Czech and Chinese researchers have obtained the first gap-free sequence of the horseradish genome. Combining data from Illumina, Oxford Nanopore Technology, PacBio HiFi, and Chromatin Conformation Capture (Hi-C) sequencing, they generated the first telomere-to-telomere (T2T) genome assembly of the allotetraploid horseradish genome (Armoracia rusticana). The genome sequence allowed the researchers to investigate the genetic basis of the biosynthesis of glucosinolates (GSLs) and horseradish peroxidases. While GSLs are precursors of isothiocyanates responsible for the characteristic pungent and spicy taste of horseradish, horseradish peroxidases are frequently used as a reporter enzyme in diagnostics and histochemistry. The first T2T assembly of the horseradish genome expands our understanding of polyploid genome evolution and provides a fundamental genetic resource for breeding and genetic improvement of horseradish. The study, led by Fei Shan (Beijing Academy of Agriculture and Forestry Sciences) and Martin Lysak (CEITEC Masaryk University), has now been published in Nature Communications.
Horseradish (Armoracia rusticana), which like cabbage or wasabi belongs to the mustard family, contains glucosinolates (GLSs) that break down into isothiocyanates with characteristic pungency. Horseradish is grown for its root, which, when grated, becomes pungent and is processed into spicy condiments. GLSs or their breakdown products provide numerous benefits to the human body, including anti-cancer, anti-inflammatory, and anti-microbial properties. Despite its increasing importance as a “super health food” limited genomic resources have prevented the application of advanced breeding techniques to horseradish and the elucidation of the genetic basis of its important traits.
The research team, led by Fei Shen from the Institute of Biotechnology Research, Beijing Academy of Agriculture and Forestry Sciences, and Martin Lysak from the Central European Institute of Technology (CEITEC), Masaryk University, reported the telomere-to-telomere (T2T) gap-free reference genome of allotetraploid horseradish sequenced using a comprehensive strategy. Analysis of the first T2T assembly of an allotetraploid genome (i.e., genome consisting of two parental subgenomes) in the mustard family demonstrated the role of transposable DNA elements (long terminal repeat retrotransposon) and DNA methylation in subgenome differentiation. Using advanced genomic techniques, scientists have fully characterized the epigenomic architecture and 3D chromatin structure of two horseradish subgenomes and deciphered the dramatic contribution of divergence and bursts of DNA repeats to subgenomic divergence. The in-depth analysis of the horseradish peroxidase family provides important resources for studying the full spectrum of horseradish isoenzymes. In addition, researchers have identified the genetic basis underlying the wide diversity of GSLs and their degradation products in horseradish. Allopolyploidization and continuous tandem duplications have allowed preferential retention of GSL genes, contributing to the wide diversity of GSLs and their degradation products in horseradish.
Overall, the first T2T assembly of the allotetraploid horseradish genome, together with its epigenomic architecture and 3D chromatin structure, expands our understanding of polyploid genome evolution and provides a fundamental genetic resource for breeding and genetic improvement of horseradish. The high-quality horseradish genome will be a valuable genomic resource for biologists, biochemists, and agricultural scientists.
The publication in Nature Communications is available also here.