Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger

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Authors

Cheng, Shi-Ping
Jia, Kai-Hua
Liu, Hui
Zhang, Ren-Gang
Li, Zhi-Chao
Zhou, Shan-Shan
Shi, Tian-Le
Ma, Ai-Chu
Yu, Cong-Wen
Gao, Chan

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Publisher

Springer Nature

Abstract

Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.

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Keywords

Ginger (Zingiber officinale), Gene expression, Gene regulation, Plant evolution

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Citation

Cheng, SP., Jia, KH., Liu, H. et al. Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. Horticulture Research 8, 188 (2021). https://doi.org/10.1038/s41438-021-00599-8.