Study of TE evolution in a population of genomes

panEDTA annotation of NAM genomes

• bin: scripts to summarize panEDTA annotations
• data:
  • B73v5.NAM-illumina_filtered-pass-only-two-round-gatk-snps.homo.chr.gt.pres.25k.h: 25k NAM SNPs using B73v5 as the reference
  • NAM.EDTA1.9.0.MTEC02052020.TE.v1.anno.intact.LTR.sort.gz: Intact LTR superfamily classification based on TEsorter
  • NAM.EDTA2.0.0.MTEC02052020.TElib.fa: panEDTA library generated for NAM genomes
  • NAM.intact.LTR.genedist.gz: physical distance of intact LTRs to the nearest genes.
  • pan_TE_bootstrap1000.summary26.txt: the occurrance of 1000 bootstrap resampling of panTE families in NAM genomes
  • soloLTR.txt: All solo LTRs found in NAM
  • TE_Fam_stats.txt: Statistics and descriptions of pangenome TE families
  • individual_genomes: panEDTA annotation results generated for each NAM genome

Population genomics of intact LTR elements

• 1.pairwise: identification of syntenic LTRs between any two NAM genomes
  • bin: scripts to identify pairwise syntenic LTRs
  • data: syntenic LTR information for each genome pair
• 2.combine: combine pairwise information to a pangenome table
  • bin: scripts to combine pairwise syntenic LTRs
  • data/final_27_genome_TE_resolved_B73_added_v2.txt.gz: syntenic LTR information in 26 NAM genomes
• 3.rooting: identify ancestral states of LTR insertions using a teosinte genome
  • bin: scripts to root syntenic LTRs
  • data: syntenic LTR information in a teosinte genome
• 4.site_frequency_spectrum: SFS studies for both SNP and syntenic LTRs
  • SNP_calling: scripts to call SNPs
  • data: VCF and SFS files for both SNPs nad syntenic LTRs

Methylation analysis of intact LTR elements

• data: UMR information of each NAM genomes using B73v5 as the reference

Expression analysis of TE families

• scripts: scripts to map short reads to each genome
• TEexpression: scripts to generate per-family read counts
• data: raw count data for each TE family in each RNA library

LTR neighborhoods of NLR genes

• nlrannotator: Annotating NLR genes in the NAM genomes
• ltr: LTR annotation for each NAM line used for the analysis
• clustering: Clustering of NLR genes and background genes based on physical distance
• nlr_neighborhood_age: Analysis of young and old LTRs in the neighborhoods of foreground and background gene sets
• nlr_neighborhood_amplified: Analysis of tropical-amplifying and not tropical-amplifying LTRs in the neighborhoods of foreground and background gene sets in tropical and temperate NAM lines
• plots: Pre-computed results tables and plotting script for visualising the main results

R commands to compile all data (except expression) and generate most figures

R commands for expression-related analyses