WDR93_CFAP46

This GitHub repository contains the data for paper "Concurrent loss of ciliary genes WDR93 and CFAP46 in phylogenetically distant birds".

Buddhabhushan Girish Salve, Amia Miriam Kurian, Nagarjun Vijay

Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India *Correspondence: nagarjun@iiserb.ac.in

Graphical abstract

Folder Structure

• Assembly_verification: Contain the bam, bed, and UCSC screenshot for long-read verification at WDR93 and CFAP46 gene locus for the Acanthisitta chloris, Anas platyrhynchos, Anser cygnoides, Calypte anna, and Gallus gallus. (Fig. 2, Fig. S4, S27, S29-31, S34-36)
• CFAP46_blast_results: Contains the raw read blastn result for the CFAP46 gene for the species in which WDR93 loss and query sequence is used in BLASTN.
• CFAP46_deletion: Contains the fasta sequence used to get dot-plot and UCSC browser track data for deletion size comparison with Mallard. (Fig. 8, Fig. S32-S33)
• CLANS: Contains the WDR93 and NDUFS4 domain containing clans results. (Fig. S1)
• Events: The blastn output supporting the gene pseudogenization and MView html file for the Geese and other species where WDR93 is lost. ( Anser brachyrhynchus, Anser cygnoides, Anser indicus, Branta canadensis, Acanthisitta chloris, Calidris pugnax, Calypte anna, and Colius striatus) (Fig. 3, 4, 7, Fig. S2, S3, S5)
• Main_figures: Contains the main and abstract figures and the inputs required to get figures like phylogenetic trees from TimeTree and iTOLs. (Fig. 1-8, abstract_figure)
• WDR93_mol_evo_analysis: Selection pressure analysis of WDR93 gene across clades, checked using RELAX, codeML, gBGC, MEME (Mixed Effects Model of Evolution), and FEL (Fixed Efects Likelihood).
• CFAP46_mol_evo_analysis: Selection pressure analysis of CFAP46 gene across clades, checked using RELAX and gBGC (GC-biased gene conversion).
• Pairwise_alignment: Contains the pairwise alignment between Mallard and chicken in the CFAP46 region.
• Synteny: Contains the NCBI synteny images for WDR93. (Fig. 1)
• Transcriptome_analysis: Contains the input files for coverage plots. Also, contain an IGV screenshot for the WDR93 gene. (Fig. 5-6, Fig. S6-26)
• WDR93_blast_results: Contains the Genome and SRA blastn results for WDR93 for finding the gene disrupting changes and their confirmation.

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Prerequisites:

• TOGA (v1.1.2)
• make_lastz_chains (https://github.com/hillerlab/make_lastz_chains.git)
• PAML (4.9f)
• BLASTN 2.9.0+
• phastBias(1.6)
• mapnh(1.3.0)
• HYPHY 2.5.48(MP)
• HYPHY-MEME 2.3.14.20181224beta(MP)
• HYPHY-FEL 2.3.14.20181224beta(MP)
• BWA(0.7.17-r1188)
• Samtools (1.3)
• bedtools (v2.26.0)
• ea-utils (https://github.com/ExpressionAnalysis/ea-utils.git)
• seqtk (1.2-r94)
• Guidance (v2.02)
• PRANK (v.150803)
• IGV (2.8.13)
• STAR (2.7.0d)
• MegaX
• MView (Version 1.67)
• CLANS
• Pfam (34.0)
• R (4.1.0)
• Pymol (Version 2.3.0)

R packages:

• ape (5.5)
• phytools (0.7-90)
• ggplot2 (3.3.5)
• ggrepel (0.9.1)
• cowplot (1.1.1)
• dplyr (1.0.7)
• ggplotify (0.1.0)
• grid (4.1.1)
• gridExtra (2.3)
• reshape2 (1.4.4)