Internet Archive Scholar

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

Shi-Ping Cheng, Kai-Hua Jia, Hui Liu, Ren-Gang Zhang, Zhi-Chao Li, Shan-Shan Zhou, Tian-Le Shi, Ai-Chu Ma, Cong-Wen Yu, Chan Gao, Guang-Lei Cao, Wei Zhao (+14 others)
2021 Horticulture Research  

Preserved Fulltext

fulltext thumbnail
Web Archive Capture PDF (2.3 MB)
https://web.archive.org/web/20211003055753/https://biblio.ugent.be/publication/8721910/file/8721911.pdf

A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL. The file type is application/pdf.

AbstractGinger (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
more » ... ith 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.
doi:10.1038/s41438-021-00599-8 fatcat:slyx3q4zefe63h2yxntra6kfva
DOAJ
Citation

Shi-Ping Cheng, Kai-Hua Jia, Hui Liu, Ren-Gang Zhang, Zhi-Chao Li, Shan-Shan Zhou, Tian-Le Shi, Ai-Chu Ma, Cong-Wen Yu, Chan Gao, Guang-Lei Cao, Wei Zhao, Shuai Nie, Jing-Fang Guo, Si-Qian Jiao, Xue-Chan Tian, Xue-Mei Yan, Yu-Tao Bao, Quan-Zheng Yun, Xin-Zhu Wang, Ilga Porth, Yousry A. El-Kassaby, Xiao-Ru Wang, Zhen Li, Yves Van de Peer, Jian-Feng Mao. "Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger." Horticulture Research 8.1 (2021)