This is a consolidation two current Arnqvist projects - namely uppstore2017218 and uppstore2017212. Overall, these projects gather DNA and RNA seq data on four different seed beetle model species. They involve four de novo genome assemblies, large amounts of poolseq data for several populations and selection lines (of two different species), RNA seq data for several species and experimental populations / selection lines as well as incoming Hi-G seq data for two species. Data in this project is being used in a variety of collaborative efforts between the Arnqvist group at IEG/EBC and other researchers at UU. The project is primarily funded by The European Research Council (ERC) and the Swedish Research Council (VR) through grants to the PI.
uppstore2017218 and uppstore2017212 currently uses 14 TB but not all data needs to be migrated to the new project. We estimate a gross need of a bit less than 11 TB which, using a expansion factor of 2.5X yield a total net need of 27 TB.
Some of the daughter projects are:
b2016139 - De novo genome assembly of Callosobruchus chinensis
This project will assemble the male genome of the beetle Callosobruchus maculatus, a major pest of legume crops globally. Genome size is 717 Mb.
b2016158 - De novo genome assembly of Callosobruchus analis
This project will assemble the male genome of the beetle Callosobruchus maculatus. Genome size is 971 Mb. This project forms part of a larger project on comparative genomics of a group of beetles of the genus Callosobruchus. Other projects deal with C. maculatus and C. chinensis.
b2016194 - Pool seq of mtDNA
We will estimate mtDNA haplotype freq in samples from artficial selection lines of a beetle, using Illumina pool seq data. Here, samples represent 100 individual beetles pooled together, to estimate mtDNA haplotype frequency in the samples (individuals carry either three different haplotypes). This concerns the management and analyses of this pool seq Illumina seq data.
b2016443 - De novo genome assembly of Acanthoscelides obtectus
This project will assemble the male genome of the beetle Acanthoscelides obtectus. Genome size is 949 Mb - determined by flow cytometry. We will use long-read data generated by the NGS PacBio platform. gDNA will be delivered to the platform in the next few days (contact: Olga Vinnere Pettersson). Project funed by VR and ERC.
b2017004 - Pool seq of A obtectus lines
Pool seq re-seq of Acanthoscelides obtectus selection lines, to determine regions of genome under selection.
b2017005 - RNA seq of A obtectus lines
RNA seq of Acanthoscelides obtectus selection lines, to assemble transcriptome and to analyse differential gene expression.
uppstore2017212 - Genome and transcriptome assembly of the beetle Callosobruchus maculatus, including differential gene expression. This form part of a major ERC and VR funded project in evolutionary genetics relating to this insect, which is a global agricultural pest species on legume crops. The project involves several different types of data with partly overlapping aims.