Abstract
Syagrus coronata (Martius) Beccari belongs to the Arecaceae family, an economically and ecologically important species of palm tree. It grows in northeastern Brazil and has a widespread geographic distribution in the “Caatinga” (a seasonally dry tropical forest biome) and Atlantic forest domains (a rain forest biome). The aim of this study was to perform a genome survey and develop SSR markers using high-throughput sequencing. We obtained 78,231,881 million Illumina single-end and paired-end reads, and these reads were used to obtain contigs with a minimum of 500 nucleotides using Ray software. Mining of the SSRs was performed with Phobos software, while the primers were designed by Primer3. Thirty loci were analyzed, three of which were not amplified, 12 were monomorphic, and 15 were polymorphic. Five to 11 alleles per locus were observed, with the observed and expected heterozygosity at 0.06–0.63 and 0.73–0.88, respectively. Here, we report the first set of microsatellite markers developed for S. coronata, and their polymorphism levels indicate they can be used as powerful tools for evaluating genetic diversity and population structure, and thus contribute to conservation studies.
This is a preview of subscription content, log in via an institution to check access.
References
Ambreen H, Kumar S, Variath MT et al (2015) Development of genomic microsatellite markers in Carthamus tinctorius L. (safflower) using next generation sequencing and assessment of their cross-species transferability and utility for diversity analysis. PLoS ONE 10:1–22. https://doi.org/10.1371/journal.pone.0135443
An J, Yin M, Zhang Q et al (2017) Genome survey sequencing of Luffa cylindrica L. And microsatellite high resolution melting (SSR-HRM) analysis for genetic relationship of luffa genotypes. Int J Mol Sci. https://doi.org/10.3390/ijms18091942
Boisvert S, Raymond F, Godzaridis E et al (2012) Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol 13:R122. https://doi.org/10.1186/gb-2012-13-12-r122
de Andrade Martins W, Ramos MA, Souto WMS et al (2015) Knowledge, uses and practices of the Licuri Palm (Syagrus Coronata (Mart.) Becc.) around protected areas in Northeastern Brazil holding the endangered species Lear’s Macaw (Anodorhynchus Leari). Trop Conserv Sci 8:893–911. https://doi.org/10.1177/194008291500800403
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Hodel RGJ, Segovia-Salcedo MC, Landis JB et al (2016) The report of my death was an exaggeration: a review for researchers using microsatellites in the 21st century. Appl Plant Sci 4:1600025. https://doi.org/10.3732/apps.1600025
Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405. https://doi.org/10.1093/bioinformatics/btn129
Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23:1289–1291. https://doi.org/10.1093/bioinformatics/btm091
Kumar M, Choi J-Y, Kumari N et al (2015) Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica. Front Plant Sci 6:1–13. https://doi.org/10.3389/fpls.2015.00688
Mayer C (2008) Phobos, a tandem repeat search tool for complete genomes. Version 3. 3:12. http://www.rub.de/ecoevo/cm/cm_phobos.htm
Motalebipour EZ, Kafkas S, Khodaeiaminjan M et al (2016) Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: development of novel SSR markers and genetic diversity in Pistacia species. BMC Genom 17:1–14. https://doi.org/10.1186/s12864-016-3359-x
Moura RF, Dawson DA, Nogueira DM (2017) The use of microsatellite markers in neotropical studies of wild birds: a literature review. An Acad Bras Cienc 89:145–154. https://doi.org/10.1590/0001-3765201620160378
Portis E, Portis F, Valente L et al (2016) A genome-wide survey of the microsatellite content of the globe artichoke genome and the development of a web-based database. PLoS ONE 11:1–20. https://doi.org/10.1371/journal.pone.0162841
Souza MCP, Moura F, Silva JV, Almeida C (2018) Phylogeography of the palm Syagrus coronata (Martius) Beccari (Arecaceae): distribution in the “Caatinga” and Atlantic forest domains. Braz J Bot. https://doi.org/10.1007/s40415-018-0498-0
Sumathi M, Yasodha R (2014) Microsatellite resources of eucalyptus: current status and future perspectives. Bot Stud 55:1–16. https://doi.org/10.1186/s40529-014-0073-3
Taheri S, Lee Abdullah T, Yusop M et al (2018) Mining and development of Novel SSR markers using next generation sequencing (NGS) data in plants. Molecules 23:399. https://doi.org/10.3390/molecules23020399
Vieira MLC, Santini L, Diniz AL, Munhoz CDF (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39:312–328. https://doi.org/10.1590/1678-4685-GMB-2016-0027
Wei X, Wang L, Zhang Y et al (2014) Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey. Molecules 19:5150–5162. https://doi.org/10.3390/molecules19045150
Acknowledgements
We acknowledge the Federal University of Alagoas for the laboratories, the financial support of Fundação de Apoio à Pesquisa de Alagoas (FAPEAL), and the National Council for the Improvement of Higher Education (CAPES).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Author contributions
Barbosa SN performed the experiments, and Almeida C analyzed the data and wrote the manuscript.
Conflict of interest
The authors declare that they have no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Fig. S1
Number of repeats by all motifs and di- to hexanucleotides motifs (TIFF 16899 kb)
Rights and permissions
About this article
Cite this article
Barbosa, S.N., Almeida, C. Genome survey and development of 15 microsatellite molecular markers in Syagrus coronata (Martius) Beccari (Arecaceae) by next-generation sequencing. Braz. J. Bot 42, 195–200 (2019). https://doi.org/10.1007/s40415-018-0507-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s40415-018-0507-3