beroe_forskalii_mitogenome

• This repository contains additional files for the manuscript, "Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii"
• To recreate most of the figures for the manuscript, please install snakemake, cuttlery, and pauvre, then navigate to this directory and run the snakemake pipeline by executing the command snakemake in your terminal.

Installation

To install everything, use the following commands

# If on linux, execute the following command to ensure that everything plots correctly
sudo apt-get install dvipng

# install the requirements
pip install pauvre
pip install cuttlery
pip install snakemake

# Clone the repository and recreate the figures of the plot. Takes several hours.
https://github.com/conchoecia/beroe_forskalii_mitogenome
cd beroe_forskalii_mitogenome
snakemake --cores 4

Abbreviations

• Pb - Pleurobrachia bachei
• Ml - Mnemiopsis leidyi
• Bf - Beroe forskalii

Additional Files

Directory -- 16S_structure

Files in this directory are related to determining the 16S structure of the B. forskalii mitochondrial genome. The files in this directory are:

• mnemiopsis_rrnl_final.sto is a structural Stockholm file. This encodes the M. leidyi 16S rRNA structure from Pett et al 2011.
• mnemi16S.cm is the infernal covariance model built using mnemiopsis_rrnl_final.sto.
• Bf1311_against_mnemi16S.txt is the infernal results file when the Bf1311 mitochondrial genome was searched against using the mnemi16S.cm covariance model.

Directory -- ARWEN

This directory contains the fasta files of each B. forskalii mitochondrial genome and the ARWEN results. The files in this directory are:

• MG655622.fasta- The Bf201706 mitochondrial genome.
• MG655622_results.txt - The Bf201706 ARWEN results.
• MG655623.fasta - The Bf201606 mitochondrial genome.
• MG655623_results.txt - The Bf201606 ARWEN results.
• MG655624.fasta- The Bf201311 mitochondrial genome.
• MG655624_results.txt - The Bf201311 ARWEN results.

Directory -- ATP6

Files in this directory pertain to ATP6 of all ctenophores. This directory contains:

• README.md contains notes about where to locate the P. bachei and M. leidyi ATP6 sequences.
• PB_ML_ATP6_nucl.fasta contains the Pb and Ml ATP6 transcript DNA sequences.
• PB_ML_ATP6_prot.fasta contains the Pb and Ml ATP6 protein sequences.
• ATP6_to_BF.txt contains the tblastn results using the Pb and Ml ATP6 sequences to query the Bf transcriptome
• BF_ATP6_hits.fasta contains the transcript sequences of the Bf ATP6 blast hits.
• BF_ATP6.fasta contains the most likely Bf ATP6 transcript based on protein sequence similarity to other ctenophore ATP6 sequences.
• DS12*/DS12*_mapdepthavg.txt contains the average map depth average when the DS121 and DS122 libraries were mapped against the B. forskalii ATP6 transcript using bwa mem.

Directory -- Biosample_accessions

Text files in this directory contain the NCBI BioSample Accession numbers for all four B. forskalii ctenophore individuals.

Directory -- CREx

This directory contains the file crex_results_summary.pdf, which is the CREx mitochondrial rearrangement analysis results for the M. leidyi, B. forskalii, and P. bachei mitochondrial genomes.

Directory -- FTGwindow

This directory contains files used in the Fourier Transform analysis to predict which regions of the mitochondrial genome contain protein-coding DNA.

Directory -- assembly

This directory contains a single file, bf_raw_mito.fa, which is the raw mitochondrial genome assembly produced by canu.

Directory -- fasta_sequences

This directory contains fasta files used in various analyses, including nucleotide and amino acid sequences, as well as various alignments. The files in this directory are

• Directory BF201706_prot
  • Directory TM_results
    • contains html file results from TMHMM for COX1, COX2, COX3, CYTB, ND1-6, URF1, and URF2.
  • Directory TM_txtfiles
    • Contains text files with transmembrane domain predictions by TMHMM. There are files for COX1, COX2, COX3, CYTB, ND1-6, URF1, and URF2.
  • file Bf201706_prot.fasta - the protein sequences from MG655622/Bf201706. These were used in generating the transmembrane domain prediction with TMHMM.
• Directory alignments
  • Directory concatenated_after_guidance
    • concatenated_prot.phy is the COX1, COX2, COX3, CYTB, ND1, ND3, and ND5 alignments concatenated together. These are the the protein alignments that have had sites removed using Guidance2.
  • Directory concatenated_noguidance
    • concatenated_noguidance.phy is the COX1, COX2, COX3, CYTB, ND1, ND3, and ND5 alignments concatenated together. No columns were removed using Guidance2.
  • Directory ctenos_all_proteins_noguidance
    • all_proteins_ctenos_monoallo_noguidance.phy is the concatenated alignment for COX1, COX2, COX3, CYTB, and ND1-6 for all ctenophores and two outgroups.
  • Directory guidance_alignments - This directory contains files and a script, run_guidance.sh, that produces alignments with columns removed using Guidance2.
  • Directory prot_cteno_aln contains nucleotide alignments for 12S and 16S for all ctenophore mitochondrial genomes, as well as protein alignments for all ctenophores for genes COX1, COX2, COX3, CYTB, and ND1-ND6.
  • file 12S.fasta - 12S alignment from Pb and other ctenophores.
  • file 16S.fasta - 16S alignment from Bf and other ctenophores.
• Directory coding_seqs contains all of the nucleotide sequences for Bf for COX1, COX2, COX3, CYTB, and ND1-6.
• Directory non-beroe contains directories of nucleotide sequences for coding and noncoding regions of the following organisms: Chlamydomonas, Daphnia, Drosophila, Human, and Strongylocentrotus.
• Directory noncoding_seqs contains all of the Bf nucleotide sequences for the noncoding regions COX1 to ND6, COX3 to ND3, ND2 to CYTB, ND5 to URF1, URF1 to URF2, and URF2 to ND2.
• Directory test_seqs contains all of the Bf nucleotide sequences for URF1 and URF2.
• file bf_mitogenomes_alignment.fasta - the whole-mitogenome Bf alignment used to generate the table listing indels.

Directory -- figures

When the snakemake pipeline is run, the figures and associated text files are output to this directory.

Directory -- final_annotations

Text files in this directory include the final DNA sequences of the mitochondrial genomes of individuals Bf1311, Bf1706, and Bf1606. In addition, we include the scripts map_depth_extract.sh and FastqPairedEndValidator.pl used to isolate genomic reads that map to the mitochondrial sequences.

Directory -- gff_files

This directory contains GFF files used in plotting mitochondrial genomes for synteny.

Directory -- indels

Contains scripts and files to analyze the number and distribution of indels between individuals.

• file Bf_alignment.fasta is a whole-mitogenome alignment for all three individuals of B. forskalii
• file Bf_alignment.geneious - the same alignment, in geneious format.
• file Bforsk_indels.txt - a table of indels, the sample in which they occur, the position, and the size.
• file print_gaps.py - a python script that produces Bforsk_indels.txt from Bf_alignment.fasta

Directory -- itasser_results

Text and HTML files in this directory are from the ITASSER protein structure prediction. Additionally there are structure files that can be opened with protein viewing software.

Directory - phylogeny

Files in this directory contain phylogenetic analyses. All subdirectories listed below are in the directory phylogeny/201904_rooted_tree.

• Directory RAxML_ctenos_allgenes_noguidance - RAxML analysis conducted on COX1, COX2, COX3, CYTB, and ND1-6 using only ctenophores with two outgroups. Guidance2 was not used to remove columns from the amino acid matrix.
• Directory RAxML_protcatwag_guidance - RAxML analysis conducted on COX1, COX2, COX3, CYTB, ND1, ND3, and ND5 using ctenophores and many outgroups. Guidance2 was used to remove columns from the amino acid matrix.
• Directory RAxML_protcatwag_noguidance - RAxML analysis conducted on COX1, COX2, COX3, CYTB, ND1, ND3, and ND5 using ctenophores and many outgroups. Guidance2 was not used to remove columns from the amino acid matrix.
• Directory phylobayes_ctenos_allgenes_noguidance - Phylobayes analysis conducted on COX1, COX2, COX3, CYTB, and ND1-6 using only ctenophores with two outgroups. Guidance2 was not used to remove columns from the amino acid matrix.
• Directory phylobayes_guidance - Phylobayes analysis conducted on COX1, COX2, COX3, CYTB, ND1, ND3, and ND5 using ctenophores and many outgroups. Guidance2 was used to remove columns from the amino acid matrix.
• Directory phylobayes_noguidance - Phylobayes analysis conducted on COX1, COX2, COX3, CYTB, ND1, ND3, and ND5 using ctenophores and many outgroups. Guidance2 was not used to remove columns from the amino acid matrix.

Directory - tRNAscanSE

Contains HTML files of results from running tRNAscanSE on the whole mitochondrial genomes for Bf201706, Bf201606, and Bf201311.