Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives

Abstract

Background: Tree species in the genus Cedrela P. Browne are threatened by timber overexploitation across theNeotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in thetaxonomic and source validation of protected species and populations of Cedrela. However, few genetic resourcesexist that enable both species and source identification of Cedrela timber products. We developed several ‘omicresources 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 futureresearch on this widespread Neotropical tree genus.Results: We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaftissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptomefor C. odorata, and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript modelssuccessfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probesworked effectively for five Cedrela species, with each species showing similar mean on-target sequence yield anddepth. The probes showed greater enrichment efficiency for Cedrela species relative to the other three distantlyrelated Meliaceae species. We provide a set of candidate SNPs for species identification of four of the Cedrelaspecies included in this analysis, and present draft chloroplast genomes for multiple individuals of eight speciesfrom four genera in the Meliaceae.Conclusions: Deforestation and illegal logging threaten forest biodiversity globally, and wood screening toolsoffer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources describedhere provide the foundation required to develop genetic screening methods for Cedrela species identification andsource validation. Due to their transferability across the genus and family as well as demonstrated applicability for bothfresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studiesexamining the ecology and evolutionary history of Cedrela and related species in the Meliaceae.

Citation

Finch, Kristen N.; Jones, F. Andrew; Cronn, Richard C. 2019. Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives. BMC Genomics. 20(1): 1-17. https://doi.org/10.1186/s12864-018-5382-6.