Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes

Abstract

Plants in the Burseraceae are globally recognized for producing resins and essential oils with medicinal properties and have economic value. In addition, most of the aromatic and non-aromatic components of Burseraceae resins are derived from a variety of terpene and terpenoid chemicals. Although terpene genes have been identified in model plant crops (e.g., Citrus, Arabidopsis), very few genomic resources are available for non-model groups, including the highly diverse Burseraceae family. Here we report the assembly of a leaf transcriptome of Protium copal, an aromatic tree that has a large distribution in Central America, describe the functional annotation of putative terpene biosynthetic genes and compare terpene biosynthetic genes found in P. copal with those identified in other Burseraceae taxa. The genomic resources of Protium copal can be used to generate novel sequencing markers for population genetics and comparative phylogenetic studies, and to investigate the diversity and evolution of terpene genes in the Burseraceae.

Keywords: Protium; RNA-sequencing; copal resin; de novo assembly; terpenoid.

Figure 1

(a) Diagram of sequence length for the transcriptome assembly of Protium copal (Burseraceae). (b) The N50 value, the shortest transcript length at which 50% of assembled bases can be found, calculated only for the top percentile of expressed transcripts. The maximum exN50 value is at 75% expression, with an N50 of 1639. (c) Benchmarking Universal Single-Copy Orthologs (BUSCO) results of the Protium copal transcriptome assembly in comparison to two other transcriptomes in Burseraceae (Bursera simaruba and Boswellia sacra).

Figure 2

(a) The species distribution of BLAST hits used to assign sequence descriptions and Gene Ontology terms to transcripts for annotation. The majority of transcripts had BLAST hits from the genus Citrus, a member of the same order Sapindales. (b) Top 20 Gene Ontology terms (Level 2) for each of the three main sub-categories, Molecular Function (MF), Biological Process (BP), and Cellular Component (CC), based on the number of transcripts assigned that GO term.

Figure 3

Expected abundance of transcripts expressed in transcripts per million (TPM) for different GO terms in Protium copal (Burseraceae). TPM is the abundance one would expect to find in a pool of a million transcripts.

Figure 4

Maximum likelihood phylogeny of 57 putative TPS genes in P. copal and known TPS genes from angiosperm and gymnosperm taxa. Bootstrap support values greater than 50 are shown.

Figure 5

(a) Venn diagram of inferred terpene orthologous gene clusters for Protium copal, Boswellia sacra, and Bursera simaruba produced using OrthoVenn. (b) Total numbers of inferred terpene orthologous gene clusters for each species are given in the bar plot.