RT Journal Article
T1 Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers.
A1 Olsson, Sanna
A1 Seoane-Zonjic, Pedro
A1 Bautista, Rocio
A1 Claros, M Gonzalo
A1 Gonzalez-Martinez, Santiago C
A1 Scotti, Ivan
A1 Scotti-Saintagne, Caroline
A1 Hardy, Olivier J
A1 Heuertz, Myriam
K1 Clusiaceae
K1 draft genome
K1 microsatellites
K1 single nucleotide polymorphisms
K1 transcriptomic
AB Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST  = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
PB Wiley-Blackwell Publishing Ltd.
YR 2016
FD 2016-10-16
LK http://hdl.handle.net/10668/10519
UL http://hdl.handle.net/10668/10519
LA en
NO Olsson S, Seoane-Zonjic P, Bautista R, Claros MG, González-Martínez SC, Scotti I, et al. 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. 2017 Jul;17(4):614-630
NO This study was funded by the Spanish Ministry of Science andInnovation (MICINN) under the project AFFLORA (CGL2012-40129-C02-02), cofunded by the ERDF (European RegionalDevelopment Fund) and Plan Andaluz de Investigaci on, Desar-rollo e Innovaci on under the grant P10-CVI-6075, the FrenchNational Research Agency (ANR) under the project FLAG(ANR-12-ADAP-0007) and the Research Council of Norway(203822/E40). This work has benefited from support of a grantfrom Investissement d’Avenir grants of the ANR (CEBA:ANR-10-LABX-25-01). Research Permits for sample collection wereissued by the Ministry of Science and Innovation, Cameroon.Genotyping services were carried out at the Spanish ‘ParqueCient ıfico’ in Madrid (CSIC—PCM). We acknowledge comput-ing resources and expertise used at the CSC—Finnish IT Centerfor Science, the Finnish grid infrastructure (FGI), and computingresources, technical expertise and assistance provided by theSCBI (Supercomputing and Bioinformatics) centre of the Univer-sity of Malaga. MH acknowledges a ‘Ram on y Cajal’ fellowship(RYC2009-04537) from the Spanish Ministry of Science and Inno-vation (MICINN), and a Marie-Curie Intra-European fellowship (PIEF-GA-2012-329088). We thank CarmenGarc ıa Barriga, Zaida Lorenzo, Henri Caron and Val erie Trois-poux for assistance with laboratory work and Katharina B.Budde, Katrin Heer, Peter Mambo, Bonaventure Sonk e, GillesDauby and Saintomer Cazal for help with fieldwork.
DS RISalud
RD May 11, 2025