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Applications in Plant Sciences

Si-Si Wang, Yang Zhang, De-Chen Liu, Xiao-Wei Sun, Rong Wang, Yuan-Yuan Li
PREMISE OF THE STUDY: To quantify the population-level genetic characteristics of Cunninghamia lanceolata (Taxodiaceae), an important timber conifer, we developed 30 pairs of microsatellite primers based on the nuclear genome. METHODS AND RESULTS: Using the streptavidin-biotin capture system, we developed 14 polymorphic and 16 monomorphic microsatellites. Polymorphisms were detected in 14 loci using 94 individual trees that were collected from three C. lanceolata populations in Hubei and Zhejiang provinces and in Chongqing Municipality, China...
September 2017: Applications in Plant Sciences
Elisa Lagostina, Francesco Dal Grande, Sieglinde Ott, Christian Printzen
PREMISE OF THE STUDY: Usnea antarctica and U. aurantiacoatra (Parmeliaceae) are common lichens in the maritime Antarctic. These species share the same habitats on King George Island (South Shetland Islands, Antarctica) and are distinguishable based on reproductive strategies. METHODS AND RESULTS: We developed 23 fungus-specific simple sequence repeat (SSR) markers that cross-amplify between the two species. We used a low-coverage genome-skimming approach on one sample of each species to identify SSR repeats in the two species...
September 2017: Applications in Plant Sciences
Joyce G Chery, Chodon Sass, Chelsea D Specht
PREMISE OF THE STUDY: We developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted introns of single-copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline. METHODS AND RESULTS: Transcriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single-nucleotide polymorphisms are called, generating a "pseudoreference" closer to the lineage of interest...
September 2017: Applications in Plant Sciences
Rachel A van Heugten, Marie L Hale, Stacey Bryan, Bart van Griensven, Sophia Satter, Lily Brailsford, Hannah L Buckley
PREMISE OF THE STUDY: Ficinia spiralis (Cyperaceae) is a declining sand-binding sedge of ecological and cultural importance. Microsatellite primers were developed in F. spiralis to investigate how population genetic structure is related to the pronounced morphological, physiological, and ecological variation observed in this species. METHODS AND RESULTS: A 454 shotgun-sequencing approach was used to generate 157,274 raw sequence reads, 536 of which contained microsatellites...
September 2017: Applications in Plant Sciences
Maribeth Latvis, Sarah J Jacobs, Sebastian M E Mortimer, Melissa Richards, Paul D Blischak, Sarah Mathews, David C Tank
PREMISE OF THE STUDY: We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility. METHODS AND RESULTS: We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family...
September 2017: Applications in Plant Sciences
Maribeth Latvis, Sebastian M E Mortimer, Diego F Morales-Briones, Samuel Torpey, Simon Uribe-Convers, Sarah J Jacobs, Sarah Mathews, David C Tank
PREMISE OF THE STUDY: Chloroplast primers were developed from genomic data for the taxonomically challenging genus Castilleja. We further tested the broader utility of these primers across Orobanchaceae, identifying a core set of chloroplast primers amplifying across the clade. METHODS AND RESULTS: Using a combination of three low-coverage Castilleja genomes and sequence data from 12 Castilleja plastomes, 76 primer combinations were specifically designed and tested for Castilleja...
September 2017: Applications in Plant Sciences
Xiao-Yan Wang, Ze-Xin Jin, Jian-Hui Li, Yuan-Yuan Li
PREMISE OF THE STUDY: Thirty-one microsatellite markers were developed for Sinocalycanthus chinensis (Calycanthaceae), an endemic endangered species in China. METHODS AND RESULTS: Twenty-one polymorphic and 10 monomorphic microsatellite markers of S. chinensis were developed using methods of biotin-streptavidin capture and capillary electrophoresis. The number of alleles per locus was one to 20 with an average of 4.677 in 90 individuals taken from two populations in Zhejiang Province and one population in Anhui Province in China...
September 2017: Applications in Plant Sciences
Bronwyn M Ayre, Janet M Anthony, David G Roberts, Richard J N Allcock, Siegfried L Krauss
PREMISE OF THE STUDY: Microsatellites were developed for the future assessment of population genetic structure, mating system, and dispersal of the perennial kangaroo paw, Anigozanthos manglesii (Haemodoraceae), and related species. METHODS AND RESULTS: Using a Personal Genome Machine (PGM) semiconductor sequencer, ca. 4.03 million sequence reads were generated. QDD pipeline software was used to identify 190,000 microsatellite-containing regions and priming sites...
August 2017: Applications in Plant Sciences
Johany Peñailillo, Wenhsi Kuo, Gabriela Olivares, Gerardo Silva-Poblete, Barbara Peña-Ahumada, Sofía Muñoz, Ximena Moncada, Kuo-Fang Chung, Daniela Seelenfreund, Andrea Seelenfreund
PREMISE OF THE STUDY: Broussonetia papyrifera (Moraceae) is native to Asia and is used as a medicinal plant and as a source of fiber for making paper. It was dispersed into the Pacific region as a fiber source for making nonwoven textiles (barkcloth). Microsatellites were developed to trace the human-mediated dispersal of this species into the Pacific region. METHODS AND RESULTS: A set of 36 microsatellites was isolated and initially assayed on 10 accessions to assess polymorphism...
August 2017: Applications in Plant Sciences
Mariana Bulgarella, Patrick J Biggs, Peter J de Lange, Lara D Shepherd
PREMISE OF THE STUDY: Microsatellite markers were developed for Arthropodium cirratum (Asparagaceae) to study population genetic structure and translocation of this species. These markers were tested for cross-amplification in two other Arthropodium species. METHODS AND RESULTS: Sixteen microsatellite markers were developed from a genomic library and tested in three populations of A. cirratum. The loci exhibited one to five alleles per locus, with private alleles present in each of the populations...
August 2017: Applications in Plant Sciences
Ricardo Gutiérrez-Ozuna, Matthew B Hamilton
PREMISE OF THE STUDY: Twenty-three polymorphic microsatellite loci (simple sequence repeats) were identified and characterized for Liriodendron tulipifera (Magnoliaceae), a species native to eastern North America, to investigate its genetic diversity, population structure, and mating system. METHODS AND RESULTS: Using Illumina HiSeq paired-end reads from genomic DNA, searches for repeat motifs identified approximately 280,000 potentially amplifiable loci. Of 77 loci tested, 51 amplified consistently...
August 2017: Applications in Plant Sciences
Emily L Gillespie, Annabella G Pauley, Megan L Haffner, Nikolai M Hay, Matt C Estep, Zack E Murrell
PREMISE OF THE STUDY: Microsatellite primers were developed for a widespread limestone endemic sedge, Carex eburnea, to facilitate investigation of the genetic diversity and phylogeography of this taxon and its closest relative, C. mckittrickensis. METHODS AND RESULTS: Forty-eight primer pairs were designed from Illumina sequence data and screened for suitability. Fourteen of these primer pairs were polymorphic and generated one to seven alleles per locus. Cross-species amplifications were conducted for all four members of Carex sect...
August 2017: Applications in Plant Sciences
Benjamin S T Morgan, Louise M Egerton-Warburton
PREMISE OF THE STUDY: Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples...
August 2017: Applications in Plant Sciences
Ning Miao, Lei Zhang, Maoping Li, Liqiang Fan, Kangshan Mao
PREMISE OF THE STUDY: We developed transcriptome microsatellite markers (simple sequence repeats) for Taxillus nigrans (Loranthaceae) to survey the genetic diversity and population structure of this species. METHODS AND RESULTS: We used Illumina HiSeq data to reconstruct the transcriptome of T. nigrans by de novo assembly and used the transcriptome to develop a set of simple sequence repeat markers. Overall, 40 primer pairs were designed and tested; 19 of them amplified successfully and demonstrated polymorphisms...
August 2017: Applications in Plant Sciences
Karla Quiroz, Jessica Saavedra, Hermine Vogel, Gabriela Verdugo, Peter D S Caligari, Rolando García-Gonzáles
PREMISE OF THE STUDY: Chloraea crispa is a terrestrial Orchidaceae species native to Chile, characterized by a beautiful and showy inflorescence. The species has a great potential for commercial exploitation in the cut flower industry, but it is essential to improve propagation methods to avoid endangering its natural populations. Because this species is hard to propagate using traditional greenhouse techniques, in vitro techniques offer an effective tool for its large-scale production in terms of germination, growth, and propagation...
August 2017: Applications in Plant Sciences
Catherine J Nock, Martin S Elphinstone, Gary Ablett, Asuka Kawamata, Wayne Hancock, Craig M Hardner, Graham J King
[This corrects the article DOI: 10.3732/apps.1300089.].
August 2017: Applications in Plant Sciences
Xianggang Shi, Haidan Wu, Hongxian Xie, Yi Zheng, Yelin Huang, Shixiao Yu
PREMISE OF THE STUDY: Sixteen microsatellite markers were developed to study the fine-scale spatial genetic structure of Eurya acuminatissima, a dioecious tree species of Theaceae endemic to southern China. METHODS AND RESULTS: A total of 30 primer pairs were initially designed and tested on the basis of the transcriptome data of E. acuminatissima, of which 16 were successfully amplified and showed clear polymorphism. For these microsatellites, one to 17 alleles per locus were identified...
July 2017: Applications in Plant Sciences
James P Riser, Anna L Schwabe, Jennifer Ramp Neale
PREMISE OF THE STUDY: Microsatellite primers were developed to characterize genetic diversity and structuring in the genus Phacelia (Hydrophyllaceae) and to further conservation efforts for P. formosula. METHODS AND RESULTS: Fifteen novel microsatellite primers were developed for P. formosula. These were characterized for genetic variation in three separate P. formosula populations. Two to nine alleles were found per locus. Overall observed heterozygosity and expected heterozygosity ranged from 0...
July 2017: Applications in Plant Sciences
Yu-Ping Liu, Xu Su, Wen-Chun Luo, Ting Lv, Ke-Long Chen, A J Harris, Sayed Afzal Shah
PREMISE OF THE STUDY: Transcriptomes were used to develop microsatellite markers for the plant genus Orinus (Poaceae), which comprises three species of grasses (O. thoroldii, O. kokonoricus, and O. intermedius) that are widely distributed in the Qinghai-Tibetan Plateau. METHODS AND RESULTS: Primer pairs were developed for 16 high-quality simple sequence repeats (SSRs) using transcriptomes. SSRs were amplified in 248 individuals representing the three species of Orinus; the number of alleles per locus ranged from one to seven, with an average of 2...
July 2017: Applications in Plant Sciences
Félicien Tosso, Jean-Louis Doucet, Jérémy Migliore, Kasso Daïnou, Esra Kaymak, Franck S Monthe Kameni, Olivier J Hardy
PREMISE OF THE STUDY: Microsatellite primers (simple sequence repeats [SSRs]) were developed in Guibourtia ehie (Fabaceae, Detarioideae) to study population genetic structure and the history of African vegetation. METHODS AND RESULTS: We isolated 18 polymorphic SSRs from a nonenriched genomic library. This set of primer pairs was tested on four populations, and the results showed two to 16 alleles per locus with mean observed and expected heterozygosities of 0.27 ± 0...
July 2017: Applications in Plant Sciences
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