Abstract
BackgroundTree 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.ResultsWe 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.ConclusionsDeforestation 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.
Highlights
Tree species in the genus Cedrela P
The third challenge for the genetic identification of Cedrela timber is a lack of specimens of known geographic origin which are necessary for the construction of a comprehensive reference genomic database for taxonomic and source validation of confiscated timber
28% (14,508) of gene models were greater than 1000 bp ( kilobase pairs (Kbp)) in length, and they range in length from 37,635 bp to 200 bp
Summary
Tree species in the genus Cedrela P. Spatial genetic structure among populations of C. odorata and C. fissilis [8, 9, 13,14,15,16,17] has been examined using multiple genetic markers (nuclear rDNA, chloroplast noncoding genes, chloroplast microsatellites), and these studies identified spatial structure across broad geographic regions: a latitudinal gradient in chloroplast and nuclear haplotypes for C. odorata populations across the extent of its range [8], and a longitudinal gradient among C. fissilis flanking the ‘Cerrado’ savanna ecoregion of Brazil and Bolivia [13, 14] While these markers may be useful for coarse-level regional assignment, it is unclear if they could provide fine-scale classification accuracy necessary for differentiating timber from protected concessions, or differentiating timber from neighboring countries that offer contrasting levels of protection for Cedrela species. The third challenge for the genetic identification of Cedrela timber is a lack of specimens of known geographic origin which are necessary for the construction of a comprehensive reference genomic database for taxonomic and source validation of confiscated timber
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