DOI: 10.5281/zenodo.1258011

Rana temporaria_transcriptome_sex bias_tissue specificity

This projects intends to assemble the most comprehensive transcriptome of Rana temporaria, collecting samples from five developmental stages and three adult tissues. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with evolutionary rate.

A brief pipeline for this project is as follows:

Step1: Transcriptome is firstly assembled with Trinity v2.3.0.

Following a few filtering steps, transcripts were filtered with possible transposable element insertions by masking the transcriptome assembly using a custom repeat library of Rana temporaria using RepeatMasker, only retaining transcripts that were at least 75% unmasked.

the custom repeat library can be found in folder /TE_library TE_repeats.fasta

Step2: Quantifying abundances of transcripts from RNA-Seq reads with Kallisto v0.43.0.

see the scripts in folder /script/ amm_kallisto_pipeline.sh am23_matrix.sh am27_matrix.sh am31_matrix.sh am43_matrix.sh am46_matrix.sh amm_goand_matrix.sh amm_brain_matrix.sh amm_liver_matrix.sh

Step 3 Analyse differential (sex-biased) gene expression with edgeR v3.4.

see the scripts in folder /script/ edgeR_main.r. stacked_barchart.R

Step 4 Gene divergence analysis (dN/dS), with PRANK v140603 and codeml in PAML.

see the scripts in folder /script/ Amm_dn_ds.R Prank_and_PAML.sh for_loop_codeml.sh

Step 5 Tissue specificity Tau calculation, investigating relationship among dN/dS, Tau and sex bias.

see the scripts in folder /script/ tau.R 5groups_venn.R Expression_slidingwindow.r

Step6 Gene ontology (GO enrichment) analysis

see the scripts in folder /script/ GO_analysis_05.sh GO_BP.R GO_CC.R GO_MF.R

Step7 Sex bias gene expression with RPKM and related analysis

see the scripts in folder /script/ RPKM.R