Development of microsatellite markers for the endangered Pedicularis ishidoyana (Orobanchaceae) using next-generation sequencing1

  title={Development of microsatellite markers for the endangered Pedicularis ishidoyana (Orobanchaceae) using next-generation sequencing1},
  author={Won-Bum Cho and In-Su Choi and Byoung-Hee Choi},
  journal={Applications in Plant Sciences},
Premise of the study: Microsatellite primers were developed for Pedicularis ishidoyana (Orobanchaceae), an endangered and hemiparasitic plant that is narrowly endemic to Korea. Because its populations are threatened by loss of suitable habitat, conservation efforts are required. Methods and Results: We developed polymorphic microsatellite loci through reference mapping of 300-bp paired-end reads obtained from Illumina MiSeq data. In all, 74 primer pairs were designed and 32 were amplified. Of… 
Development of 26 microsatellite markers in Bupleurum latissimum (Apiaceae), an endangered plant endemic to Ulleung Island, Korea
These developed markers will be useful for understanding evolutionary patterns of B. latissimum in an oceanic island system and for establishing suitable conservation strategies at the genetic level.
New polymorphic microsatellite markers for the endangered fern Ceratopteris thalictroides (Parkeriaceae)
This work used the Mi-Seq platform to develop three sets of 25 polymorphic microsatellite markers for C. thalictroides, which is endangered in Korea, and these markers will be useful for evaluating the genetic status and conserving Korean populations more effectively.
A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak (Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization
It is suggested that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU) and improve the understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks.
Diverse trajectories of plastome degradation in holoparasitic Cistanche and the whereabouts of the lost plastid genes.
It is identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences on entire plastome, long single copy region and non-coding region, and different patterns of the retention/loss of functional genes.
Beneficial health applications and medicinal values of Pedicularis plants: A review.
Pedicularis L. Genus: Systematics, Botany, Phytochemistry, Chemotaxonomy, Ethnopharmacology, and Other
This work represents the first total comprehensive review on this genus and particular emphasis was given to phytochemistry and ethnopharmacology, since several classes of natural compounds have been reported within this genus.


Pedicutlaris, a genus of the Scrophulariaceae, is one of the largest genera of temperate flowering plants with somewhat around 600-800 species, yet as a whole the genus is so thoroughly natural that attempts to subdivide it into subgeneric groupings are not even made.
Disintegration of the scrophulariaceae.
A molecular systematic study of Scrophulariaceae sensu lato using DNA sequences of three plastid genes revealed at least five distinct monophyletic groups, which are newly erected herein to recognize the phylogenetic distinctiveness of tribe Calceolarieae.
Pollen morphology of the Orobanchaceae and rhinanthoid Scrophulariaceae
The resulting data showed no clear differences between the pollen of the Orobanchaceae and that of the rhinanthoid Scrophulariaceae.
New iridoids from Pedicularis artselaeri.
Three new iridoids, named artselaenin I, II and III, were isolated from the whole plants of Pedicularis artselaeri, along with 11 known compounds, 8-epiloganic acid, 7-deoxy-8-epiloganic acid,
SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data.
SSR_pipeline, a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data, is implemented in the Python programming language and can be used from nearly any computer operating system.
Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: many losses of photosynthesis and complex patterns of rate variation.
It is suggested that there may be substantial molecular evolutionary changes to the plastid genome of parasites before the loss of photosynthesis, and independent patterns of synonymous and nonsynonymous rate acceleration in rps2 point to distinct mechanisms underlying rate variation in different lineages.
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses
Micro-Checker: Software for identifying and correcting genotyping errors in microsatellite data
MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
Trimmomatic: a flexible trimmer for Illumina sequence data
Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
genepop’007: a complete re‐implementation of the genepop software for Windows and Linux
  • F. Rousset
  • Computer Science
    Molecular ecology resources
  • 2008
This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of