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.
Highlights
At the dawn of civilization, spices were sought after as eagerly as gold and precious gems
After mapping the Illumina reads to the final assembly, SNPs were identified with SAMtools v1.813, and we obtained a SNP heterozygosity of ~0.041% and a single-base error rate of ~0.0014%, suggesting that there were only a few regions with high sequence similarity that were not well resolved
99.85% of the Illumina short reads could be successfully mapped to the genome assembly, and ~99.5% of the assembly was covered by at least 20X Oxford Nanopore Technologies (ONT) long reads, indicating that the current assembly covered most unique genomic regions and was highly accurate
Summary
At the dawn of civilization, spices were sought after as eagerly as gold and precious gems. Ginger (Zingiber officinale) was initially cultivated and utilized by Austronesian people more than 3000 years ago and was subsequently introduced to South India following Austronesian expansion[1]. The Latin name of the genus, Zingiber, is derived from the Greek word zingiberis, whose. Ginger is an economically important and widely used spice and folk medicine worldwide. According to the Food and Agriculture Organization of the United Nations, the production of ginger had reached 2.78 million tons from a. Cheng et al Horticulture Research (2021)8:188 harvested area of 373,120 ha as of 2018, with 81.7% of the global production taking place in Asia Despite the worldwide use of ginger, the genetic research and development efforts associated with it have not been commensurate with its importance
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