Skip to content

Files

Latest commit

qiao-xinqiao-xin
Update README.md
Feb 24, 2019
efe00a3 · Feb 24, 2019

History

History

detect_gene_conversion

README.md

A pipeline used to detect gene conversion events

This pipeline incorporated a sophisticated method that was firstly reported in a previous study (Wang et al. 2007) to detect gene conversion events. This method was originally developed by Dr. Xiyin Wang, and was applied to subsequent a series of studies (Wang et al. 2009; Wang et al. 2011; Liu et al. 2014).
Authors Xin Qiao (qiaoxin)
Xiyin Wang (PGML)
Andrew Paterson (PGML)
Email qiaoxinqx2011@126.com

Dependencies

Installation

git clone https://github.com/qiao-xin/Scripts_for_GB.git

Preparing input files

Here, we used this pipeline to detect gene conversion events in WGD-derived gene pairs for Arabidopsis thaliana (Ath) using Arabidopsis lyrata (Aly) as outgroup.

Before running this pipline, some data files should be prepared:

  • Ath.wgd.pairs: duplicate gene pairs derived from different modes of gene duplication or WGD events of different ages.
  • Ath.cds and Aly.cds: whole-genome CDS sequences (FASTA format) of investigated species (Ath) and outgroup species (Aly).
  • Ath_Aly.collinearity: the execution of MCScanX will output this file, containing pairwise collinear blocks as follows:
## Alignment 0: score=64951.0 e_value=0 N=1326 Aly-scaffold_1&Ath-Chr1 plus
  0-  0:	Aly333558	AT1G02210.1	  3e-11
  0-  1:	Aly470187	AT1G02260.1	      0
  0-  2:	Aly470188	AT1G02270.1	      0
  0-  3:	Aly311338	AT1G02280.1	      0
  0-  4:	Aly470192	AT1G02310.1	      0
  0-  5:	Aly470194	AT1G02335.1	 4e-152

Running

USAGE:

perl GeConScan.pl species_A_abbr species_B_abbr gene_order_in_collinearity paralog_pairs_in_A

The parameter species_A_abbr and species_B_abbr indicates scientific name abbreviation you defined for the investigated species and outgroup species respectively, for example, "Ath" and "Aly". You can set the option gene_order_in_collinearity by 'f' or 'r'. If the target genome gene_id located before the outgroup genome gene_id in file "xyz.collinearity", please use 'f'. paralog_pairs_in_A indicates the input file containing paralogous gene pairs from target species.

A typical command could look like this:

perl GeConScan.pl Ath Aly r Ath.wgd.pairs.example

This command will produce:

  1. Ath_Aly.homologous.quartets
Duplicate 1	Homolog 1	Duplicate 2	Homolog 2
Ath.AT1G17380.1	Aly.Aly312706	Ath.AT1G72450.1	Aly.Aly476379
Ath.AT1G17400.1	Aly.Aly471945	Ath.AT1G72490.1	Aly.Aly476382
Ath.AT1G17455.1	Aly.Aly471952	Ath.AT1G72630.1	Aly.Aly339481
Ath.AT1G17480.1	Aly.Aly471956	Ath.AT1G72670.1	Aly.Aly476404
Ath.AT1G17530.1	Aly.Aly471960	Ath.AT1G72750.1	Aly.Aly476412
Ath.AT1G17590.1	Aly.Aly471968	Ath.AT1G72830.2	Aly.Aly339498
  1. Ath_Aly.quartets.K.CV.BP.txt
Homologous_quartets	Pa(Ath-1, Ath-2)	Ps(Ath-1, Ath-2)	Pa(Aly-1, Aly-2)	Ps(Aly-1, Aly-2)	Pa(Ath-1, Aly-1)	Ps(Ath-1, Aly-1)	Pa(Ath-2, Aly-2)	Ps(Ath-2, Aly-2)	Is_conversion_between_Ath-1_and_Ath-2	Is_conversion_between_Aly-1_and_Aly-2	Bootstrap_percentage_Ks_Ath-1_Ath-2	Bootstrap_percentage_Ka_Ath-1_Ath-2	Bootstrap_percentage_Ks_Aly-1_Aly-2	Bootstrap_percentage_Ka_Aly-1_Aly-2
Ath.AT1G17380.1_Ath.AT1G72450.1_Aly.Aly312706_Aly.Aly476379	0.2493	1.0510	0.2763	0.9870	0.0493	0.1356	0.0394	0.1723	N	N	
Ath.AT1G17400.1_Ath.AT1G72490.1_Aly.Aly471945_Aly.Aly476382	0.2136	1.0556	0.2100	1.1067	0.0122	0.1398	0.0327	0.2425	N	N	
Ath.AT1G17455.1_Ath.AT1G72630.1_Aly.Aly471952_Aly.Aly339481	0.0695	0.8170	0.0738	0.7803	0.0000	0.0449	0.0040	0.2151	N	N	
Ath.AT1G17480.1_Ath.AT1G72670.1_Aly.Aly471956_Aly.Aly476404	0.1680	1.0117	0.1634	0.9545	0.0200	0.1268	0.0112	0.1642	N	N	
Ath.AT1G17530.1_Ath.AT1G72750.1_Aly.Aly471960_Aly.Aly476412	0.0888	0.9736	0.0900	0.9477	0.0224	0.1566	0.0074	0.1205	N	N	
Ath.AT1G17590.1_Ath.AT1G72830.2_Aly.Aly471968_Aly.Aly339498	0.2331	0.5479	0.1989	0.5094	0.0859	0.1327	0.0455	0.1487	N	N

Note:

  • Ath-1 and Ath-2 show two Ath paralogous genes, Aly-1 and Aly-2 show two Aly paralogous genes.
  • Pa () shows nonsynonymous nucleotide substitution difference, Ps () shows synonymous nucleotide substitution difference.
  • 'N' shows no gene converison found between the Ath or Aly paralogs.
  • 'R' shows that the two Ath paralogs have been affected by gene covnersion.
  • 'S' shows that the two Aly paralogs have been affected by gene covnersion.

Citation

Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH: Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants. Genome Biology 2019, 20:38.