The genomics of speciation and rapid range expansion in Cochlearia danica
Current progress includes:
Step 1: Subgenome coverage assessment of Cochlearia species against a synthetic C. danica genome
1.) Created a concatenated pseudo-C. danica hybrid genome composed of C. excelsa (n = 6) and C. groenlandica (n = 7).
2.) Constructed C. danica genome was mapped against multiple individuals of different Cochlearia populations using NGS pipe.
3.) The alignment outputs of these mappings were assessed for coverage using bedtools intersect, samtools coverage and flagstat (Using scripts samtools_coverage.sh and samtools_flagstat.sh). Bedtools_intersect.sh was used to create non-repeat region (masked) BAMs.
Step 2: Draft assembly of HiFi reads, QC and genomica analysis of C. danica
1.) Generated assemblies for C. danica using the program Hifiasm (and script hifiasm.sh)
2.) Use Quast and BUSCO for QC of assembly (quast.sh and busco.sh)
3.) Generate ploidy and heterozygosity analysis with Genomescope and Smudgeplot (Scope_and_smudges.sh)
4.) Generate dotplots by creating alignments between C. danica assembly and reference genomes using mummer (mummer_coords_shortq.sh) and running them through the web-based application Dot.
5.) Used Syri to visualise synteny between C. danica and reference genomes. Alignment files were generated (minimap2.sh), homologous chromosomes were extracted using Grep -e commands, chromosomes were sorted and configured using the Fixchr tool (fixchr_Chr1_Chr3.sh), synteny calculated using Syri (syri_Chr1_Chr3.sh) and visualised using Plotsr (plotsr_Chr1_Chr3.sh).