Development of microsatellite markers for Hosta capitata (Asparagaceae) and amplification in related taxa
Article information
Abstract
Microsatellite markers were developed as a tool for phylogeographic studies of Hosta capitata. We also assessed cross-amplification in species closely related to Hosta capitata. We produced 28 polymorphic microsatellite markers by mapping 300 bp paired-end reads obtained from Illumina MiSeq data of H. capitata. In H. capitata, the number of alleles per locus ranged from 1 to 13. Observed and expected heterozygosity ranged from 0.000 to 0.844 and 0.000 to 0.832, respectively. Additionally, 13 loci were successfully transferable to the related species of H. minor and H. venusta. These markers will provide a powerful genetic tool not only for elucidating the phylogeographic patterns of H. capitata populations but also for studying the genetic delimitation of H. capitata from its related species.
The temperate climate zones in East Asia are one of the biodiversity hotspots with increased endemism and plant species richness in East Asian temperate forests (Qian and Ricklefs, 2000). Many phylogeographic surveys covering countries in Asia, such as China, Korea, and Japan, have demonstrated that the high plant diversity is largely derived from dynamic changes in land configurations during the Quaternary climate oscillations (e.g., Qiu et al., 2011; Lee et al., 2013). The processes and mechanisms underlying lineage diversification are major topics in evolutionary biology, and phylogeographic analysis is an essential tool to understand the speed and spatial scale of an organism’s diversification (Crisp et al., 2011; Donoghue and Edwards, 2014). In addition, differences in behaviors, such as life cycles, seed dispersal modes, and pollinators, can explain complex patterns of speciation. Thus, understanding the phylogeographic history of a given species concerning ecological factors is critical for resolving systematic controversies (Sakaguchi et al., 2018).
The genus Hosta Tratt. is widely used in gardening owing to its ground cover, shiny leaf surfaces, leaf pattern, and brilliant purple to white flowers (Jones, 1989; Chung, 1990). With ca. 45 species, Hosta is naturally distributed in Korea, Japan, China, and some parts of Russia, mainly on the edge of the forest or on grasslands in alpine regions (Chen and David, 2000; Chung, 2018). This genus was traditionally under Liliaceae (Maekawa, 1940; Fujita, 1975; Chung, 1990; Chung et al., 1991; Schmid, 1991), but more recently it has been placed in Asparagaceae (The Angiosperm Phylogeny Group et al., 2016; Jo and Kim, 2017; Lee et al., 2018). In general, the infrageneric classification of Hosta includes 3 subgenera and 10 sections (Schimid, 1991).
Hosta capitata (Kodiz.) Nakai [sect. Lamellatae F. Maek., subg. Bryocles (Salisb.) F. Maek.] shows the disjunct distribution by occurring in the main mountain range (Baekdudaegan) of Korea and western parts of Japan (Fujita, 1975; Chung et al., 1991). This species is distinguished in sect. Lamellatae by its capitate raceme (Lee et al., 2018). However, this species still has a systematic ambiguous relationship especially with its closely related H. minor (Baker) Nakai, H. venusta F. Maek., and H. nakaiana F. Maek. within the section. In particular, H. nakaiana has been treated as a synonym of H. cpitata (Tamura and Fujita, 2016; Jo and Kim, 2017), but its phylogenetic identity is still controversial (Schimid, 1991; Sauve et al., 2005). In addition, despite population genetic analyses based on allozyme (Park and Chung, 1997) and isozyme (Chung, 1994) data for H. capitata, its phylogeography and evolutionary history have not been clearly addressed so far (Schmid, 1991). Accordingly, we isolated and characterized a set of polymorphic microsatellite markers from H. capitata to provide a basis for analyses of evolutionary patterns driven by historical factors in East Asia. We also tested cross-amplification in its related species, H. minor and H. venusta of sect. Lamellatae.
Materials and Methods
To acquire an NGS library for H. capitata, we used the DNeasy Plant Kit (Qiagen, Seoul, Korea) to extract genomic DNA from a fresh leaf of a single plant sample collected from Baegunsan Mt., Gwangyang-si, Jeollanam-do, Korea (Table 1). We evaluated the quality of the DNA using a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA). The DNA passed the quality check (concentration 317.95 ng/μL; A260/280 = 1.83; A260/230 = 2.37) was sequenced on the Illumina MiSeq platform (LAS Inc., Seoul, Korea). To identify microsatellites, sequence reads were screened using SSR-pipeline version 0.951 (Miller et al., 2013). The parameter settings for the detection of di-, tri-, or tetranucleotide motifs were flanking regions larger than 100 bp and a minimum of 10, 6, and 4 repeats, respectively. In addition, AT and TA repeats, G + C contents under 30%, and G + C contents above 80%, as well as reads with additional repeat were removed. The resulting sequences were grouped by the repeat motives and mapped to the reference using Geneious R 10.1.3. For each assembled contig, sites with identities < 80% and qualities < 50% were removed. We selected fragments with unique patterns that had less than 20 reads, two separate alleles, little variation at the site to which the primer was attached, and no additional single nucleotide polymorphisms in the flanking region. The final selected reads were deduplicated through de novo assembly and used to develop microsatellite markers. Primer pairs were designed using Primer 3 (Rozen and Skaletsky, 2000), and three sets of M13 tag sequences were added (5′-CACGACGTTGTAAAACGAC-3′, 5′-TGTGGAAT TGTGAGCGG-3′, and 5′-CTATAGGGCACGCGTGGT-3′) to the forward primer with 6FAM, VIC, and NED fluorescent dyes, respectively. For multiplex PCR (nine primer sets), each marker was 100–300 bp. To select microsatellite markers with infraspecific polymorphism for H. capitata, 90 microsatellite markers were verified using 32 individuals collected from Baegunsan Mt. The PCR protocol consisted of initial denaturation at 95°C for 10 min, followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 56°C for 1 min 30 s, and extension for 1 min at 72°C, and a final extension at 4°C for 10 min. The PCR products were analyzed using an ABI 3730XL sequencer with the GeneScan 500LIZ Size Standard (Thermo Fisher Scientific, Waltham, MAs, USA). Allele sizes and peaks for each sample were determined using Peak Scanner version 2.0 (Thermo Fisher Scientific). The number of alleles and the values for HE (expected heterozygosity) and HO (observed heterozygosity) were analyzed using GeneAlEx 6.5 (Peakall and Smouse, 2005). Deviations from Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium were estimated using GENEPOP 4.0 (Rousset, 2008). In addition, Micro-checker version 2.2.3 (Van Oosterhout et al., 2004) was used to determine the null allele frequencies and scoring errors.
Locality and voucher information for the Hosta species examined in this study.
Results and Discussion
Using the 90 newly designed primer pairs, we developed 28 polymorphic microsatellite loci from H. capitata (Table 2). The number of alleles per locus ranged from 1 to 13 (average, 4.7). HE and HO values ranged from 0.000 to 0.832 and from 0.000 to 0.844, respectively. After Bonferroni correction, three markers (Hca069, Hca70, and Hca72) showed a significant deviation from HWE (p < 0.0018), but the deviation was not consistent across the three populations of H. capitata (Table 3). We tested the 28 loci for cross-amplification in its two closely related species of H. minor and H. venusta (Table 4). From the results, 13 loci were successfully amplified and were polymorphic in both H. minor and H. venusta, with 2–10 alleles per locus. The newly developed microsatellite markers will provide a powerful genetic tool for elucidating the phylogeographic patterns of Hosta capitata populations in Korea and Japan. Furthermore, these results will be beneficial for studying the genetic delimitation of H. capitata and its related species in sect. Lamellatae.
Characterization of the 28 microsatellite loci developed from Hosta capitata.
Genetic properties of 28 microsatellite loci in separate populations of Hosta capitata.
Results of cross-amplication and genetic properties of 28 microsatellite loci developed from Hosta capitata in H. minor and H.venusta.
Acknowledgements
This work was supported by grants from the National Institute of Biological Resources, funded by the Ministry of Environment of the Republic of Korea (NIBR202007103).
Notes
Conflict of Interest
The authors declare that there is no conflict of interest.