Dendroctonus ponderosae Assembly and Gene Annotation

About Dendroctonus ponderosae

Dendroctonus ponderosae, the mountain pine beetle, is a destructive pest of pine trees in increasingly large regions of North America [1]. The beetle carries blue-stain fungus (Grosmannia clavigera [2]), a symbiont that enables the beetles to extract nutrients from the tree. Infestation by many beetles (which coordinate attacks with pheromones) can be fatal to the tree because the fungus produces filaments that block water transport. The Tria project provides genomic resources for the mountain pine beetle, blue-stain fungus, pine tree, and related-species, to assist researchers in understanding the ecological dynamics of these species.

The mountain pine beetle is the second coleopteran genome to be sequenced (the other is Tribolium castaneum), and provides a valuable comparative resource for this inordinately speciose order.

Picture credit (public domain): Forest Service (USDA) 2005

Assembly

The D. ponderosae genome was assembled at the University of British Columbia and Canada’s Michael Smith Genome Sciences Centre, into 8,188 scaffolds, spanning 204Mbp, with a scaffold N50 of 629Kbp. The life cycle of the beetle makes laboratory rearing infeasible, so the assembly consists of high-coverage paired-end short reads from a field-collected male, scaffolded with short read data from a mixed-sex pool of field-collected pupae [1]. The assembly was refined with EST and RNA-seq data from different tissues and life stages.

Annotation

Genes were generated with MAKER, which used ab initio predictions (from AUGUSTUS, Snap, and GeneMark), and alignments of EST sequences, RNA-seq data, and Tribolium castaneum proteins. Protein-coding genes are imported into Ensembl Genomes from the ENA records that were submitted by the same team responsible for the assembly [1]. Non-coding RNA genes were added using the Ensembl Genomes pipeline, and BLAST hits and protein features have been computed.

References

1. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest.
   Keeling CI, Yuen MM, Liao NY, Docking TR, Chan SK, Taylor GA, Palmquist DL, Jackman SD, Nguyen A, Li M et al. 2013. Genome Biology. 14:R27.
2. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.
   Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, Holt RA, Hirst M et al. 2009. Genome Biology. 10:R94.

More information

General information about this species can be found in Wikipedia.