DupGen_finder

The DupGen_finder was developed to identify different modes of duplicated gene pairs. MCScanX algorithm was incorporated in this pipeline.

Authors	Xin Qiao (Xin Qiao)
	Qionghou Li (Qionghou Li)
	Yupeng Wang (Yupeng Wang)
	Shaoling Zhang (Shaoling Zhang)
	Andrew H. Paterson (PGML)
Email	[email protected]

The schematic diagram of DupGen_finder pipeline

Figure 1: The flowchart of DupGen_finder pipeline

Contents

• Dependencies
• Installation
• Preparing input files
• Running
• Result Files
• Citation

Dependencies

• Perl

Installation

cd ~/software  # or any directory of your choice
git clone https://github.com/qiao-xin/DupGen_finder.git
cd DupGen_finder
make
chmod 775 DupGen_finder.pl
chmod 775 DupGen_finder-unique.pl
chmod 775 set_PATH.sh
source set_PATH.sh

Test you can run DupGen_finder:

DupGen_finder.pl

DupGen_finder should print its 'help' text.

**Note**

DupGen_finder software package includes a custom MCScanX algorithm which can output sorted gff files such as Ath.gff.sorted, and is slightly different from the original MCScanX algorithm implemented in MCScanX software package.

Preparing input files

Pre-computed BLAST results (-outfmt 6) and gene location information (GFF format) are required for running DupGen_finder successfully.

1. For the target genome in which gene duplicaiton modes will be classified, please prepare two input files:

   • target_species.gff, a gene position file for the target species, following a tab-delimited format. For example, "Ath.gff".
   • target_species.blast, a blastp output file (-outfmt 6) for the target species (self-genome comparison). For example, "Ath.blast".

2. For the outgroup genome, please prepare two input files:

   • [target_species]_[outgroup_species].gff, a gene position file for the target_species and outgroup_species, following a tab-delimited format.
   • [target_species]_[outgroup_species].blast, a blastp output file (-outfmt 6) between the target and outgroup species (cross-genome comparison).

For example, assuming that you are going to classify gene duplication modes in Arabidopsis thaliana (Ath), using Nelumbo nucifera (Nnu) as outgroup, you need to prepare 4 input files: Ath.gff,Ath.blast, Ath_Nnu.gff, Ath_Nnu.blast

gff file

Ath.gff is in the following format (tab separated):

Species_abbrev-Chr_ID	gene_ID	start_position	end_position

The data in Ath.gff looks like this (tab separated):

Ath-Chr1	AT1G01010.1	3631	5899
Ath-Chr1	AT1G01020.1	5928	8737
Ath-Chr1	AT1G01030.1	11649	13714
Ath-Chr1	AT1G01040.2	23416	31120
Ath-Chr1	AT1G01050.1	31170	33153

The below command can be used to creat Ath_Nnu.gff:

cat Ath.gff Nnu.gff >Ath_Nnu.gff

The data in Ath_Nnu.gff looks like this (tab separated):

Ath-Chr1	AT1G01010.1	3631	5899
Ath-Chr1	AT1G01020.1	5928	8737
...
Nnu-megascaffold_32	NNU_00001-RA	57481	63788
Nnu-megascaffold_32	NNU_00002-RA	32491	41125
...

blast file

Ath.blast is in the following format:

query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score

The data in Ath.blast looks like this (tab separated):

ATCG00500.1	ATCG00500.1	100.00	488	0	0	1	488	1	488	0.0	 932
ATCG00510.1	ATCG00510.1	100.00	37	0	0	1	37	1	37	2e-19	73.9
ATCG00280.1	ATCG00280.1	100.00	473	0	0	1	473	1	473	0.0	 876
ATCG00890.1	ATCG01250.1	100.00	389	0	0	1	389	1	389	0.0	 660
ATCG00890.1	ATCG00890.1	100.00	389	0	0	1	389	1	389	0.0	 660

Here is the typical parameter setting for generating the xyz.blast file:

The example file Ath.pep contains the whole genome protein sequences (FASTA format) of Arabidopsis.

• For BLAST software

# Create a reference database
makeblastdb -in Ath.pep -dbtype prot -title Ath -parse_seqids -out Ath
# Align protein query sequences against the reference database
blastp -query query_file -db database -evalue 1e-10 -max_target_seqs 5 -outfmt 6 -out xyz.blast
# For example
blastp -query Ath.pep -db Ath -evalue 1e-10 -max_target_seqs 5 -outfmt 6 -out Ath.blast

• For DIAMOND software

# Create a reference database
diamond makedb --in Ath.pep -d Ath
# Align protein query sequences against the reference database
diamond blastp -d Ath -q Ath.pep -o Ath.blast -p 20 --sensitive --max-target-seqs 5 --evalue 1e-10 --quiet

---

NOTE: All above input files should be stored under the same folder (the "-i" option). For more parameters please see below.

Running

Run the following command to get help information about DupGen_finder:

DupGen_finder.pl

This command will print a full list of options:

Usage: DupGen_finder.pl -i data_directory -t target_species -c outgroup_species -o output_directory
#####################
Optional:
-a 1 or 0(are segmental duplicates ancestral loci or not? default: 1, yes)
-d number_of_genes(maximum distance to call proximal, default: 10)
#####################
The following are optional MCScanX parameters:
-k match_score(cutoff score of collinear blocks for MCScanX, default: 50)
-g gap_penalty(gap penalty for MCScanX, default: -1)
-s match_size(number of genes required to call a collinear block for MCScanX, default: 5)
-e e_value(alignment significance for MCScanX, default: 1e-05)
-m max_gaps(maximum gaps allowed for MCScanX, default: 25)
-w overlap_window(maximum distance in terms of gene number, to collapse BLAST matches for MCScanX, default: 5)

A typical command to identify different modes of duplicated gene pairs in a given species could look like this:

DupGen_finder.pl -i data -t Ath -c Nnu -o results

Here, DupGen_finder attempts to identify the different modes of duplicated gene pairs in A.thaliana by using N.nucifera as outgroup. All required data files should be stored under this directory data. The output files will be stored under this directory results. For more details please see below. Ath: A.thaliana, Nnu: N.nucifera.

Note: We recommend that the "data_directory" or "output_directory" should be given a full path. For example, /home/the_path_to_your_data_directory/

DupGen_finder-unique

Moreover, to eliminate redundant duplicate genes among different modes, we provide a stricter version of DupGen_finder named DupGen_finder-unique by which each duplicate gene was assigned to a unique mode after all of the duplicated gene pairs were classified into different gene duplication types. The priority of the duplicate genes is as follows: WGD > tandem > proximal > transposed > dispersed.

DupGen_finder-unique.pl -i data -t Ath -c Nnu -o results

Result Files

1 - Duplicated gene pairs:

• Ath.wgd.pairs
• Ath.tandem.pairs
• Ath.proximal.pairs
• Ath.transposed.pairs
• Ath.dispersed.pairs

These files includes duplicated gene pairs derived from five modes of gene duplication, including WGD (Ath.wgd.pairs), tandem duplication (Ath.tandem.pairs), proximal duplication (Ath.proximal.pairs), transposed duplication (Ath.transposed.pairs), dispersed duplication (Ath.dispersed.pairs). The gene pairs contained in these files looks like this (tab separated):

Duplicate 1	Location	Duplicate 2	Location	E-value
AT1G01010.1	Ath-Chr1:3631	AT4G01550.1	Ath-Chr4:673862	5e-52
AT1G01020.1	Ath-Chr1:5928	AT4G01510.1	Ath-Chr4:642733	5e-74
AT1G01030.1	Ath-Chr1:11649	AT1G13260.1	Ath-Chr1:4542168	3e-45
AT1G01050.1	Ath-Chr1:31170	AT3G53620.1	Ath-Chr3:19880504	6e-126
AT1G01060.1	Ath-Chr1:33666	AT5G17300.1	Ath-Chr5:5690227	3e-30

2 - Ath.singletons

It includes genes that have no homologous genes within target species.

GeneID	Location
AT2G32600.1	Ath-Chr2:13833545
AT5G11810.1	Ath-Chr5:3808720
AT4G16610.1	Ath-Chr4:9354321
AT1G66520.1	Ath-Chr1:24816128
AT1G51110.1	Ath-Chr1:18935329

3 - Ath.stats

The number of duplicated gene pairs derived from different modes.

Types	NO. of gene pairs
WGD-pairs	4352
TD-pairs	2063
PD-pairs	788
TRD-pairs	4447
DSD-pairs	16130

4 - Collinearity files

• Ath.collinearity
• Ath_Nnu.collinearity

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.