title: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers.
abstract: 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.
authors.affiliation: Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.
authors.forename: Sanna
authors.initials: S
authors.lastname: Olsson
authors.affiliation: Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Seoane-Zonjic
authors.affiliation: Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain.
authors.forename: Rocío
authors.initials: R
authors.lastname: Bautista
authors.affiliation: Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain.
authors.forename: M Gonzalo
authors.initials: MG
authors.lastname: Claros
authors.affiliation: Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.|UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France.
authors.forename: Santiago C
authors.initials: SC
authors.lastname: González-Martínez
authors.affiliation: INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France.
authors.forename: Ivan
authors.identifier: http://orcid.org/0000-0002-8951-2680
authors.initials: I
authors.lastname: Scotti
authors.affiliation: INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Scotti-Saintagne
authors.affiliation: Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium.
authors.forename: Olivier J
authors.initials: OJ
authors.lastname: Hardy
authors.affiliation: Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.|UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France.|Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium.
authors.forename: Myriam
authors.initials: M
authors.lastname: Heuertz
mesh_terms: D001938:Brazil; D002163:Cameroon; D028084:Clusiaceae / Q000235:genetics*; D005616:French Guiana; D005819:Genetic Markers; D005828:Genetics, Population; D018745:Genome, Plant; D018895:Microsatellite Repeats; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers
keywords: Clusiaceae; draft genome; microsatellites; single nucleotide polymorphisms; transcriptomic