Helitron-like elements (Helitron, Helentron and Helitron2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging to identify. Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements.
- python = 3.9.0
- r-base = 4.1
- biopython
- pybedtools = 0.9.0 =py39hd65a603_2
- r-bedtoolsr
- r-seqinr = 4.2_16 = r41h06615bd_0
- bedtools = 2.30.0
- dialign2 = 2.2.1
- mafft
- cd-hit = 4.8.1
- blast = 2.2.31
- emboss = 6.6.0
- hmmer = 3.3.2
- genometools-genometools = 1.6.2 = py39h58cc16e_6
- rnabob = 2.2.1
If mamba is not installed on your system, you can install it with the following commands easily.
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh -b
Then you can install HELIANO with mamba.
#create the HELIANO environment
mamba create -n HELIANO
#activate the HELIANO environment
mamba activate HELIANO
# install
mamba install zhenlisme::HELIANO -c conda-forge -c bioconda
mamba deactivate
#create the HELIANO environment
conda create -n HELIANO
#activate the HELIANO environment
conda activate HELIANO
# installation
conda install zhenlisme::HELIANO -c conda-forge -c bioconda
conda deactivate
Before installation , you need to be sure that all dependencies have been installed in your computer and that their path are defined into your environmental variables. All dependencies could be installed via conda/mamba.
- download the latest HELIANO package.
git clone https://github.com/Zhenlisme/HELIANO.git - switch to the source code dorectory that you cloned at the last step.
cd HELIANO/ - run configure file.
bash configure.sh - You can find HELIANO in the bin directory.
conda activate HELIANO
heliano -h
usage: heliano [-h] -g GENOME [-w WINDOW] [-dm DISTANCE_DOMAIN] [-pt {0,1}] [-is1 {0,1}] [-is2 {0,1}] [-sim_tir {100,90,80}] [-p PVALUE] -o OPDIR [-n PROCESS] [-v]
HELIANO can detect and classify different variants of Helitron-like elements: Helitron and Helentrons. Please visit https://github.com/Zhenlisme/HELIANO/ for more information. Email us:
zhen.li3@universite-paris-saclay.fr
optional arguments:
-h, --help show this help message and exit
-g GENOME, --genome GENOME
The genome file in fasta format.
-w WINDOW, --window WINDOW
To check terminal signals within a given window bp upstream and downstream of ORF ends, default is 10 kb.
-dm DISTANCE_DOMAIN, --distance_domain DISTANCE_DOMAIN
The distance between HUH and Helicase domain, default is 2500.
-pt {0,1}, --pair_helitron {0,1}
For Helitron, its 5' and 3' terminal signal pairs should come from the same autonomous helitorn or not. 0: no, 1: yes. default no.
-is1 {0,1}, --IS1 {0,1}
Set the insertion site of autonomous Helitron as A and T. 0: no, 1: yes. default no.
-is2 {0,1}, --IS2 {0,1}
Set the insertion site of autonomous Helentron/Helitron2 as T and T. 0: no, 1: yes. default no.
-sim_tir {100,90,80}, --simtir {100,90,80}
Set the simarity between short inverted repeats(TIRs) of Helitron2/Helentron. Default 100.
-p PVALUE, --pvalue PVALUE
The p-value for fisher's exact test.
-o OPDIR, --opdir OPDIR
The output directory.
-n PROCESS, --process PROCESS
Maximum of threads to be used.
-v, --version show program's version number and exit
Here we will use the chromosome 18 of Fusarium oxysporum strain Fo5176 as an example, where you can find it in file test.fa .
Perform the following code:
heliano -g test.fa -is1 0 -is2 0 -o test_opt -w 15000
You will find two main result files when HELIANO program runs successfully.
- RC.representative.bed: the predicted Helitron/Helentron coordinates in bed format (available in the file test.opt.tbl in this repository).
- RC.representative.fa: the predicted Helitron/Helentron sequences in fasta format. Other files or directories are intermediate outputs.
- TIR_count.tbl: Table for counts of terminal inverted repeats of each HLE subfamily.
- Boundary.tbl: Table for the conservation of flanking regions of each HLE subfamily.
- Helitron/ or Helentron/: Directory for intermediate files when detecting Helitron/Helentron.
There are 11 columns in RC.representative.bed file:
| chrm-id | start | end | subfamily | occurence | strand | pvalue | TS_blastn_identity | variant | type | name |
|---|---|---|---|---|---|---|---|---|---|---|
| CP128282.1 | 53617 | 59046 | Helentron_left_18-Helentron_right_18 | 7 | - | 6.3390e-07 | 60 | Helentron | auto | insertion_Helentron_auto_1 |
| CP128282.1 | 83425 | 88824 | Helentron_left_18-Helentron_right_18 | 7 | - | 6.3390e-07 | 60 | Helentron | auto | insertion_Helentron_auto_2 |
| CP128282.1 | 94525 | 99924 | Helentron_left_18-Helentron_right_18 | 7 | + | 6.3390e-07 | 60 | Helentron | auto | insertion_Helentron_auto_3 |
| CP128282.1 | 306838 | 312276 | Helentron_left_18-Helentron_right_18 | 7 | + | 6.3390e-07 | 60 | Helentron | auto | insertion_Helentron_auto_4 |
| CP128282.1 | 665681 | 668554 | Helentron_left_33-Helentron_right_32 | 3 | - | 1.3547e-05 | 60 | Helentron | nonauto | insertion_Helentron_nonauto_1 |
| CP128282.1 | 668719 | 671599 | Helentron_left_33-Helentron_right_32 | 3 | + | 1.3547e-05 | 60 | Helentron | nonauto | insertion_Helentron_nonauto_2 |
| CP128282.1 | 855863 | 858738 | Helentron_left_33-Helentron_right_32 | 3 | + | 1.3547e-05 | 60 | Helentron | nonauto | insertion_Helentron_nonauto_3 |
| CP128282.1 | 855863 | 880806 | Helentron_left_33-Helentron_right_32 | 3 | + | 1.3547e-05 | 60 | Helentron | auto | insertion_Helentron_auto_5 |
| CP128282.1 | 926221 | 928267 | CP128282.1-926221-928267 | 1 | - | 1 | 0 | Helentron | orfonly | insertion_Helentron_orfonly_1 |
| CP128282.1 | 963556 | 968985 | Helentron_left_18-Helentron_right_18 | 7 | + | 6.3390e-07 | 60 | Helentron | auto | insertion_Helentron_auto_6 |
| CP128282.1 | 1107206 | 1112635 | Helentron_left_18-Helentron_right_18 | 7 | + | 6.3390e-07 | 60 | Helentron | auto | insertion_Helentron_auto_7 |
| CP128282.1 | 1259412 | 1264991 | Helentron_left_18-Helentron_right_18 | 7 | - | 6.3390e-07 | 60 | Helentron | auto | insertion_Helentron_auto_8 |
Notice: The insertions that encode Rep/helicase are considered putative autonomous HLEs.
| Columns | Explaination |
|---|---|
| chrm-id | chromosome id |
| start | start site of HLE |
| stop | stop site of HLE |
| subfamily | heliano classification |
| occurence | how often this subfamily occurred in genome |
| strand | the insertion is on which strand |
| pvalue | pvalue of fisher's exact test, indicating the significance of the prediction. The lower, the more significant. |
| TS_blastn_identity | the average identity of RTS and LTS to their representative counterparts |
| variant | the insertion is Helitron or Helentron |
| type | the mobility of HLE, either autonomous (auto) or nonautonomous (nonauto) |
| name | unique identifier for each insertion |
The HELIANO package also provides a program (heliano_cons) for generating consensus sequences of HLE.
Check the usage of heliano_cons:
heliano_cons -h
usage: heliano_cons [-h] -g GENOME -r REPSENBED -o OPDIR [-n PROCESS] [-v]
Making consensus for Helitron-like sequences. Please visit https://github.com/Zhenlisme/heliano/ for more information. Email us: zhen.li3@universite-paris-saclay.fr
optional arguments:
-h, --help show this help message and exit
-g GENOME, --genome GENOME
The genome file in fasta format.
-r REPSENBED, --repsenbed REPSENBED
The representative bed file (RC.representative.bed).
-o OPDIR, --opdir OPDIR
The output directory.
-n PROCESS, --process PROCESS
Maximum of threads to be used.
-v, --version show program's version number and exit
Li Z , Gilbert C , Peng H , Pollet N. "Systematic annotation of Helitron-like elements in eukaryote genomes using HELIANO." bioRxiv (2024): 2024-02. doi: 10.1101/2024.02.08.579435
Li Z , Gilbert C , Peng H , Pollet N. "HELIANO: a Helitron-like element annotator." Zenodo (2024). doi: 10.5281/zenodo.10625239
HELIANO is designed to predict complete insertions of Helitron-like elements (HLE), with the limitation that fragmented insertions will not be reported. To identify fragmented insertions, we recommend running RepeatMasker or BLASTN using HELIANO predictions as the query. Before you run RepeatMasker or BLASTN, we suggest mask the HLE query with a trusted non-HLE TE database because other non-HLE TEs might insert into long HLEs which would inflates sequence length and result in misannotation.
For a precise and quick search, you can use the strigent parameter '-pt 1 -is1 1 -is2 1 -p 1e-5 -s 30 -pt 1 -sim_tir 100' that considered the preferred insertion sites of HLE. For big or complex genomes (e.g., maize genome), I just recommed you use the strigent parameter set. But not all HLEs obey their regular preferring insertion sites. If you want to explore more in your interested genome, you can use the loose parameter set, e.g., '-is1 0 -is2 0 -sim_tir 90', and you will have more predictions and longer execution time. Note that the parameters 'is2' and '-sim_tir' are only for Helentrons, and 'is1' and '-pt' are only for Helitrons.
For any questions, please open an issue in the 'issues' section or email us: zhen.li3@universite-paris-saclay.fr or nicolas.pollet@universite-paris-saclay.fr