Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. Cheng, S., Jia, K., Liu, H., Zhang, R., Li, Z., Zhou, S., Shi, T., Ma, A., Yu, C., Gao, C., Cao, G., Zhao, W., Nie, S., Guo, J., Jiao, S., Tian, X., Yan, X., Bao, Y., Yun, Q., Wang, X., Porth, I., El-Kassaby, Y. A., Wang, X., Li, Z., Van de Peer, Y., & Mao, J. Horticulture Research, 8(1):188, August, 2021. doi abstract bibtex 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.
@article{cheng_haplotype-resolved_2021,
title = {Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger},
volume = {8},
issn = {2662-6810},
doi = {10/gmhq7d},
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.},
language = {eng},
number = {1},
journal = {Horticulture Research},
author = {Cheng, Shi-Ping and Jia, Kai-Hua and Liu, Hui and Zhang, Ren-Gang and Li, Zhi-Chao and Zhou, Shan-Shan and Shi, Tian-Le and Ma, Ai-Chu and Yu, Cong-Wen and Gao, Chan and Cao, Guang-Lei and Zhao, Wei and Nie, Shuai and Guo, Jing-Fang and Jiao, Si-Qian and Tian, Xue-Chan and Yan, Xue-Mei and Bao, Yu-Tao and Yun, Quan-Zheng and Wang, Xin-Zhu and Porth, Ilga and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Li, Zhen and Van de Peer, Yves and Mao, Jian-Feng},
month = aug,
year = {2021},
pages = {188},
}
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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. 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