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

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.

热带植物的群体遗传学研究往往颇具挑战，这是因为其分类学、系统发育关系与分布范围信息有限，基因组资源匮乏，且采样存在后勤难题。本研究针对古热带乔木树种Symphonia globulifera L.f.（藤黄科，Clusiaceae）开发了一套稳健且普适性强的遗传标记开发策略，仅需投入适度的基因组资源开发工作；该树种是非洲与新热带雨林中的关键物种（keystone species）。我们对来自喀麦隆的单株个体进行了低覆盖度（11X）测序，获得了碎片化的草图基因组（draft genome），组装序列总长1.027 Gbp，约占预估基因组大小的67.5%。对565个支架（scaffold，总长7.57 Mbp）进行注释后，预测得到1046个候选基因（其中231个包含完整开放阅读框）以及1523个精确的简单序列重复（simple sequence repeats，SSRs，微卫星）。将法属圭亚那群体的已发表转录组与该草图基因组进行比对，得到了923个高质量单核苷酸多态性（single nucleotide polymorphisms，SNPs）。我们还通过计算机（in silico）预先筛选出了在广泛地理范围内保守且具有多态性的基因内SSRs，从而减少了针对稀缺DNA样本的标记开发测试工作量。在测试的23个SSRs中，19个可成功扩增，18个可在来自南美洲（巴西与法属圭亚那）和非洲（喀麦隆与圣多美岛）的4个S. globulifera种群中完成有效基因分型，群体分化系数FST=0.34。多数位点仅表现出群体特异性的哈迪-温伯格平衡偏离，这指向了局部群体效应（例如无效等位基因（null alleles））。本研究开发的基因组资源对于Symphonia属的进化研究以及植物比较研究均具有重要价值。所采用的方法对于分布广泛的热带类群或DNA可获取性有限的濒危类群而言尤其具有应用价值。