Acromyrmex inquiline social parasite comparative genomics

This repository holds all the code that was used in the Acromyrmex inquiline comparative genomics project.

---

These files hold the workflows to analyse the basic quality of the genomes used in the comparison.

Local and remote copies of files and folders

# mac
macbase=/Users/lukas/sciebo/inquilineGenomics18/
# pallas
base=/corefac/cse/lukas/inqGen18/

Raw assemblies & annotations (v.2.0)

The latest assemblies and annotations delivered from BGI are located on Pallas. The raw files are located at /usr/local/home/lschrader/data/genomes/inquilines_2.0/

Acromyrmex charruanus:  ./Acha.files.txt
Acromyrmex insinuator:  ./Ains.files.txt
Acromyrmex heyeri:      ./Ahey.files.txt
Pseudoatta argentina:   ./Parg.files.txt

assembly v2.1/annotation v2.1

Clean genomes and annotations of fungal and mitochondrial scaffolds.

./QC/filterContaminants/inquilines2.0-to-2.1.sh

# location on pallas
$base/inquilines_v2.1/
$base/inquilines_v2.1/Acromyrmex_charruanus.2.1/Acromyrmex_charruanus.v2.1.files.tree
$base/inquilines_v2.1/Acromyrmex_heyeri.2.1/Acromyrmex_heyeri.v2.1.files.tree
$base/inquilines_v2.1/Acromyrmex_insinuator.2.1/Acromyrmex_insinuator.v2.1.files.tree
$base/inquilines_v2.1/Pseudoatta_argentina.2.1/Pseudoatta_argentina.v2.1.files.tree

QC

Code, programs and scripts used for quality control of assemblies and annotations are provided below.

BUSCO

BUSCO (v3) was run on v2.1 assembly and annotation of the new genomes and on the reannotated previously published attine genomes.

# newly sequenced genomes
./QC/busco/runBUSCO_inq.v2.1.sh

# previously published attines
./QC/busco/runBUSCO_7ants.sh

Quast

Quast (v5.0.2) was run to assess N50 contig and scaffold sizes and other assembly parameters.

./QC/N50/runQuast.sh

TransposonPSI

TransposonPSI (v.08222010) was run to identify putative TE-encoded proteins.

./QC/transposonPSI/runTransposonPsi.sh

GAG

GAG v2.0.1 was run on all newly sequenced genomes (see ./QC/filterContaminants/inquilines2.0-to-2.1.sh) and also on reannoated attines.

./QC/gag/runGAG_7attines.sh

Ortholog inference

I used orthofinder (v.2.2.6) to identify orthologs and orthogroups between different species.

./orthology/runOrthofinder.sh

Species Phylogeny

Orthologous 4-fold degenerate site alignment

Alignment of single copy orthologs, testing for recombination and extraction of 4d sites.

./singleCopyOrthologs/runSCOalignment.sh

Phylogenetic inference

Phylogenetic inference with PAUP, PhyML, MrBayes, and RaxML

./phylogeny/runPhylogeny.sh

Tree divergence dating

Divergence estimates with mcmcTree

./TreeDating/treeDating.workflow.sh

Gene Family Evolution

The complete workflow for analysing gene family evolution with CAFE is described here:

./geneFamilies/README.md

# This readme refers to the following scripts:
  run.geneFamilies.mcl.sh
  run.CAFError.sh
  run.CAFE.sh
  analyseCAFEmodels.Rmd
  CAFE.lhtest.R
  analyseCAFEoutput.Rmd

Demographic inference with MSMC2

Demographic history for A. insinuator and A. echinatior with MSMC2:

./Ne/MSMC2.refAech.md ./Ne/plotMSMC2.Rmd

Evolutionary rate analyses

Evolutionary rate analyses and signatures of selection (SOS) on single copy orthologs with HyPhy (v2.3.14)

./SOS/AnalyseDNDS.hyphy.sh
./SOS/RELAX.summary.Rmd
./SOS/absREL.summary.Rmd
./SOS/analyseSOS.Rmd

Gene Ontology (GO) enrichment

GO enrichment analyses were run on genes under relaxed, intensified, and positive selection and on shrinking gene families.

./GOenrichment/RELAX.GOenrichment.Rmd
./GOenrichment/absREL.GOenrichment.Rmd
./GOenrichment/CAFE.GOenrichment.Rmd
# scripts for revigo plots
./GOenrichment/revigoPlots/

Whole genome alignment

Whole genome alignment with progressiveCactus v0.1

./WGA/run.progressiveCactus.sh

Synteny Analysis

Synteny was analyzed with i-adhore v3.0.1

./synteny/run.iadhore.sh
./synteny/analyse.synteny.Rmd

# analysis of annotated OR genes only
./synteny/run.iadhore.ORs.sh
./synteny/plotOR.synteny.Rmd

Analysis of the attine OR gene family

OR annotation

The full annotation pipeline is contained in

./ORevolution/clean/ORannotation.190408.sh

The following scipts are called in the above bash script:

ORannotation.190408.sh
filterForDomain.sh
runGeMoMa.pipe.sh
runExonerate.sh
runEVM.sh
prepareEVM.sh
addIncompleteGenes.sh
rename.R
runExonBlast.sh
runGeMoMa.sh
runExonerate.pl
processExonerate2Fa.pl
cleanExonerateGFF.pl
translateCDS2AA.pl
processExonerate2GFF.pl
addGeneGFF.pl
identify_geneLS.pl
hsp2bed.pl

# final annotations appropriate for v2.1 and published attine genomes
./ORevolution/results/annotations/

OR phylogeny

Scripts for OR alignments, alignment QC, tree inference, tree plotting, and analyses.

./ORphylogeny/ORphylogeny.sh
./ORphylogeny/ORplotTreeClean.Rmd
./ORphylogeny/analyseTree.Rmd

OR gene tree reconciliation

Scripts for clade-wide OR alignments, alignment QC, tree inference, tree plotting, and analyses.

./ORevolution/reconciliation/allClades.Rmd
./ORevolution/reconciliation/DLCpar.md
./ORevolution/reconciliation/plotReconTreeDLCpar.Rmd
./ORevolution/reconciliation/runAllDLCpar.sh

Evolutionary rate analyses in ORs with HyPhy (v2.3.14)

./ORevolution/OR.SOS/hyphy.ORs.sh
./ORevolution/OR.SOS/summary.RELAX.OR.Rmd
./ORevolution/OR.SOS/summary.absREL.OR.Rmd

# Detailed analysis of clade 285
./ORevolution/OR.SOS/analyseClade285.Rmd

Annnotation & analysis of other gene families

# MRJPs
./genePhylogenies/MRJPevolution/MRJP.annotation.sh
./genePhylogenies/MRJPevolution/MRJP.phylogeny.sh
./genePhylogenies/MRJPevolution/plotMRJP.tree.Rmd
./genePhylogenies/MRJPevolution/mrjp.analyseTree.Rmd

# Gustatory Receptors (GR)
./genePhylogenies/GRevolution/annotateGRs.sh
./genePhylogenies/GRevolution/phylogenyGRs.sh
./genePhylogenies/GRevolution/plotGRtree.Rmd

# Elongases
./genePhylogenies/ELONGASEevolution/annotate.ELNG.sh
./genePhylogenies/ELONGASEevolution/phylogeny.ELNG.sh
./genePhylogenies/ELONGASEevolution/plotELGtree.Rmd

# Cuticular Proteins (CPRs)
./genePhylogenies/CPRevolution/annotateCPR.sh
./genePhylogenies/CPRevolution/phylogenyCPR.sh
./genePhylogenies/CPRevolution/plotCPRtree.Rmd

Script to plot barplots for all analyzed gene families

./genePhylogenies/barplot.Rmd