Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA.
Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.
BMC Genomics. 2019 Jan 18;20(1):58. doi: 10.1186/s12864-018-5382-6.
Tree species in the genus Cedrela P. Browne are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several 'omic resources including a leaf transcriptome, organelle genome (cpDNA), and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin and enable future research on this widespread Neotropical tree genus.
We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaf tissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptome for C. odorata, and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript models successfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probes worked effectively for five Cedrela species, with each species showing similar mean on-target sequence yield and depth. The probes showed greater enrichment efficiency for Cedrela species relative to the other three distantly related Meliaceae species. We provide a set of candidate SNPs for species identification of four of the Cedrela species included in this analysis, and present draft chloroplast genomes for multiple individuals of eight species from four genera in the Meliaceae.
Deforestation and illegal logging threaten forest biodiversity globally, and wood screening tools offer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources described here provide the foundation required to develop genetic screening methods for Cedrela species identification and source validation. Due to their transferability across the genus and family as well as demonstrated applicability for both fresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studies examining the ecology and evolutionary history of Cedrela and related species in the Meliaceae.
在整个新热带地区，由于过度采伐木材，贝壳杉属的树种受到威胁。对加工木材进行基因鉴定可以与木材解剖学结合使用，以协助分类学和受保护物种和种群的来源验证。然而，能够同时识别贝壳杉木材产品的物种和来源的遗传资源很少。我们开发了一些“组学”资源，包括叶转录组、细胞器基因组（cpDNA）和诊断单核苷酸多态性（SNP），这可能有助于将贝壳杉标本分类为物种和地理起源，并为这个广泛分布在新热带地区的贝壳杉属树种的未来研究提供支持。
我们设计了杂交捕获探针，从新鲜保存的叶片组织和 8 种楝科植物标本中富集了数千个基因。我们首先为 C. odorata 组装了一个新的转录组草图，然后鉴定了可能的低拷贝基因。10001 个转录模型的杂交探针成功富集了 9795 个（98%）目标基因，并且目标捕获效率分析表明，这些探针对 5 种贝壳杉物种有效，每个物种的目标序列产量和深度相似。与其他三种亲缘关系较远的楝科物种相比，这些探针对贝壳杉物种的富集效率更高。我们为本次分析中包括的 4 种贝壳杉物种提供了一组候选 SNP 用于物种鉴定，并为楝科 4 属 8 种多个个体提供了叶绿体基因组草案。
森林砍伐和非法采伐威胁着全球森林生物多样性，而木材筛选工具为执法机构提供了识别非法采伐木材的新方法。这里描述的基因组资源为开发贝壳杉物种鉴定和来源验证的遗传筛选方法提供了所需的基础。由于这些资源在属和科内具有可转移性，并且已经证明适用于新鲜叶片和标本，因此这里描述的基因组资源为研究贝壳杉属和楝科相关物种的生态学和进化历史提供了额外的工具。
