Overview

Bradysia coprophila is a fungus gnat (fly) that carries germline restricted chromosomes (GRCs or 'L' chromosomes). We sequenced the germ tissue in B. coprophila and identified the GRCs using K-mer and coverage based techniques. We then compared the genes on the GRCs to those in the core genome (i.e. autosomes and X chromosome) to explore how the GRCs evolved in this species. The code in this repository was used in the analyses in this manuscript (https://doi.org/10.1101/2021.02.08.430288).

Note:

Within this repository, L is a synonym of germ-line restricted chromosome (GRC).

Project data

Later paths should be replaced by URLs in public repositories.

• raw reads: ENA project PRJEB44837 https://www.ebi.ac.uk/ena/browser/view/PRJEB44837?show=reads

• data used to generate all figures in manuscript: tables/figure_data.tar.gz

• softmasked genome (Illumina): /data/ross/mealybugs/analyses/sciara_coprophila/18_repeat/repeats/Scop_repeatmask/scop.spades2.min1kb.trimmed.fasta.masked

• annotation: /data/ross/mealybugs/analyses/sciara_coprophila/20_braker/braker.gff3

• pacbio genome: /data/ross/mealybugs/analyses/sciara_coprophila/Pacbio/4_racon2_sr/sciara.germ.pb.illumina1.rb.racon6pe.fasta

• RNAseq of germ and soma (Males and Females): /data/ross/mealybugs/raw/11791_Ross_Laura/raw_data/20190812/ and Mgerm/body or Fgerm/body directory

• all vs all blasts

  • genes (nucleotides) data/genome_wide_paralogy/genes_all_vs_all.blast
  • proteins (transcribed genes) data/genome_wide_paralogy/proteins_all_vs_all.blast

• repeatmodeler/masker for genome annotation: /data/ross/mealybugs/analyses/Sciara-L-chromosome/data/repeats

Analysis documentation

Below is a list of manuscript sections containing analysis documentation and scripts used for those analyses

Genome assembly and annotation

• associated data:

• table linking Illumina contigs to annotated genes with assignments: data/gene.assignment.tab.tsv
  • associated r script: scripts/gene.num.tab.R
• gene ID and mean coverage for that gene: data/gene_cov_table.tsv

Chromosome classification of the Sciara genome to GRC/X/A

• analysis documentation
• associated scripts
• table with scores and assignments for all Illumina contigs data/scaffold_assignment_tab_full.tsv

Genome wide paralogy to identify GRC homologs and colinearity analysis

• analysis documentation

• scripts

• associated data

  • table with gene pairs in reciprocal blasts and gene cov, percent alignment between the blast pairs, length of genes, and assignments for genes. Before filtering based or gene/alignment length: data/ntgene_recip_blast_cov.tsv
  • table with all info from paralog exploration, paralog ID, cov, type, and paralog freq after filtering based on gene/alignment length : data/filtered_paralog_tab.tsv

• associated data for colinearity analysis

  • table of colinear blocks between chromosomes. Contains gene ID, chromosome assignment, scf in Illumina, scf in colinear block, block info, order in block and paralog ID, and assignment, and mean gene cov: data/full_colinear_tab.tsv
  • associated r script: scripts/colinear_exploration.R

GRC scaffold coverage analysis

• analysis documentation

• associated data

• per gene coverage: data/gene.cov.braker.annotation.tsv

Phylogenetic placement of B. coprophila BUSCO genes

• analysis documentation

• associated scripts

  • make_BUSCO_scf_tab.R
  • busco.sp.count.hist.R

• associated data

  • Table of assigment of BUSCO genes

GRC homolog identification in the M. destructor (Cecidomyiidae) genome

• analyses documentation

Important places to look at

• Google drive "Sciara_L_chromosome" (written documents; you should have access if you are supposed to have an access)
• Code that decides about assigments what is L / Lc / Lk / Lp / AX / AXp (we can latter one separate A and X using either male coverage or the reference genome). In total the assigment fractions now are (Mbp):

L	Lc	A	Ac	X	Xc	NA
154.1	6.8	162.4	9	52.9	2.4	10.1