HEB_categories

Identification of the homoeologous expression bias (HEB) categories for each quadruplet

Introduction

The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops (Ramírez-González et al., 2018). Identification the patterns of HEB category for each quadruplet (1:1:1:1) could help us better study the diversity of octoploid species phenotypes. This study defined nine ideal categories of quadruplets and determined the category of each quadruplet by comparing the shortest distance between each quadruplet with the nine ideal quadruplets.

Dependencies

Practical Extraction and Report Language (Perl v5.26.2 is more recommended in this study)

Installation

git clone https://github.com/jinxin112233/HEB_categories
cd HEB_categories-main
chmod +x HEB_categories.perl
export PATH=/your/path/to/HEB_categories-main

Input file format

Example input file: input.fpkm.txt

Tips: The values in the table represent the expression of each homoeologous (FPKM or TPM is recommended).

Usage

A typical command line looks like:

# Identification of HEB categories
HEB_categories.perl input.fpkm.txt

# Output file processing
sed 1d input.fpkm.txt | awk '{print$1}' - > tmp1.txt && awk '{print$5}' input.fpkm.txt_summary > tmp2.txt && paste tmp1.txt tmp2.txt > output.Categories.txt && rm -r tmp1.txt tmp2.txt

Output file

Example output file: output.Categories.txt

Tips: A dominant (AD), B dominant (BD), C dominant (CD), D dominant (DD), A suppressed (AS), B suppressed (BS), C suppressed (CS) and D suppressed (DS).

Note

Before you start running your data, we recommend that you run test data (input.fpkm.txt).

Limitations

Please input each quadruple with a total expression > 0.5 (not normalized) or input the normalized data. If you input a quadruple with total expression < 0.5, the above command you use to process may get an error that the category does not match the quadruple id.

Reference

Ramírez-González, R. H. et al. The transcriptional landscape of polyploid wheat. Science. 361, eaar6089 (2018).

Ye, C. Y. & Wu, D. Y. et al. The Genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven Adaptation. Mol. Plant. 13, 1298–1310 (2020).

Citations

Jin, X., Du, H., Zhu, C., Wan, H., Liu, F., Ruan, J., Mower, J. P., & Zhu, A. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. Nature plants 9, 1252–1266 (2023).

Contact

Any interseting comments and questions are welcome (jinxin@mail.kib.ac.cn).

jinxin112233/HEB_categories

About

Resources

Stars

Watchers

Forks

Releases

Packages 0

Languages

Packages