Data from: Transcriptome-wide mining, characterization, and development of microsatellite markers in Lychnis kiusiana (Caryophyllaceae)

Background: Lychnis kiusiana Makino is an endangered perennial herb native
to wetland areas in Korea and Japan. Despite its conservational and
evolutionary significance, population genetic resources are lacking for
this species. Next-generation sequencing has been accepted as a rapid and
cost-effective solution for the identification of microsatellite markers
in nonmodel plants. Results: Using Illumina HiSeq 2000 sequencing
technology, we assembled 67,498,600 reads into 91,900 contigs and
identified 11,403 microsatellite repeat motifs in 9,563 contigs. A total
of 4,510 microsatellite-containing transcripts had Gene Ontology (GO)
annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis
identified 124 pathways with significant scores. Many microsatellites in
the L. kiusiana leaf transcriptome were linked to genes involved in the
plant response to light intensity, salt stress, temperature stimulus, and
nutrient and water deprivation. A total of 12,486 single-nucleotide
polymorphisms (SNPs) were identified on transcripts harboring
microsatellites. The analysis of nucleotide substitution rates for 2,389
unigenes indicated that 39 genes were under strong positive selection. The
primers of 6,911 microsatellites were designed, and 40 of 50 selected
primer pairs were consistently and successfully amplified from 51
individuals. Twenty-five of these were polymorphic, and the average number
of alleles per SSR locus was 6.96, with a range from 2 to 15. The observed
and expected heterozygosities ranged from 0.137 to 0.902 and 0.131 to
0.827, respectively, and locus-specific FIS estimates ranged from -0.116
to 0.290. Eleven of the 25 primer pairs were successfully amplified in
three additional species of Lychnis: 56% in L. wilfordii, 64% in L.
cognata and 80% in L. fulgens. Conclusions: The transcriptomic SSR markers
of Lychnis kiusiana provide a valuable resource for understanding the
population genetics, evolutionary history, and effective conservation
management of this species. Furthermore, the identified microsatellite
loci linked to the annotated genes should be useful for developing
functional markers of L. kiusiana. The developed markers represent a
potentially valuable source of transcriptomic SSR markers for population
genetic analyses with moderate levels of cross-taxon portability.