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Applications in Plant Sciences

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https://www.readbyqxmd.com/read/28529837/fifteen-microsatellite-markers-for-herbertia-zebrina-iridaceae-an-endangered-species-from-south-american-grasslands
#1
Cristiane Forgiarini, Manuel Curto, Eudes Maria Stiehl-Alves, Christian Bräuchler, Johannes Kollmann, Harald Meimberg, Tatiana Teixeira de Souza-Chies
PREMISE OF THE STUDY: Polymorphic microsatellite loci were developed and used to genotype individuals of Herbertia zebrina (Iridaceae) as a first step for assessment of intraspecific genetic diversity. METHODS AND RESULTS: Primer pairs for 47 markers were developed: 20 from a microsatellite-enriched library and 27 from a next-generation sequencing run using the Illumina MiSeq platform. Of those, 15 loci were considered successful, of which 12 were polymorphic and three were monomorphic...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28529836/chloroplast-and-mitochondrial-microsatellites-for-millettia-pinnata-fabaceae-and-cross-amplification-in-related-species
#2
Yanling Wang, Hongxian Xie, Yi Yang, Yelin Huang, Jianwu Wang, Fengxiao Tan
PREMISE OF THE STUDY: Chloroplast and mitochondrial microsatellites were identified to study the population genetics of Millettia pinnata (Fabaceae). METHODS AND RESULTS: Based on publicly available plastid genome sequence data of M. pinnata, 42 primer pairs were developed, of which 17 displayed polymorphisms across 89 individuals from four populations. For chloroplast loci, two to six alleles were recovered and the unbiased haploid diversity per locus ranged from 0...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28529835/a-new-set-of-microsatellite-primers-for-coelogyne-fimbriata-orchidaceae-and-cross-amplification-in-c-ovalis
#3
Wei-Chang Huang, Kai Jiang, Chao Hu, Yue-E Xiao, Barnabas C Seyler, Yuan-Yuan Li
PREMISE OF THE STUDY: Declining orchid populations have made it necessary to prioritize the study of population structure and genetic diversity for species including Coelogyne fimbriata (Orchidaceae). METHODS AND RESULTS: A biotin-streptavidin capture method was used to construct a microsatellite library for C. fimbriata. A total of 15 polymorphic nuclear microsatellite loci were isolated and characterized using 47 C. fimbriata individuals from two natural populations in China...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28529834/development-and-characterization-of-est-ssr-markers-for-begonia-luzhaiensis-begoniaceae
#4
Yu-Hsin Tseng, Han-Yau Huang, Wei-Bin Xu, Hsun-An Yang, Yan Liu, Ching-I Peng, Kuo-Fang Chung
PREMISE OF THE STUDY: Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. METHODS AND RESULTS: Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28529833/development-and-evaluation-of-microsatellite-markers-for-the-critically-endangered-birch-betula-chichibuensis-betulaceae
#5
Yuji Igarashi, Hiroki Aihara, Yoshihiro Handa, Hiroshi Katsumata, Masanori Fujii, Koichiro Nakano, Toshihide Hirao
PREMISE OF THE STUDY: Microsatellite markers were developed and characterized for the critically endangered birch Betula chichibuensis (Betulaceae) to investigate the genetic structure of this species for conservation purposes. METHODS AND RESULTS: Sixteen microsatellite markers with di-, tri-, and tetranucleotide repeat motifs were developed and optimized using MiSeq paired-end sequencing. Of these, 14 were polymorphic, with two to five alleles per locus, in 47 individuals from two newly discovered populations of B...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28529832/application-of-a-simplified-method-of-chloroplast-enrichment-to-small-amounts-of-tissue-for-chloroplast-genome-sequencing
#6
Shota Sakaguchi, Saneyoshi Ueno, Yoshihiko Tsumura, Hiroaki Setoguchi, Motomi Ito, Chie Hattori, Shogo Nozoe, Daiki Takahashi, Riku Nakamasu, Taishi Sakagami, Guillaume Lannuzel, Bruno Fogliani, Adrien S Wulff, Laurent L'Huillier, Yuji Isagi
PREMISE OF THE STUDY: High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. METHODS: Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28529831/source-identification-of-western-oregon-douglas-fir-wood-cores-using-mass-spectrometry-and-random-forest-classification
#7
Kristen Finch, Edgard Espinoza, F Andrew Jones, Richard Cronn
PREMISE OF THE STUDY: We investigated whether wood metabolite profiles from direct analysis in real time (time-of-flight) mass spectrometry (DART-TOFMS) could be used to determine the geographic origin of Douglas-fir wood cores originating from two regions in western Oregon, USA. METHODS: Three annual ring mass spectra were obtained from 188 adult Douglas-fir trees, and these were analyzed using random forest models to determine whether samples could be classified to geographic origin, growth year, or growth year and geographic origin...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439480/development-of-microsatellite-markers-based-on-expressed-sequence-tags-in-asparagus-cochinchinensis-asparagaceae
#8
Bo-Yun Kim, Han-Sol Park, Jung-Hoon Lee, Myounghai Kwak, Young-Dong Kim
PREMISE OF THE STUDY: Transcriptome-derived simple sequence repeat (SSR) markers were developed in Asparagus cochinchinensis (Asparagaceae). Due to its application in traditional medicine, its wild populations are threatened by over-collection even in protected areas, requiring immediate conservation efforts. METHODS AND RESULTS: Based on transcriptome data of A. cochinchinensis, 96 primer pairs with two to seven alleles per locus were selected for initial validation; of those, 27 primer pairs amplified across all samples, resulting in 15 polymorphic and 12 monomorphic microsatellite markers...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439479/simple-sequence-repeat-markers-for-k%C3%A4-nuka-kunzea-spp-myrtaceae-present-in-new-zealand
#9
Dagmar F Goeke, Caroline M Mitchell, Claudia Lange, Gary J Houliston
PREMISE OF THE STUDY: We developed simple sequence repeat (SSR) markers to facilitate population genetic studies on kānuka (Kunzea spp.; Myrtaceae). METHODS AND RESULTS: A shotgun sequencing library was constructed from leaf material of K. robusta using a Roche 454 Junior sequencer, and a total of 3174 putative SSR regions were identified. Sixteen polymorphic markers were optimized for multiplex PCR on 10 endemic New Zealand Kunzea species. Each of these loci cross-amplified in all tested species...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439478/development-of-microsatellite-loci-in-mediterranean-sarsaparilla-smilax-aspera-smilacaceae-using-transcriptome-data
#10
Zhe-Chen Qi, Chao Shen, Yu-Wei Han, Wei Shen, Man Yang, Jinliang Liu, Zong-Suo Liang, Pan Li, Cheng-Xin Fu
PREMISE OF THE STUDY: Although several microsatellite markers of Smilax aspera (Smilacaceae) have been reported in a previous study, due to universality issues in cross-population amplification, we have newly developed microsatellite markers for S. aspera based on transcriptome data to further investigate gene flow and genetic structure of its circum-Mediterranean, East African, and South Asian populations. METHODS AND RESULTS: A total of 4854 simple sequence repeat (SSR) primer pairs were designed from 99,193 contigs acquired from public transcriptome data of S...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439477/development-and-characterization-of-est-ssr-markers-in-stipa-breviflora-poaceae
#11
Jing Ren, Zhi-Zhen Su, Zhen-Hua Dang, Yu Ding, Pei-Xuan Wang, Jian-Ming Niu
PREMISE OF THE STUDY: Stipa breviflora (Poaceae) is one of the dominant species of the desert steppe in the eastern Eurasian grasslands. Simple sequence repeat (SSR) markers were developed for use in genetic diversity studies of this species. METHODS AND RESULTS: A total of 1954 potentially polymorphic loci were obtained by comparing transcriptome data of eight different S. breviflora individuals. We selected 81 loci to verify polymorphism and 63 loci amplified, of which 21 loci exhibited polymorphism...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439476/development-and-characterization-of-18-polymorphic-ssr-markers-for-barthea-barthei-melastomataceae
#12
Guilian Huang, Haijun Liu, Hongbin Sun, Ying Liu, Renchao Zhou, Wenbo Liao, Qiang Fan
PREMISE OF THE STUDY: To examine population differentiation, simple sequence repeat (SSR) markers were developed in Barthea barthei, a shrub with a disjunct distribution in the southern mainland of China and Taiwan. METHODS AND RESULTS: We used Illumina HiSeq technology to sequence a genomic library for SSR identification. Twenty-seven SSR loci were developed, of which 18 SSR loci were polymorphic in three populations composed of two varieties of B. barthei. At the population level, the number of alleles ranged from one to seven, and the observed and expected heterozygosity varied from 0 to 0...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439475/transcriptomic-resources-for-an-endemic-neotropical-plant-lineage-gesneriaceae
#13
Martha L Serrano-Serrano, Anna Marcionetti, Mathieu Perret, Nicolas Salamin
PREMISE OF THE STUDY: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. METHODS AND RESULTS: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439474/digitizing-specimens-in-a-small-herbarium-a-viable-workflow-for-collections-working-with-limited-resources
#14
Kari M Harris, Travis D Marsico
PREMISE OF THE STUDY: Small herbaria represent a significant portion of herbaria in the United States, but many are not digitizing their collections. METHODS: At the Arkansas State University Herbarium (STAR), we have created a viable workflow to help small herbaria begin the digitization process, including suggestions for publishing data on the Internet. We calculated hourly rates of each phase of the digitization process. We also mapped accessions at the county level to determine geographic strengths in the collection...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337395/isolation-and-characterization-of-microsatellite-loci-for-smilax-sieboldii-smilacaceae
#15
Yalu Ru, Ruijing Cheng, Jing Shang, Yunpeng Zhao, Pan Li, Chengxin Fu
PREMISE OF THE STUDY: Polymorphic microsatellite markers were developed for Smilax sieboldii (Smilacaceae), a member of the S. hispida group with a biogeographic disjunction between eastern Asia and North America, to study the phylogeography and incipient speciation of this species and its close relatives. METHODS AND RESULTS: Transcriptome sequencing produced 47,628 unigenes. Seventeen loci were developed from 122 randomly selected primer pairs. Polymorphism and genetic variation were evaluated for 68 accessions representing five populations of S...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337394/chloroplast-microsatellite-markers-for-pseudotaxus-chienii-developed-from-the-whole-chloroplast-genome-of-taxus-chinensis-var-mairei-taxaceae
#16
Qi Deng, Hanrui Zhang, Yipeng He, Ting Wang, Yingjuan Su
PREMISE OF THE STUDY: Pseudotaxus chienii (Taxaceae) is an old rare species endemic to China that has adapted well to ecological heterogeneity with high genetic diversity in its nuclear genome. However, the genetic variation in its chloroplast genome is unknown. METHODS AND RESULTS: Eighteen chloroplast microsatellite markers (cpSSRs) were developed from the whole chloroplast genome of Taxus chinensis var. mairei and successfully amplified in four P. chienii populations and one T...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337393/development-and-validation-of-est-ssr-markers-for-fokienia-hodginsii-cupressaceae
#17
Mingyan Ding, Kaikai Meng, Qiang Fan, Weizheng Tan, Wenbo Liao, Sufang Chen
PREMISE OF THE STUDY: Fokienia hodginsii (Cupressaceae) is a Tertiary relict evergreen conifer of the monotypic genus Fokienia. Polymorphic microsatellite markers were developed to investigate its genetic diversity and population structure. METHODS AND RESULTS: RNA transcripts of F. hodginsii were sequenced and de novo assembled into 85,818 unigenes, and 1892 simple sequence repeat (SSR) markers were detected from the unigenes. A total of 273 expressed sequence tag-SSR primer pairs were designed and tested, and 129 successfully amplified...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337392/microsatellite-markers-for-population-studies-of-the-salt-marsh-species-juncus-roemerianus-juncaceae
#18
Hayley R Tumas, Brian M Shamblin, Mark S Woodrey, Campbell J Nairn
PREMISE OF THE STUDY: Juncus roemerianus (Juncaceae) is a foundational species and ecosystem engineer of salt marshes in the Gulf of Mexico. These ecosystems provide coastal flood attenuation, nurseries for important species, and other ecosystem services, but are experiencing significant decline. Nuclear microsatellite markers were developed for J. roemerianus to study genetic diversity and population structure for conservation and restoration efforts. METHODS AND RESULTS: Illumina NextSeq high-throughput sequencing was used to develop a panel of 19 polymorphic microsatellite markers that were tested across individuals from three populations on the Gulf Coast...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337391/an-efficient-field-and-laboratory-workflow-for-plant-phylotranscriptomic-projects
#19
Ya Yang, Michael J Moore, Samuel F Brockington, Alfonso Timoneda, Tao Feng, Hannah E Marx, Joseph F Walker, Stephen A Smith
PREMISE OF THE STUDY: We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. METHODS AND RESULTS: A total of 216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens. RNA was extracted, stranded mRNA libraries were prepared, and libraries were sequenced on Illumina HiSeq platforms...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337390/an-rbcl-reference-library-to-aid-in-the-identification-of-plant-species-mixtures-by-dna-metabarcoding
#20
Karen L Bell, Virginia M Loeffler, Berry J Brosi
PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. METHODS: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms...
March 2017: Applications in Plant Sciences
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