A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology

scientific article

A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.3732/APPS.1400059
P932PMC publication ID4259455
P698PubMed publication ID25506520
P5875ResearchGate publication ID269715246

P2093author name stringLisa E Wallace
Hanna E Dorman
Lavanya Challagundla
Gregory L Wheeler
Alenda Buchanan
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Complete plastid genome sequencing of Trochodendraceae reveals a significant expansion of the inverted repeat and suggests a Paleogene divergence between the two extant speciesQ28709289
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Complete chloroplast genome sequences of important oilseed crop Sesamum indicum LQ28729990
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Estimation of average heterozygosity and genetic distance from a small number of individualsQ29614682
The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysisQ29614978
Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare IIIQ29616844
Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population geneticsQ31024833
Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant speciesQ33523040
Assembly algorithms for next-generation sequencing dataQ33538377
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Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat speciesQ33671219
Current trends in microsatellite genotyping.Q33897404
Choosing and using a plant DNA barcodeQ33920783
Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellitesQ33942971
Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in BrachypodiumQ33945391
An evaluation of genetic distances for use with microsatellite loci.Q33964342
Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North AmericaQ34013574
Asymmetrical gene flow in a hybrid zone of Hawaiian Schiedea (Caryophyllaceae) species with contrasting mating systemsQ34031510
Gene flow among different taxonomic units: evidence from nuclear and cytoplasmic markers in Cedrus plantation forests.Q34267104
Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.Q34342285
Another look at the root of the angiosperms reveals a familiar taleQ34395825
Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other PlantsQ34608652
The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhizaQ34608728
The hidden side of invasions: massive introgression by local genesQ34775522
Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysisQ34808348
Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate treeQ35241615
Evidence for the equal resilience of Triodia spp. (Poaceae), from different functional groups, to frequent fire dating back to the late PleistoceneQ35623388
The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in GymnospermsQ36810530
A frameshift mutation of the chloroplast matK coding region is associated with chlorophyll deficiency in the Cryptomeria japonica virescent mutant Wogon-SugiQ37215463
The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asteridsQ37461572
Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant speciesQ37874712
Range-wide phylogeography and gene zones in Pinus pinaster Ait. revealed by chloroplast microsatellite markers.Q38924616
Long-term population isolation in the endangered tropical tree species Caesalpinia echinata Lam. revealed by chloroplast microsatellites.Q39182688
The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studiesQ42065829
Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomesQ42510317
Chloroplast microsatellites and mitochondrial nad1 intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila).Q42652403
Chloroplast DNA phylogeography of European ashes, Fraxinus sp. (Oleaceae): roles of hybridization and life history traitsQ42688689
Beans in Europe: origin and structure of the European landraces of Phaseolus vulgaris L.Q43057684
Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine.Q43173294
Genetic and Floral Divergence among Sympatric Populations of Gymnadenia conopsea s.l. (Orchideaceae) with Different Flowering PhenologyQ43679332
The complete chloroplast genome of Origanum vulgare L. (Lamiaceae)Q43766379
Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implicationsQ44006070
Spread of herbicide-resistant weedy rice (red rice, Oryza sativa L.) after 5 years of Clearfield rice cultivation in ItalyQ44241380
A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiospermsQ44546989
Genetic discontinuity revealed by chloroplast microsatellites in eastern North American Abies (Pinaceae).Q44873405
Chloroplast diversity in a putative hybrid swarm of Ponderosae (Pinaceae).Q46192380
Chloroplast genome analysis of Australian eucalypts--Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae).Q46640288
Phylogeographic structure of jack pine (Pinus banksiana; Pinaceae) supports the existence of a coastal glacial refugium in northeastern North AmericaQ47252546
Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine subgenus Glycine)Q47294463
Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasyQ47303232
Causes of size homoplasy among chloroplast microsatellites in closely related Clusia species.Q47424962
A set of primers for the amplification of 20 chloroplast microsatellites in PinaceaeQ48061584
Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genomeQ48070856
The development and evaluation of consensus chloroplast primer pairs that possess highly variable sequence regions in a diverse array of plant taxaQ48238783
Chloroplast microsatellites: new tools for studies in plant ecology and evolution.Q51203110
Elucidating polyploidization of bermudagrasses as assessed by organelle and nuclear DNA markersQ51492691
A case of chloroplast heteroplasmy in kiwifruit (Actinidia deliciosa) that is not transmitted during sexual reproductionQ52945205
Biparental inheritance of chloroplast DNA and the existence of heteroplasmic cells in alfalfaQ54262070
Contrasting patterns of pollen and seed flow influence the spatial genetic structure of sweet vernal grass (Anthoxanthum odoratum) populationsQ54343694
High variability of chloroplast DNA in three Mediterranean evergreen oaks indicates complex evolutionary historyQ57240513
Pollen pool heterogeneity in shortleaf pine, Pinus echinata MillQ58375366
Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related speciesQ60294666
Quantitative assessment of heteroplasmy levels in Senecio vulgaris chloroplast DNAQ60534500
Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite lociQ74161778
Sequence-repeat polymorphisms exhibit the signature of recombination in lodgepole pine chloroplast DNAQ74631657
DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis)Q77664877
High level of variation at Abies alba chloroplast microsatellite loci in EuropeQ78127716
Use of cpSSRs for the characterisation of yam phylogeny in BeninQ81045225
Phylogeographic inferences from chloroplast DNA: quantifying the effects of mutations in repetitive and non-repetitive sequencesQ83688126
Single nucleotide sequence analysis: a cost- and time-effective protocol for the analysis of microsatellite- and indel-rich chloroplast DNA regionsQ84129784
Improving sequencing quality from PCR products containing long mononucleotide repeatsQ84457385
Heteroplasmy of chloroplast DNA in MedicagoQ86839165
Variable length chloroplast markers for population genetic studies in Acmispon (Fabaceae)Q87356031
P433issue12
P921main subjectbotanyQ441
P577publication date2014-11-20
P13046publication type of scholarly workreview articleQ7318358
P1433published inApplications in Plant SciencesQ27724431
P1476titleA review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology
P478volume2

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