Transposable elements in Magnaporthe oryzae

This repository contains code used for the analysis of transposable elements (TEs) in Magnaporthe oryzae. It is organized following the order of the manuscript, which is preprinted here: DOI 10.1101/2022.11.27.518126 and additional data files are available on Zenodo: DOI 10.5281/zenodo.7366416

Contents

• Gene annotation and genome phylogeny
• TE annotation pipeline and phylogeny
• Divergence analyses
  • GC content
  • LTR divergence
  • Jukes-Cantor distance
• Solo LTR analysis
• POT2 transfer analysis
• Region of recombination analysis

Details

Gene annotation and genome phylogeny

• fungap_run.sh - gene prediction using FunGap for each genome
• makeTree.sh - runs OrthoFinder to find SCOs, uses them to build a genome tree
• effector_analysis.sh - predicting effectors in the proteome of each genome

TE annotation pipeline and phylogeny

1. robustTE_denovo.sh - run on each representative genome to produce de novo repeat annotations
2. repTE_make_lib.sh - use only the representative genome de novo elements + RepBase to make TE library, cluster and scan library for domains
3. repTE_group_by_dom.sh - group TEs by the domains they contain, align the domains and produce phylogenies
4. Manually curate the phylogeny results and calssify individual TEs by clade
5. repTE_classi_lib.sh - use manual classifications to classify each individual TE of interest in the library
6. repTE_RMask.sh - run RepeatMasker on the genomes using classified library, scan for domains, get TE copy number data
7. repTE_indiv_trees.sh - produce a tree for each individual TE of interest using all RepeatMasker hits
8. domseq_TE_trees.sh - generate domain based ML phylogenies for each individual TE of interest

Divergence analyses

GC content

• GC_content.sh - determining GC content of TE copies to assess RIP

LTR divergence

1. preprocess_for_LTR.sh - filter all annotations of each LTR-retrotransposon of interest for those included in the domain-based ML TE phylogenies
2. blast_LTR.sh - determine the LTR sequence for each LTR-retrotransposon of interest
3. align_LTRs.sh - align and generate consensus sequences for each LTR
4. rmask_LTRs.sh - run RepeatMasker on representative genomes using a library of the LTR consensus sequences
5. flank_LTR.sh - identify flanking LTRs for each LTR-retrotransposon of interest and find the divergence between them

Jukes-Cantor distance

• JC_dist_ref.sh - determine JC distances between each TE and the consensus (one consensus for all lineages)
• JC_dist_lin.sh - determine JC distances between each TE and the consensus (individual consenses for each lineage)
• JC_dist_gen.sh - determine JC distances for representative genomes

Solo LTR analysis

• soloLTR_analysys.sh - use previous LTR annotations and locations of all full elements to identify solo LTRs

POT2 transfer analysis

• POT2_mummer.sh - find any POT2 + flanking sequences that have synteny
• POT2_flank.sh - look at flanking genes of POT2 copies

Region of recombination analysis

• b71_colocate.sh - see if any protein-sequence gene trees with POT2 tree topology are co-located in the B71 genome
• nuc_tree_POT2_topo.sh - make nucleotide-sequence based gene trees to see if POT2 topology holds
• full_region_tree.sh - make a phylogeny for the full region on chr7 containing POT2 topology genes
• characterize region.sh - characterize any PAV or effectors for the genes in the potential region of recombination
• GO_PFAM_pot2topo.sh - determine GO terms and PFAM domains for the genes in the potential region of recombination

Generating visualization files

• visualize_OGs.sh - generate bed files to visualize all genes, SCOs, and effectors in each genome
• visualize_TEs.sh - generate bed files to visualize JC distance along with TE position
• genomewide_GC.sh - generate seg files to visualize GC content across each genome

Contact

Anne Nakamoto - annen@berkeley.edu