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Applications in Plant Sciences

Janet M Anthony, Richard J N Allcock, Mark P Dobrowolski, Siegfried L Krauss
Premise of the study: Microsatellite markers were developed for population genetic analysis in the rare shrub Styphelia longissima (Ericaceae). Methods and Results: We generated ca. 2.5 million sequence reads using a Personal Genome Machine semiconductor sequencer. Using the QDD pipeline, we designed primers for >12,000 sequences with PCR product lengths of 80-480 bp. From these, 30 primer pairs were selected and screened using PCR; of these, 16 loci were found to be polymorphic, four loci were monomorphic, and 10 loci did not amplify reliably for S...
November 2017: Applications in Plant Sciences
Eva Kondrysová, Karol Krak, Bohumil Mandák
Premise of the study: Microsatellite primers were developed to characterize the genetic diversity and structure of the annual herb Atriplex tatarica (Amaranthaceae) and to facilitate ecological and evolutionary studies of A. tatarica and its relatives. Methods and Results: Sixteen novel microsatellite primers were developed for A. tatarica based on high-throughput sequencing of enriched libraries. All markers were polymorphic, with the number of alleles per locus ranging from three to 25 and observed and expected heterozygosity ranging from 0...
November 2017: Applications in Plant Sciences
Zhi-Zhong Li, Meng-Xue Lu, Josphat K Saina, Andrew W Gichira, Qing-Feng Wang, Jin-Ming Chen
Premise of the study: Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Methods and Results: Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis. One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively...
November 2017: Applications in Plant Sciences
Zuo-Zhou Li, Hua Tian, Jin-Ju Zhang
Premise of the study: Polymorphic microsatellite markers were developed to reveal the genetic diversity of extant populations and the mating system of Sinowilsonia henryi (Hamamelidaceae). Methods and Results: In this study, nuclear simple sequence repeat (SSR) markers were developed using the Illumina high-throughput sequencing technique (RNA-Seq). The de novo-assembled transcriptome generated a total of 64,694 unique sequences with an average length of 601 bp...
November 2017: Applications in Plant Sciences
Jenna L Wingfield, Lauren G Ruane, Joshua D Patterson
Premise of the study: The three-dimensional structure of tree canopies creates environmental heterogeneity, which can differentially influence the chemistry, morphology, physiology, and/or phenology of leaves. Previous studies that subdivide canopy leaves into broad categories (i.e., "upper/lower") fail to capture the differences in microenvironments experienced by leaves throughout the three-dimensional space of a canopy. Methods: We use a three-dimensional spatial mapping approach based on spherical polar coordinates to examine the fine-scale spatial distributions of photosynthetically active radiation (PAR) and the concentration of ultraviolet (UV)-absorbing compounds (A300) among leaves within the canopies of black mangroves (Avicennia germinans)...
November 2017: Applications in Plant Sciences
Brendan F Kohrn, Jessica M Persinger, Mitchell B Cruzan
Premise of the study: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole-genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single-nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure...
November 2017: Applications in Plant Sciences
Theresa M Culley
We are now in an era where sharing and making data widely accessible are not only expected within many disciplines, but also required by federal granting agencies and many scientific journals. In addition, there are practical reasons why authors should deposit their data into permanent data repositories: (1) it prevents data loss due to accidents, theft, or death of the researcher; (2) it enables published research to be reproduced by others; (3) publications associated with accessible data sets can have higher citation rates; (4) deposited data sets are increasingly recognized for scholarly recognition and professional advancement; and (5) stored and accessible data can be used in the future for projects that are unanticipated today...
October 2017: Applications in Plant Sciences
Lijing Sun, Kaikai Meng, Boyong Liao, Chunmei Li, Yue Zhang, Wenbo Liao, Sufang Chen
Premise of the study: The genus Anneslea (Pentaphylacaceae) contains four species and six varieties, most of which are locally endemic. Here, simple sequence repeat (SSR) markers were developed for the conservation of these species. Methods and Results: The genome of A. fragrans was sequenced and de novo assembled into 445,162 contigs, of which 30,409 SSR loci were detected. Primers for 100 SSR loci were validated with PCR amplification in three populations of A...
October 2017: Applications in Plant Sciences
Ping Wang, Karin Tremetsberger, Estrella Urtubey, Karl-Georg Bernhardt
Premise of the study: We developed microsatellite markers to study clonal growth and interspecific hybridization in the Patagonian and subantarctic plant Hypochaeris incana (Asteraceae) and its closest relatives. Methods and Results: We developed primers for microsatellite loci from 454 sequence reads of genomic DNA of H. incana. We tested them on individuals of H. acaulis, H. hookeri, H. incana, H. palustris, and H. tenuifolia. We selected 15 polymorphic microsatellite loci, which delivered clearly scorable fragments in most or all species...
October 2017: Applications in Plant Sciences
Haijun Liu, Zhihua Yan, Hualing Xu, Chunmei Li, Qiang Fan, Wenbo Liao, Boyong Liao
Premise of the study: Brainea insignis (Aspleniaceae) is an endangered tree fern in China whose wild populations have been seriously damaged due to overexploitation. Expressed sequence tag-simple sequence repeat (EST-SSR) primers were developed to investigate its genetic diversity and provide resources for future conservation studies. Methods and Results: We obtained 72,897 unigenes of B. insignis using transcriptome sequencing and detected 15,006 SSRs in 12,058 unigenes...
October 2017: Applications in Plant Sciences
Maila Beyer, Alison G Nazareno, Lúcia G Lohmann
Premise of the study: We developed chloroplast microsatellite markers (cpSSRs) to be used to study the patterns of genetic structure and genetic diversity of populations of Stizophyllum riparium (Bignonieae, Bignoniaceae). Methods and Results: We used genomic data obtained through an Illumina HiSeq sequencing platform to develop a set of cpSSRs for S. riparium. A total of 36 primer pairs were developed, of which 28 displayed polymorphisms across 59 individuals from three populations...
October 2017: Applications in Plant Sciences
Brent A Berger, Jiahong Han, Emily B Sessa, Andrew G Gardner, Kelly A Shepherd, Vincent A Ricigliano, Rachel S Jabaily, Dianella G Howarth
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes...
October 2017: Applications in Plant Sciences
Yueqin Cheng, Pingping Li, Yi Yang, Jianhang Zhang, Fengming Yan, Hongwei Wang
Premise of the study: Phytolacca acinosa (Phytolaccaceae) is a traditional Chinese herb with multiple medicinal uses and is an important pigment source. Due to excessive human harvesting, the population numbers and sizes have decreased dramatically. Methods and Results: Using an enriched genomic library, we developed and characterized 15 microsatellite primers for P. acinosa, 13 of which were polymorphic. The number of alleles varied from two to seven. The observed heterozygosity and expected heterozygosity per locus ranged from 0...
October 2017: 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
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