General workflow of analysis used in "The effect of parental conflict on imprinted genes in A. lyrata", Audrey Le Veve et al,. https://doi.org/10.1101/2024.08.01.606153

G LO BA L WO R K F L O W F O R A N A LYS I S O F I M P R I N T E D G E N E S I N E N D OS P E R M I N L E VEVE E T A L , 2 0 2 6 Candidate genes in bedfile Phytozome database brasicacee (Fasta+gff3) Input Intermediate files github link Biological question * Bootstrap pipeline https://github.com/thelovelab/DESeq2 Fasta reference genome (zenodo.17287897) List PEG/MEG (Klosinska et al, 2016 RNAseq of 5 tissues in 10 individuals of 2 lineages DEG endosperm Fasta file of genes *** PEG/MEG more expressed than endosperm genes? *https://github.com/le veveaudrey/bootstrap Variation of GC/size of genes od CDS in PEG/MEG compared to endosperm genes? DNSDS, presence/absence in species phylogenetic trees RF distance, length branches Phylogenetic signal of directional selection in PEG/MEG compared to endosperm genes? R libraries TreeDist+ape * Read pooseq Willi et al, 2018 SNP by population in vcf π,Tajima’s D Genetic signal of directional selection in PEG/MEG in allogamous populationscompared to endosperm genes? PHE score of each codon in Sahoo et al,. 2019 Proportion of amino acid and codon Biaised of codon/AA usage in PEG/MEG compared to endosperm genes? Variations PHE in PEG/MEG compared to endosperm genes? https://github.com/levevea udrey/POOLSEQ-analysisof-polymorphism Bedtools https://github.com/levevea udrey/alignment-and-snpcalling * * https://github. com/leveveau drey/codonbias * https://github.com/levevea udrey/phylogenetic_analys e_brassicacee https://github.com/levevea udrey/permutation-test-