CRABS CLAW-independent floral nectary development in Penstemon barbatus

Data and Scripts for the "CRABS CLAW-independent floral nectary development in Penstemon barbatus" manuscript.

Scripts:

fastp.sh - filter and quality trim reads using fastp on all samples

1ribo_detect.sh - detect and filter rRNA. Example script for 1 sample.

gffread.sh - convert P. barbatus genome annotation GFF to a GTF for use in STAR

star_initalize.sh - initalize STAR for the P. barbatus genome

1star_ribo.sh - Example script for aligning reads from 1 sample to the genome.

htseq_ribo.sh - counting reads for each sample using HTseq

deseq2_code.R - R script for running the transcriptome tissue comparisons in DEseq2 with the output from HTseq.

deseq_PCA.R - R script for the generation of the PCA plots for the samples. To be used in conjuction with the deseq2_code.R script.

20230321_topGO_script.R - R script for Gene Ontology analyses in topGO.

area_perimeter_cor.R - R script for vasculature ANOVAs.

Data:

Genome files

4_LG_2022_maker.all.maker.proteins.fasta - protein sequences for all genes in the P. barbatus genome in Wessinger et al. 2023

4_LG_2022_maker.all.maker.noseq.gff - GFF file for all genes in the P. barbatus genome in Wessinger et al. 2023

HTseq output trimmed to only the counts (excludes other log information) - trimmed_htseq_35404342.txt

DEseq2 output 

Early stage

barb_early_nect_nonect_FDR0.01_LFC0.csv

barb_early_nect_nonect_FDR0.01_LFC0.annotated.csv

Late stage

barb_late_nect_nonect_FDR0.01_LFC0.csv

barb_late_nect_nonect_FDR0.01_LFC0.annotated.csv

Nectar removal

barb_stage5_6_FDR0.01_LFC0.csv

barb_stage5_6_FDR0.01_LFC0.annotated.csv

Orthofinder output - N0.tsv

Vasculature raw data - 20231025_bud_measurements_pbarb.csv

Archive_Images directory - contains raw section images stained with either Alcian Blue & Safranin O or