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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
Horticulture Research ( IF 8.7 ) Pub Date : 2021-08-05 , DOI: 10.1038/s41438-021-00599-8
Shi-Ping Cheng 1 , Kai-Hua Jia 2 , Hui Liu 2 , Ren-Gang Zhang 3 , Zhi-Chao Li 2 , Shan-Shan Zhou 2 , Tian-Le Shi 2 , Ai-Chu Ma 4 , Cong-Wen Yu 4 , Chan Gao 4 , Guang-Lei Cao 4 , Wei Zhao 2, 5 , Shuai Nie 2 , Jing-Fang Guo 2 , Si-Qian Jiao 2 , Xue-Chan Tian 2 , Xue-Mei Yan 2 , Yu-Tao Bao 2 , Quan-Zheng Yun 3 , Xin-Zhu Wang 3 , Ilga Porth 6 , Yousry A El-Kassaby 7 , Xiao-Ru Wang 2, 5 , Zhen Li 8, 9 , Yves Van de Peer 8, 9, 10, 11 , Jian-Feng Mao 2
Affiliation  

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.

中文翻译:

栽培姜中单倍型分辨的基因组组装和等位基因特异性基因表达

姜 (生姜) 是全球最有价值的香料植物之一;它因其烹饪和民间医药应用而备受推崇,因此具有很高的经济和文化重要性。在这里,我们提出了一个单倍型分辨的染色体规模组装,用于锚定到总长度为 3.1 Gb 的 11 个假染色体对上的二倍体生姜。在单倍型之间发现了显着的结构变异,4 号染色体上大于 15 Mb 的两个倒位可能与生姜不育有关。我们对等位基因表达模式进行了全面的时空全基因组分析,发现大多数等位基因是协调表达的。表现出最大差异的等位基因表现出更接近转座因子,更大的编码序列分歧,更宽松的选择压力,和更多的转录因子结合位点差异。我们还预测了可能调节 6-姜酚生物合成的转录因子。我们的等位基因感知组装为姜中未来的功能基因组学、分子育种和基因组编辑提供了一个强大的平台。
更新日期:2021-08-05
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