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Premise: Saxifraga fortunei (Saxifragaceae) includes several infraspecific taxa that are ecologically and morphologically distinct. To investigate the evolutionary history of phenotypic polymorphisms in this species, we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers for S . fortunei ., Methods and Results: We developed 26 polymorphic markers based on transcriptome data obtained from Illumina HiSeq 2000. Within three populations of S . fortunei var. incisolobata , the number of alleles ranged from four to 25, and the levels of observed and expected heterozygosity ranged from 0.200 to 0.847 and from 0.209 to 0.930, respectively. Furthermore, all 26 loci showed transferability for S . fortunei var. obtusocuneata and S . fortunei var. suwoensis , and 18 loci were also successfully amplified in S . acerifolia ., Conclusions: These newly developed EST-SSR markers will prove useful to infer the evolutionary history of S . fortunei var. incisolobata and its relatives in population genetic studies.

Premise of the Study: Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for Carex angustisquama  (Cyperaceae) to investigate the evolutionary history of this plant that is endemic to solfatara fields in northern Japan., Methods and Results: Using RNA-Seq data generated by the Illumina HiSeq 2000, 20 EST-SSR markers were developed. Polymorphisms were assessed in C. angustisquama and the closely related species C. doenitzii and C. podogyna . In C. angustisquama , many loci were monomorphic within populations; the average number of alleles ranged from one to five, and levels of expected heterozygosity ranged from 0.000 to 0.580, while all markers were polymorphic in a population of C. doenitzii . This indicates that low genetic polymorphism of C. angustisquama is likely due to the species' population dynamics, rather than to null alleles at the developed markers., Conclusions: These markers will be used to assess genetic diversity and structure and to investigate evolutionary history in future studies of C. angustisquama and related species.

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., Results: Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully., Discussion: This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species).

Premise of the Study: Microsatellite markers were developed and characterized in the vulnerable plant Hepatica nobilis var. japonica (Ranunculaceae) to investigate its genetic diversity, population structure, and gene flow., Methods and Results: Fourteen microsatellite markers were developed. The number of alleles per locus ranged from one to 12, and the expected heterozygosity per locus ranged from 0.043 to 0.855. Eleven markers were successfully amplified in the cultivar 'Mego' from Japan., Conclusions: These microsatellite markers can be used to investigate the genetic diversity, population structure, and gene flow of H. nobilis var. japonica.

Premise of the Study: Microsatellite loci were developed for Vitex rotundifolia, an endangered species isolated to Lake Biwa, to investigate its genetic diversity and population structure. •, Methods and Results: Ten primer sets were identified in Japanese populations of V. rotundifolia. The number of alleles per locus ranged from one to six and gene diversity per locus ranged from 0.040 to 0.697 between two populations. In addition, all loci could be successfully amplified in V. trifolia. •, Conclusions: These markers will be useful for studies of genetic diversity and population structure of endangered species isolated to Lake Biwa of V. rotundifolia, to aid in the development of conservation strategies.

Premise of the Study: Microsatellite markers were characterized in Tricyrtis macrantha (sect. Brachycyrtis, Convallariaceae), a vulnerable species endemic to Japan, to investigate its genetic diversity and population structure. •, Methods and Results: Eleven microsatellite markers were developed. The number of alleles per locus ranged from one to seven, and genetic diversity per locus ranged from 0.142 to 0.812. Four markers were successfully amplified in other species of sect. Brachycyrtis (T. ishiiana, T. ishiiana var. surugensis, and T. macranthopsis). •, Conclusions: The microsatellite markers can be used to investigate the genetic diversity and population structure of the vulnerable and endangered species of Tricyrtis sect. Brachycyrtis, to aid in the development of conservation strategies for each species.