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Applications in Plant Sciences

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https://www.readbyqxmd.com/read/27843729/development-and-characterization-of-microsatellite-loci-for-lindera-glauca-lauraceae
#1
Biao Xiong, Shubin Dong, Ji Qi, Limei Zhang, Denglong Ha, Yuxi Ju, Zhixiang Zhang
PREMISE OF THE STUDY: Microsatellite primers were developed to investigate population genetic structure in Lindera glauca (Lauraceae). METHODS AND RESULTS: Twenty-five microsatellite primers were developed and optimized for L. glauca using Illumina's Solexa sequencing technology. These novel primers were found to be polymorphic in nine wild L. glauca populations with 81 total alleles confirmed and genotyped via capillary gel electrophoresis. The total number of alleles, observed heterozygosity, and expected heterozygosity for each population ranged from one to four, from 0...
November 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27843728/microsatellite-primers-for-the-rare-shrub-acacia-adinophylla-fabaceae
#2
Paul G Nevill, Grant Wardell-Johnson
PREMISE OF THE STUDY: Microsatellite primers were developed for the rare shrub Acacia adinophylla (Fabaceae) to assess genetic diversity and its spatial structuring. METHODS AND RESULTS: Shotgun sequencing on an Illumina MiSeq produced 6,372,575 reads. Using the QDD pipeline, we designed 60 primer pairs, which were screened using PCR. Seventeen loci were developed, of which 12 loci were identified that were polymorphic, amplified reliably, and could be consistently scored...
November 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27843727/microsatellite-primers-for-the-rare-sedge-lepidosperma-bungalbin-cyperaceae
#3
Paul G Nevill, Grant Wardell-Johnson
PREMISE OF THE STUDY: Microsatellite markers were developed for the rare sedge Lepidosperma bungalbin (Cyperaceae) to assess genetic variation and its spatial structuring. METHODS AND RESULTS: We conducted shotgun sequencing on an Illumina MiSeq and produced 6,215,872 sequence reads. The QDD pipeline was used to design 60 primer pairs that were screened using PCR. We developed 17 loci, of which 12 loci were identified that were polymorphic, amplified reliably, and could be consistently scored...
November 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27843726/development-of-ssr-markers-for-a-tibetan-medicinal-plant-lancea-tibetica-phrymaceae-based-on-rad-sequencing
#4
Zunzhe Tian, Faqi Zhang, Hairui Liu, Qingbo Gao, Shilong Chen
PREMISE OF THE STUDY: Lancea tibetica (Phrymaceae), a Tibetan medicinal plant, is endemic to the Qinghai-Tibet Plateau. The over-exploitation of wild L. tibetica has led to the destruction of many populations. To enhance protection and management, biological research, especially population genetic studies, should be carried out on L. tibetica. Simple sequence repeat (SSR) markers of L. tibetica were developed to analyze population diversity. METHODS AND RESULTS: Four thousand four hundred and forty-one SSR loci were identified for L...
November 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27843725/development-of-highly-transferable-microsatellites-for-panax-ginseng-araliaceae-using-whole-genome-data
#5
Peng Jiang, Feng-Xue Shi, Ya-Ling Li, Bao Liu, Lin-Feng Li
PREMISE OF THE STUDY: Highly transferable expressed sequence tag (EST) microsatellites were developed for Panax ginseng (Araliaceae), one of the most celebrated traditional Chinese medicines and an endangered species in East Asia, using whole-genome data. METHODS AND RESULTS: Twenty-one EST microsatellites were characterized from next-generation sequencing and were composed of di- and trinucleotide repeats. Polymorphisms and genetic diversity were evaluated for 45 accessions of three ginseng landraces...
November 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27843724/complete-chloroplast-genome-of-a-valuable-medicinal-plant-huperzia-serrata-lycopodiaceae-and-comparison-with-its-congener
#6
Zhi-You Guo, Hong-Rui Zhang, Nawal Shrestha, Xian-Chun Zhang
PREMISE OF THE STUDY: Here we report the complete chloroplast genome of the important medicinal species Huperzia serrata (Lycopodiaceae) and compare it to the chloroplast genome of the congeneric species H. lucidula. METHODS AND RESULTS: The whole chloroplast genome of H. serrata was sequenced using an Illumina platform and assembled with Geneious version R9.0.5. The genome size of H. serrata was 154,176 bp, with 36.3% GC content. The complete chloroplast genome contained 120 unique genes, including 86 coding genes, four rRNA genes, and 30 tRNA genes...
November 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27843723/development-of-single-nucleotide-polymorphism-markers-for-bromus-tectorum-poaceae-from-a-partially-sequenced-transcriptome
#7
Keith R Merrill, Craig E Coleman, Susan E Meyer, Elizabeth A Leger, Katherine A Collins
PREMISE OF THE STUDY: Bromus tectorum (Poaceae) is an annual grass species that is invasive in many areas of the world but most especially in the U.S. Intermountain West. Single-nucleotide polymorphism (SNP) markers were developed for use in investigating the geospatial and ecological diversity of B. tectorum in the Intermountain West to better understand the mechanisms behind its successful invasion. METHODS AND RESULTS: Normalized cDNA libraries from six diverse B...
November 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785388/transcriptomic-resources-and-marker-validation-for-diploid-and-polyploid-veronica-plantaginaceae-from-new-zealand-and-europe
#8
Eike Mayland-Quellhorst, Heidi M Meudt, Dirk C Albach
PREMISE OF THE STUDY: Polyploidy may generate novel variation, leading to adaptation and species diversification. An excellent natural system to study polyploid evolution in a comparative framework is Veronica (Plantaginaceae), which comprises several parallel, recently evolved polyploid series. METHODS: Over 105 million Illumina paired-end sequence reads were generated from cDNA libraries of leaf tissue from eight individuals representing three European and four New Zealand species...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785387/characterization-of-polymorphic-microsatellite-markers-in-pinus-armandii-pinaceae-an-endemic-conifer-species-to-china
#9
Wan-Lin Dong, Ruo-Nan Wang, Xiao-Hao Yan, Chuan Niu, Lin-Lin Gong, Zhong-Hu Li
PREMISE OF THE STUDY: Pinus armandii (Pinaceae) is an important conifer tree species in central and southwestern China, and it plays a key role in the local forest ecosystems. To investigate its population genetics and design effective conservation strategies, we characterized 18 polymorphic microsatellite markers for this species. METHODS AND RESULTS: Eighteen novel polymorphic and 16 monomorphic microsatellite loci of P. armandii were isolated using Illumina MiSeq technology...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785386/polymorphic-microsatellite-markers-in-anthoxanthum-poaceae-and-cross-amplification-in-the-eurasian-complex-of-the-genus
#10
Irene Lema-Suárez, Elvira Sahuquillo, Neus Marí-Mena, Manuel Pimentel
PREMISE OF THE STUDY: Nonplastid microsatellite primers were developed for the first time in the Euro-Siberian complex of Anthoxanthum (Poaceae), a genus of temperate grasses in which reticulate evolution is common. METHODS AND RESULTS: A microsatellite-enriched genomic DNA library allowed the detection of 500 fragments containing a microsatellite motif. Fifteen primer pairs were selected for an extended primer test. A preliminary analysis was conducted on the Eurasian diploid lineages of Anthoxanthum, with special emphasis on three populations of the Mediterranean A...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785385/isolation-and-characterization-of-microsatellite-markers-in-the-lepisorus-clathratus-complex-polypodiaceae
#11
Cun-Feng Zhao, Myounghai Kwak, Qiao-Ping Xiang
PREMISE OF THE STUDY: Microsatellites were designed and characterized in the Sino-Himalayan fern Lepisorus clathratus complex (Polypodiaceae) to further study the phylogeography and reproductive ecology of this species. METHODS AND RESULTS: From a genomic library obtained by next-generation sequencing, 10 polymorphic and six monomorphic microsatellite loci were developed. In one population of L. clathratus from Taibaishan in central China, the number of alleles observed for these microsatellites ranged from seven to 29, and observed and expected heterozygosity ranged from 0...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785384/development-and-characterization-of-novel-est-ssr-markers-for-speranskia-tuberculata-euphorbiaceae
#12
Yi Fu, Miao-Miao Ju, Huan-Cheng Ma, Pei-Yao Xin, Cheng-Zhong He, Dong-Rui Jia, Bin Tian
PREMISE OF THE STUDY: The first set of expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for Speranskia tuberculata (Euphorbiaceae), a traditional medicinal plant endemic to northern China, to explore the effects of recent habitat fragmentation on the genetic diversity and structure of this species. METHODS AND RESULTS: In this study, a total of 18 novel polymorphic microsatellite (EST-SSR) markers were developed for S...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785383/development-of-microsatellite-markers-for-the-clonal-shrub-orixa-japonica-rutaceae-using-454-sequencing
#13
Ichiro Tamaki, Suzuki Setsuko, Kyoko Sugai, Nao Yanagisawa
PREMISE OF THE STUDY: Microsatellite markers were developed for a dioecious shrub, Orixa japonica (Rutaceae). Because O. japonica vigorously propagates by vegetative growth, microsatellite markers can be used to identify clonal relationships among its ramets. METHODS AND RESULTS: Sixteen polymorphic microsatellite markers were identified by 454 next-generation sequencing. The number of alleles and expected heterozygosity for each locus among four populations ranged from two to 10 and from 0...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785382/isolation-and-identification-of-est-ssr-markers-in-chunia-bucklandioides-hamamelidaceae
#14
Kaikai Meng, Mingwan Li, Qiang Fan, Weizheng Tan, Jian Sun, Wenbo Liao, Sufang Chen
PREMISE OF THE STUDY: Chunia bucklandioides (Hamamelidaceae), endemic to Hainan, China, is listed as threatened in the IUCN Red List and is now only found on Mt. Diaoluo and Mt. Jianfeng. Thus, microsatellite markers were developed for future conservation genetic studies of this species. METHODS AND RESULTS: A total of 115 primers were designed on the basis of the transcriptome data of C. bucklandioides. Of them, 59 successfully amplified in C. bucklandioides and polymorphisms were detected in 11; the number of alleles per locus varied from two to five, the observed heterozygosity ranged from 0...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785381/chloroplast-sequence-of-treegourd-crescentia-cujete-bignoniaceae-to-study-phylogeography-and-domestication
#15
Priscila Ambrósio Moreira, Cédric Mariac, Nora Scarcelli, Marie Couderc, Doriane Picanço Rodrigues, Charles R Clement, Yves Vigouroux
PREMISE OF THE STUDY: Crescentia cujete (Bignoniaceae) fruit rinds are traditionally used for storage vessels and handicrafts. We assembled its chloroplast genome and identified single-nucleotide polymorphisms (SNPs). METHODS AND RESULTS: Using a genome skimming approach, the whole chloroplast of C. cujete was assembled using 3,106,928 sequence reads of 150 bp. The chloroplast is 154,662 bp in length, structurally divided into a large single copy region (84,788 bp), a small single copy region (18,299 bp), and two inverted repeat regions (51,575 bp) with 88 genes annotated...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27672525/the-complete-chloroplast-genome-sequences-for-four-amaranthus-species-amaranthaceae
#16
Lindsay Chaney, Ryan Mangelson, Thiruvarangan Ramaraj, Eric N Jellen, Peter J Maughan
PREMISE OF THE STUDY: The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome. METHODS AND RESULTS: A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A...
September 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27672524/development-of-transcriptome-derived-ssr-markers-for-hoya-ledongensis-apocynaceae-and-cross-amplification-in-a-congener
#17
Zheng Chen, Yuncheng Deng, Renchao Zhou, Shaoyun He
PREMISE OF THE STUDY: To examine patterns of genetic diversity and test possible hybridization events, microsatellite markers were identified and characterized in Hoya ledongensis (Apocynaceae), and cross-amplification was tested in a congener, H. jianfenglingensis. METHODS AND RESULTS: Based on the transcriptome data of H. ledongensis, 46 microsatellite primer pairs were randomly selected for initial validation. From these, 28 primer pairs were successfully amplified, 12 of which were polymorphic in 36 individuals across three populations of H...
September 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27672523/isolation-and-characterization-of-microsatellite-loci-for-the-endangered-wetland-plant-adenophora-palustris-campanulaceae
#18
Kuniaki Otake, Toshiaki Kondo, Sonoko Watanabe, Ikuko Masumoto, Katsumi Iwahori, Yuji Isagi
PREMISE OF THE STUDY: Adenophora palustris (Campanulaceae) is an endangered wetland plant species in Japan. Although it is widely distributed in East Asia, only six extant populations are known in Japan, with fewer than 1000 individuals in total. We developed 15 microsatellite markers for this species and confirmed their utility for the closely related species A. triphylla var. japonica. METHODS AND RESULTS: Ten polymorphic loci were characterized for genetic variation within three populations of A...
September 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27672522/a-genomic-approach-for-isolating-chloroplast-microsatellite-markers-for-pachyptera-kerere-bignoniaceae
#19
Jessica N C Francisco, Alison G Nazareno, Lúcia G Lohmann
PREMISE OF THE STUDY: In this study, we developed chloroplast microsatellite markers (cpSSRs) for Pachyptera kerere (Bignoniaceae) to investigate the population structure and genetic diversity of this species. METHODS AND RESULTS: We used Illumina HiSeq data to reconstruct the chloroplast genome of P. kerere by a combination of de novo and reference-guided assembly. We then used the chloroplast genome to develop a set of cpSSRs from intergenic regions. Overall, 24 primer pairs were designed, 21 of which amplified successfully and were polymorphic, presenting three to nine alleles per locus...
September 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27672521/twenty-novel-polymorphic-microsatellite-primers-in-the-critically-endangered-melastoma-tetramerum-var-tetramerum-melastomataceae
#20
Ayu Narita, Ayako Izuno, Yoshiteru Komaki, Takefumi Tanaka, Jin Murata, Yuji Isagi
PREMISE OF THE STUDY: Microsatellite markers were identified for Melastoma tetramerum var. tetramerum (Melastomataceae), a critically endangered shrub endemic to the Bonin Islands, to reveal genetic characteristics in wild and restored populations. METHODS AND RESULTS: Using next-generation sequencing, 27 microsatellite markers were identified. Twenty of these markers were polymorphic in M. tetramerum var. tetramerum, with two to nine alleles per locus and expected heterozygosity ranging from 0...
September 2016: Applications in Plant Sciences
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