Development of Genomic Resources in Mexican Bursera (Section: Bullockia: Burseraceae): Genome Assembly, Annotation, and Marker Discovery for Three Copal Species

Abstract

Bursera comprises ~100 tropical shrub and tree species, with the center of the species diversification in Mexico. The genomic resources developed for the genus are scarce, and this has limited the study of the gene flow, local adaptation, and hybridization dynamics. In this study, based on ~155 million Illumina paired-end reads per species, we performed a de novo genome assembly and annotation of three Bursera species of the Bullockia section: Bursera bipinnata, Bursera cuneata, and Bursera palmeri. The total lengths of the genome assemblies were 253, 237, and 229 Mb for B. cuneata, B. palmeri, and B. bipinnata, respectively. The assembly of B. palmeri retrieved the most complete and single-copy BUSCOs (87.3%) relative to B. cuneata (86.5%) and B. bipinnata (76.6%). The ab initio gene prediction recognized between 21,000 and 32,000 protein-coding genes. Other genomic features, such as simple sequence repeats (SSRs), were also detected. Using the de novo genome assemblies as a reference, we identified single-nucleotide polymorphisms (SNPs) for a set of 43 Bursera individuals. Moreover, we mapped the filtered reads of each Bursera species against the chloroplast genomes of five Burseraceae species, obtaining consensus sequences ranging from 156 to 160 kb in length. Our work contributes to the generation of genomic resources for an important but understudied genus of tropical-dry-forest species.

Complete chloroplast genomes of three copal trees (Bursera: Bullockia): comparative analysis and phylogenetic relationships

“…The yield was estimated using a Qubit uorimeter (Thermo Fisher Scienti c, Waltham, MA, USA), and sequencing libraries were prepared with Illumina Truseq Nano DNA Library Prep kits (Illumina, San Diego, CA, USA) using 100 ng of high-molecular-weight DNA. Libraries were sequenced in pair-end mode with a read length of 150 bp using an Illumina NovaSeq S4 platform to obtain ~ 140-170 million reads (see [17]for more details). Genome sequencing was performed by NC State Genomic Sciences Laboratory (North Carolina, USA).…”

“…Most genetic studies in Bursera are on its phylogenetic relationships based on a few nuclear (internal and external transcribed spacers, ribosomal regions, the phosphoenolpyruvate carboxylase, and the nitrate reductase) and chloroplast genes (psbA-trnH and rps16) [12][13][14][15][16] Recently, Rico et al [17] reported the rst nuclear whole-genome sequences of three species, commonly called copales, Bursera bipinnata (Moc. & Sessé ex DC.)…”