) were developed from sequences of three Citrus species. Their transferability was tested in 63 Citrus genotypes and 19 relative genera of the subfamily Aurantioideae to estimate the potential of SNP markers, selected from a limited intrageneric discovery panel, for ongoing broader diversity analysis at the intra- and intergeneric levels and systematic germplasm bank characterization. Methods and Results: Forty-two SNP markers were developed using KASPar technology. Forty-one were successfully genotyped in all of the Citrus germplasm, where intra- and interspecific polymorphisms were observed. The transferability and diversity decreased with increasing taxonomic distance. Conclusions: SNP markers based on the KASPar method developed from sequence data of a limited intrageneric discovery panel provide a valuable molecular resource for genetic diversity analysis of germplasm within a genus and ...
TL;DR: A DNA polymerase that is tolerant to inhibitors improves PCR results, and PCR products and high-quality sequence data were obtained for 96% of samples for rbcL and 79% for matK, compared to 29% and 21% with regular Taq polymerase.
Abstract: Premise of the study: Secondary metabolites often inhibit PCR and sequencing reactions in extractions from plant material, especially from silica-dried and herbarium material. A DNA polymerase that is tolerant to inhibitors improves PCR results. Methods and Results: A novel DNA amplification system, including a DNA polymerase engineered via directed evolution for improved tolerance to common plant-derived PCR inhibitors, was evaluated and PCR parameters optimized for three species. An additional 31 species were then tested with the engineered enzyme and optimized protocol, as well as with regular Taq polymerase. Conclusions: PCR products and high-quality sequence data were obtained for 96% of samples for rbcL and 79% for matK, compared to 29% and 21% with regular Taq polymerase.
TL;DR: The standardized methodology allows the inclusion of herbarium materials as alternative sources of DNA for phylogenetic studies in Bignonieae.
Abstract: Premise of the study: New primers were developed for Bignonieae to enable phylogenetic studies within this clade using herbarium samples. Methods and Results: Internal primers were designed based on available sequences of the plastid ndhF gene and the rpl32-trnL intergenic spacer region, and the nuclear gene PepC. The resulting primers were used to amplify DNA extracted from herbarium materials. High-quality data were obtained from herbarium samples up to 53 yr old. Conclusions: The standardized methodology allows the inclusion of herbarium materials as alternative sources of DNA for phylogenetic studies in Bignonieae.
TL;DR: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species and aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.
Abstract: Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategi...
TL;DR: The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer Abies alba.
Abstract: Premise of the study: We present a protocol for the annotation of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer Abies alba. Methods and Results: A normalized cDNA library was built from an A. alba seedling. The sequencing on a 454 platform yielded more than 1.5 million reads that were de novo assembled into 25 149 contigs. Two complementary approaches were applied to annotate gene fragments that code for (1) well-known proteins and (2) proteins that are potentially adaptively relevant. Primer development and testing yielded 88 amplicons that could successfully be resequenced from genomic DNA. Conclusions: The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data. The primer set presented should be prioritized for single-nucleotide polymorphism detection in adaptively relevant genes in A. alba.
TL;DR: A version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies 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.
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, 30000 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 ac...
TL;DR: Expressed sequence tag–simple sequence repeat markers developed and characterized for size polymorphism in four Firmiana species are valuable for conservation genetics studies in the endangered Firmiana Species.
Abstract: Premise of the study: Firmiana consists of 12–16 species, many of which are narrow endemics. Expressed sequence tag (EST)–simple sequence repeat (SSR) markers were developed and characterized for size polymorphism in four Firmiana species. Methods and Results: A total of 102 EST-SSR primer pairs were designed based on the transcriptome sequences of F. danxiaensis; these were then characterized in four Firmiana species—F. danxiaensis, F. kwangsiensis, F. hainanensis, and F. simplex. In these four species, 17 primer pairs were successfully amplified, and 14 were polymorphic in at least one species. The number of alleles ranged from one to 13, and the observed and expected heterozygosities ranged from 0 to 1 and 0 to 0.925, respectively. The lowest level of polymorphism was observed in F. danxiaensis. Conclusions: These polymorphic EST-SSR markers are valuable for conservation genetics studies in the endangered Firmiana species.
TL;DR: The new markers developed for the threatened haploid lichen fungus Lobaria pulmonaria will increase the genetic resolution in studies that aim at disentangling clones in L. pulmonarius and may be useful for closely related species within Lobaria sect.
Abstract: Premise of the study: Microsatellite loci were developed for the threatened haploid lichen fungus Lobaria pulmonaria to increase the resolution to identify clonal individuals, and to study its population subdivision. Methods and Results: We developed 14 microsatellite markers from 454 DNA sequencing data of L. pulmonaria and tested for cross-amplification with L. immixta and L. macaronesica. The number of alleles per locus ranged from two to 23. Nei's unbiased gene diversity, averaged over loci, ranged from 0.434 to 0.517 in the three studied populations. Conclusions: The new markers will increase the genetic resolution in studies that aim at disentangling clones in L. pulmonaria and may be useful for closely related species within Lobaria sect. Lobaria.
TL;DR: These loci provide a valuable resource for finely resolved, genome-wide population genetic and species-level phylogenetic analyses of C. purpureus and its relatives and are illustrated the among-locus heterogeneity in the species.
Abstract: Premise of the study: We developed and tested primers for 218 nuclear loci for studying population genetics, phylogeography, and genome evolution in bryophytes. Methods and Results: We aligned expressed sequence tags (ESTs) from Ceratodon purpureus to the Physcomitrella patens genome sequence, and designed primers that are homologous to conserved exons but span introns in the P. patens genome. We tested these primers on four isolates from New York, USA; Otavalo, Ecuador; and two laboratory isolates from Austria (WT4 and GG1). The median genome-wide nucleotide diversity was 0.008 substitutions/site, but the range was large (0–0.14), illustrating the among-locus heterogeneity in the species. Conclusions: These loci provide a valuable resource for finely resolved, genome-wide population genetic and species-level phylogenetic analyses of C. purpureus and its relatives.
TL;DR: Direct shotgun pyrosequencing is a fast and relatively low-cost technique allowing identification of microsatellites in nonmodel species and will be useful in population genetic studies to infer the evolutionary history of this species.
Abstract: Premise of the study: Tuber aestivum, the most common truffle in Europe, plays an important role in the commercial truffle market. For the first time, microsatellite primers were developed to investigate polymorphism within this species. Methods and Results: Using direct shotgun pyrosequencing, 15 polymorphic microsatellites were identified out of the 7784 perfect microsatellites present in the 534620 reads obtained. Tested on 75 samples, these microsatellites were highly polymorphic. The number of alleles varied from four to 15, and the expected heterozygosity ranged from 0.266 to 0.620. A multilocus analysis allowed the identification of 63 genotypes over the 75 samples analyzed. Conclusions: Direct shotgun pyrosequencing is a fast and relatively low-cost technique allowing identification of microsatellites in nonmodel species. The microsatellites developed in this study will be useful in population genetic studies to infer the evolutionary history of this species.
TL;DR: This new staining method can be used successfully to identify downy mildew in basil, which then can significantly reduce its spread if identified early, coupled with mitigation strategies.
Abstract: Premise of the study: Demand for fresh-market sweet basil continues to increase, but in 2009 a new pathogen emerged, threatening commercial field/greenhouse production and leading to high crop losses. This study describes a simple and effective staining method for rapid microscopic detection of basil downy mildew (Peronospora belbahrii) from leaves of basil (Ocimum basilicum). Methods and Results: Fresh leaf sections infected with P. belbahrii were placed on a microscope slide, cleared with Visikol™, and stained with iodine solution followed by one drop of 70% sulfuric acid. Cell walls of the pathogen were stained with a distinct coloration, providing a high-contrast image between the pathogen and plant. Conclusions: This new staining method can be used successfully to identify downy mildew in basil, which then can significantly reduce its spread if identified early, coupled with mitigation strategies. This technique can facilitate the control of the disease, without expensive and specialized equipment.
TL;DR: Results indicate the utility of primers in S. altissima for future research on a wide range of applications, including tracking of invasion dynamics and investigating population genetics of the species.
Abstract: Premise of the study: Microsatellite markers were developed in the perennial herb Solidago altissima from populations within its introduced range in Japan to assess its population structure and to facilitate tracking of invasion expansion. Methods and Results: Using 454 pyrosequencing, 16 microsatellite primer sets were developed for S. altissima. The primer sets were tested on 70 individuals sampled from three populations in Japan. The primers amplified di- and trinucleotide repeats with five to 25 alleles per locus, and the expected heterozygosity ranged from 0.46 to 0.92. Conclusions: These results indicate the utility of primers in S. altissima for future research on a wide range of applications, including tracking of invasion dynamics and investigating population genetics of the species.
TL;DR: The results indicate that these markers will be significant for studies of population genetic structure and evolutionary history of M. spicatum as well as some of its related species.
Abstract: Premise of the study: We developed microsatellite primers to investigate genetic diversity and population genetic structure of the cosmopolitan submerged plant Myriophyllum spicatum. Methods and Results: Twenty microsatellite loci were identified in M. spicatum using the microsatellite-enriched library method. The numbers of alleles per locus ranged from one to 13, and the expected heterozygosity varied from 0 to 0.873 with a mean of 0.504 in two Chinese populations of M. spicatum. All of the loci were also found to be amplifiable in the related species M. verticillatum and M. sibiricum. Conclusions: The results indicate that these markers will be significant for studies of population genetic structure and evolutionary history of M. spicatum as well as some of its related species.
TL;DR: The microsatellites identified in this study will enable the examination of population and spatial structuring of genetic diversity in P. elliptica and P. longifolia, two priority species for mine site restoration in southwestern Australia.
Abstract: This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA) (http://creativecommons.org/licenses/by-nc-sa/4.0/)
TL;DR: Polymorphic microsatellite markers developed for Phyllostachys edulis (Poaceae), an ecologically and economically important bamboo species in China, to evaluate the genetic diversity and population genetic structure are useful for studies on the molecular ecology, population genetics, and conservation of P.Edulis.
Abstract: Premise of the study: Polymorphic microsatellite markers were developed for Phyllostachys edulis (Poaceae), an ecologically and economically important bamboo species in China, to evaluate the genetic diversity and population genetic structure of P. edulis and other Phyllostachys species. Methods and Results: Twenty microsatellite markers were developed and their polymorphisms were tested on 71 samples from three geographically disparate populations. Each locus exhibited between two and 10 alleles with an average of five alleles. Excluding monomorphic loci, observed and expected heterozygosity ranged from zero to one and from 0.041 to 0.676, respectively. Conclusions: These 20 polymorphic microsatellite loci will be useful for studies on the molecular ecology, population genetics, and conservation of P. edulis.
TL;DR: Pollination drops are a formative component in gymnosperm pollen-ovule interactions and proteomics offers a direct method for the discovery of proteins associated with this early stage of sexual reproduction via proteomics.
Abstract: Premise of the study: Pollination drops are a formative component in gymnosperm pollen-ovule interactions. Proteomics offers a direct method for the discovery of proteins associated with this early stage of sexual reproduction. Methods: Pollination drops were sampled from eight gymnosperm species: Chamaecyparis lawsoniana (Port Orford cedar), Ephedra monosperma, Ginkgo biloba, Juniperus oxycedrus (prickly juniper), Larix ×marschlinsii, Pseudotsuga menziesii (Douglas-fir), Taxus ×media, and Welwitschia mirabilis. Drops were collected by micropipette using techniques focused on preventing sample contamination. Drop proteins were separated using both gel and gel-free methods. Tandem mass spectrometric methods were used including a triple quadrupole and an Orbitrap. Results: Proteins are present in all pollination drops. Consistency in the protein complement over time was shown in L. ×marschlinsii. Representative mass spectra from W. mirabilis chitinase peptide and E. monosperma serine carboxypeptidase peptid...
TL;DR: These new microsatellite loci will be useful for conservation genetics studies of J. mandshurica and are assessed in samples collected from 98 individuals among five populations in northeastern China.
Abstract: Premise of the study: Fifty microsatellite loci were developed for the endangered species Juglans mandshurica to investigate its genetic diversity and population structure. Methods and Results: In all, 50 microsatellite markers were isolated from J. mandshurica, using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol. Twenty of these polymorphic markers were assessed in samples collected from 98 individuals among five populations in northeastern China. Across all of the J. mandshurica samples, the number of alleles per locus ranged from one to 17. Conclusions: These new microsatellite loci will be useful for conservation genetics studies of J. mandshurica.