BioProject

The pre-existing draft mountain pine beetle female genome assembly APGL01 (BioProject PRJNA179493) was scaffolded with Dovetail Genomics LLC Chicago data (Putnam, N. More...

The pre-existing draft mountain pine beetle female genome assembly APGL01 (BioProject PRJNA179493) was scaffolded with Dovetail Genomics LLC Chicago data (Putnam, N.H. et al. 2016. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Research 26: 342-350) from an individual female (PRJNA638289/SAMN14918906/SRR11965410) and HiRise software. This assembly was further scaffolded with Dovetail Genomics LLC HiC data (Lieberman-Aiden, E. et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293) from another individual female (PRJNA638296/SAMN14918916/SRR11965415) and HiRise software. In comparison with the similar assembly from the male (PRJNA638274), and linkage map information visualized with ALLMAPS (Tang, H. et al. 2015. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biology 16:3), inconsistencies were mutually resolved manually by flipping and/or shuffling scaffolds originating from the Chicago assembly. The assembly was then step-wise scaffolded and gap-filled with the corresponding assembly from the male using LINKS (Warren, R.L., Yang, C., Vandervalk, B.P., Behsaz, B., Lagman, A., Jones, S.J., and Birol, I. 2015. LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. GigaScience 4:35) and RAILS (Warren, R.L. 2016. RAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequences. The Journal of Open Source Software 1:116). Remaining gaps in scaffolds were filled using Sealer (Paulino, D., Warren, R.L., Vandervalk, B.P., Raymond, A., Jackman, S.D., and Birol, I. 2015. Sealer: a scalable gap-closing application for finishing draft genomes. BMC Bioinformatics 16:230) using shotgun sequence data used for the original draft assembly (PRJNA179493 /SAMN01121786/SRR546193). PhylOligo (Mallet, L., Bitard-Feildel, T., Cerutti, F., and Chiapello, H. 2017. PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies. Bioinformatics 33:3283-3285) was then used to remove contaminant scaffolds. Gene prediction and annotation were completed using Maker (Holt, C., and Yandell, M. 2011. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12:491), Interproscan, and BLASTp against the UniProtKB/Swiss-Prot database. Less...