Vittaria appalachiana comparative transcriptomics

Code for "Life without a sporophyte: the origin and consequences of asexual reproduction in a gametophyte-only fern" by Jessie A. Pelosi, W. Brad Barbazuk, and Emily B. Sessa.

All transcriptome assemblies are from the One Thousand Plant Transcriptome Initiatve (2019) and available here.

This repository is divided into five folders:

1. GC_content
2. dN/dS
3. genefams
4. WGD
5. TEs

The process for generating of orthologs for use in downstream anlayses is below.

Orthology Determination and Alignment

Generate pep and CDS files using TransDecoder v. 5.5 (Haas et al. 2014):

TransDecoder.LongOrfs -t [file.fasta] 

TransDecoder.Predict -t [file.fasta] 

Using OrthoFinder v. 2.3.11 (Emms and Kelly 2015, 2019) generate orthogroups as follows:

Set 1: Adiantum raddianum, V. appalachiana, V. lineata

Set 2: Pteridaceae + Asplenium platyneuon as an outgroup

orthofinder -M msa -f proteomes/ 

Retrieve single copy orthologs for OrthoFinder output and extract corresponding CDS (modify to use loop or array):

python extract_cds.py OG#######.pep transcriptome_1.cds transcriptome_2.cds transcriptome_n.cds

Align CDS files using MACSE v. 2.04 (Ranwez et al. 2011) (modify to use loop or array):

java -Xms4000m -jar macse_v2.04.jar -prog alignSequences -seq OG#######.cds 

Generate gene trees with IQTREE2 v. 2.1.0 (Minh et al. 2020, Hoang et al. 2018):

iqtree2 -s OG#######.cds_NT --alrt 1000 -B 1000 -m TEST --redo 

Generate species tree with ASTRAL-III v. 5.6.2 (Zhang et al. 2018):

cat *.treefile > OGs_treefiles.tre 
  
astral -i OGs_treefiles.tre -o OGs_sp.tre 2> OGs_sp_tre.log