Isolation of microsatellite loci in the African tree species Staudtia kamerunensis (Myristicaceae) using high-throughput sequencing
Staudtia kamerunensis (Myristicaceae) or ‘Niové’ is an evergreen tree widespread in Central African moist forests. The bark and seeds are used in traditional medicine, yet the tree is mainly harvested for its high quality, multi-purpose timber. To facilitate sustainable harvesting and conservation of the species, we aim to develop microsatellite markers that can be used to study the mating system, gene flow, genetic diversity and population structure. Genomic DNA of S. kamerunensis was sequenced on an Illumina MiSeq platform, generating 195,720 paired-end reads with 3671 sequences containing microsatellites. Amplification tests resulted in the development of 16 highly polymorphic microsatellite loci of which 14 were tested in 183 individuals of S. kamerunensis from three populations. The number of detected alleles per locus ranged from 15 to 39 and the average observed and expected heterozygosity across loci and populations were Ho = 0.713 (0.14–0.97) and He = 0.879 (0.19–0.95) respectively. The high levels of polymorphism observed in the newly developed microsatellite markers demonstrate their usefulness to study gene flow, population structure and spatial distribution of genetic diversity in S. kamerunensis.
KeywordsAfrican rainforest Microsatellites Population genetics Pycnanthus angolensis Staudtia kamerunensis Myristicaceae
This study is part of the HERBAXYLAREDD project (BR/143/A3/HERBAXYLAREDD), funded by the Belgian Belspo-BRAIN program axis 4. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant agreement N° 765000.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
Resolving with Human and Animal Participants
No Human participants and/or Animals were involved in this study.
- 1.Oyen LPA, Louppe D (2012) Staudtia kamerunensis Warb. In: Lemmens RHMJ, Louppe D, Oteng-Amoako AA (eds) Plant resources of tropical africa 7(2). Timbers 2. PROTA Foundation/CTA, Wageningen, pp 602–605Google Scholar
- 2.Tito de Morais C, Ghazoul J, Maycock CR, Bagchi R, Burslem DFRP, Khoo E, Itoh A, Nanami S, Matsuyama S, Finger A, Ismail SA, Kettle CJ (2015) Understanding local patterns of genetic diversity in dipterocarps using a multi-site, multi-species approach: implications for forest management and restoration. For Ecol Manage 356:153–165. https://doi.org/10.1016/j.foreco.2015.07.023 CrossRefGoogle Scholar
- 3.Karan M, Evans DS, Reilly D, Schulte K, Wright C, Innes D, Holton TA, Nikles DG, Dickinson GR (2012) Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity. Mol Ecol Resour 12:344–353. https://doi.org/10.1111/j.1755-0998.2011.03080.x CrossRefPubMedGoogle Scholar
- 9.Daïnou K, Blanc-jolivet C, Degen B, Kimani P, Ndiade-bourobou D, Donkpegan ASL, Tosso F, Kaymak E, Bourland N, Doucet J, Hardy OJ (2016) Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences—a case study in the tree genus Milicia. BMC Evol Biol 16:259. https://doi.org/10.1186/s12862-016-0831-9 CrossRefPubMedPubMedCentralGoogle Scholar
- 10.Sanna O, Pedro S-Z, Rocío B, Gonzalo CM, González-Martínez SC, Ivan S, Caroline S-S, Hardy OJ, Myriam H (2017) Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers. Mol Ecol Resour 17:614–630. https://doi.org/10.1111/1755-0998.12605 CrossRefGoogle Scholar
- 11.Zhao H, Yang L, Peng Z, Sun H, Yue X, Lou Y, Dong L, Wang L, Gao Z (2015) Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys. Sci Rep 5:8018. https://doi.org/10.1038/srep08018 CrossRefPubMedPubMedCentralGoogle Scholar
- 12.Verdcourt B (1997) Myristicaceae. In: Polhill RM (ed) Flora of tropical east Africa. Royal Botanic Gardens, Kew, pp 8–9Google Scholar
- 15.Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Bioinforma Methods Protoc Methods Mol Biol 132:365–386Google Scholar
- 16.Malausa T, Gilles A, Meglécz E, Blanquart H, Duthoy S, Costedoat C, Dubut V, Pech N, Castagnone-Sereno P, Délye C, Feau N, Frey P, Gauthier P, Guillemaud T, Hazard L, Le Corre V, Lung-Escarmant B, Malé PJG, Ferreira S, Martin JF (2011) High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Mol Ecol Resour 11:638–644. https://doi.org/10.1111/j.1755-0998.2011.02992.x CrossRefPubMedGoogle Scholar
- 19.Culley TM, Weller SG, Sakai AK, Putnam KA (2008) Characterization of microsatellite loci in the Hawaiian endemic shrub Schiedea adamantis (Caryophyllaceae) and amplification in related species and genera. Mol Ecol Resour 8:1081–1084. https://doi.org/10.1111/j.1755-0998.2008.02161.x CrossRefPubMedGoogle Scholar
- 20.Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. https://doi.org/10.1093/bioinformatics/bts199 CrossRefPubMedPubMedCentralGoogle Scholar
- 23.Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370. https://doi.org/10.1111/j.1558-5646.1984.tb05657.x PubMedCrossRefGoogle Scholar