Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers

Sanna Olsson (1) , Pedro Seoane Zonjic (2) , Rocío Bautista (2) , M. Gonzalo Claros (2) , Santiago Gonzalez Martinez (3, 1) , Ivan Scotti (4) , Caroline Scotti-Saintagne (4) , Olivier J. Hardy (5) , Myriam Heuertz (3, 1)

1 INIA-CIFOR - Centro de Investigacion Forestal
2 Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática
3 BioGeCo - Biodiversité, Gènes & Communautés
4 URFM - Ecologie des Forêts Méditerranéennes
5 Faculté des Sciences, Evolutionary Biology and Ecology

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 1,046 putative genes (231 of them containing a complete ORF) 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 (SNPs). 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. Out 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.

Mots clés: microsatellites; single nucleotide polymorphisms; transcriptomic; draft genome; clusiaceae; microsatellite repeats

Mots clés: symphonia globulifera; arbre tropical; transcriptome; polymorphisme nucléotidique simple (SNP); marqueur génétique; séquençage du génome; marqueur ssr; marqueur microsatellite; amérique du sud; afrique

Domaines: Biodiversité et Ecologie

Sanna Olsson, Pedro Seoane Zonjic, Rocío Bautista, M. Gonzalo Claros, Santiago Gonzalez Martinez, 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. Molecular Ecology Resources, 2016, on-line (4), ⟨10.1111/1755-0998.12605⟩. ⟨hal-01512127⟩