Ginger is a precious horticultural crop with both edible and medicinal functions. It is not only an important component of traditional Chinese medicine, but also an important condiment. It has a long history of cultivation in China. China ranks first in the world in planting area, yield and export volume of ginger. The total area of ginger in the middle and upper reaches of the Yangtze River is 2.26 million mu, accounting for 49.7% of the whole country, and it is the first choice industry to promote rural revitalization. Ginger has perennial roots, the rhizome is full of meat and contains many nutrients. Besides protein, carbohydrates, vitamins and minerals, it also contains gingerol, ginger oil, gingerol and other bioactive substances. It has the functions of seasoning, anticancer, antifungal, anti-inflammatory, antioxidant and anti-platelet aggregation, and is an important member of spice family and medicinal plant family. Gingerol is a unique flavor substance of ginger, and it is also the main functional factor of various functional activities of ginger, which has broad application prospects in condiment, cosmetics and medical care. Although ginger has remarkable economic value in the world, its molecular biology and genetic breeding have been stagnant because of its difficulty in sexual reproduction, huge genome and high heterozygosity. In addition, the lack of genome information of ginger for a long time has limited our understanding of synthesis regulation mechanism, which has led to the slow development of ginger molecular breeding.

Recently, horticultural research has continuously published the genome data of two different kinds of ginger on the Internet. They are respectively the research papers entitled "Genome Assembly and Allele-specific Gene Expression of Haplotype Analysis of Cultivated Ginger" by Pingdingshan College and Plant Genetics and Breeding Research Group of Beijing Forestry University. And the research paper entitled "The genome analysis of ginger (official ginger) haplotype and its unique pathway of gingerol biosynthesis", which was co-sponsored by Chongqing University of Arts and Sciences and Southwest University.

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The plant genetics and breeding research group of Pingdingshan University and other units analyzed the haplotype genome sequence of important traditional ginger varieties in China, revealed the differences between haplotypes, inferred the genome basis of high sterility of ginger, and preliminarily clarified the biosynthesis pathway of gingerol, which laid an important foundation for subsequent functional research and molecular design breeding.

This study takes Zhang Liangjiang, the first ginger variety registered and protected by geographical indications of agricultural products in China, as the research object. According to records, "Zhangliangjiang" has been planted for more than 2,000 years since the Han Dynasty, and is now preserved in Zhang Liangzhen, Lushan County, Pingdingshan City, Henan Province. This variety has the reputation of "the king of ginger", and has the excellent characteristics of deep yellow color, spicy fragrance, rich fragrance, silky and rich, not rotten after being boiled for a hundred times and not rotten after being stored for a long time.

In this study, the haplotype genome sequence of "Zhang Liangjiang" was analyzed by using advanced long reading and long sequencing techniques. The genetic differences between the two haplotypes were detected, and the structural variation regions related to the high gamete abortion rate of ginger were speculated. It is revealed that the difference of allele expression between the two genomes may be related to the sequence difference of cis-regulatory region and coding region, the proximity effect of transposon and selection pressure. Based on the analysis of gene * * * expression network, the gene regulation mechanism related to gingerol biosynthesis was preliminarily analyzed.

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The research of Chongqing University of Arts and Sciences and other units cracked the genome of the main variety of bamboo root ginger in southwest China, and assembled two sets of bamboo root ginger by using the strategies of short reading length (369.5 1 Gb), long reading length PacBio(285.8 1 Gb) and Hi-C (563.5438+06 GB). The haplotype genome size is 1.53 Gb (overlapping group N50: 4.68 M) and 1.5 1 GB (overlapping group N50: 5.28 m) respectively, and 98.438+0 1% sequences are anchored in 22. By allele analysis, there are 55,635 genes (72% of all genes) with homology in the two haplotypes. Of the 17226 alleles in ginger, 1 1.9% showed chromosome preference at the transcription level (Figure 2). This study found that the heterozygosity of ginger genome is 3.6%, which is the highest plant genome reported so far. The high number of repeats, including long terminal repeats (LTRs) accounting for 665,438 0.06%, may be the main reason for its large genome and high heterozygosity, and also the main driving force for the evolution of ginger genome. There was no difference in the expression of ginger alleles between the two haplotypes, and 2055 (17+0.9%) of the 65438 and 226 alleles showed chromosome preference at the transcription level.

By integrating genome, transcriptome and metabolomics data, the synthetic pathway of gingerol, a unique component of ginger, was constructed, and 12 key enzyme families (PAL, C4h, 4Cl, CST, C3'H, C3OMT, CCOMT, CSE, PKS, AOR, DHN and DHT) involved in gingerol synthesis were screened and identified.

Brief introduction of the author

Genome assembly and allele-specific expression of haplotype analysis of cultivated ginger

Associate Professor of Pingdingshan College, Dr. Jia from Beilin College (now working in Shandong Academy of Agricultural Sciences), Dr. Liu Hui and Dr. Zhang (Shandong) Gene Technology Co., Ltd. are the first authors. The correspondents are Mao Jianfeng, associate professor of Beijing Forestry University, Professor of Ghent University in Belgium, and Yves Vanderbilt, academician of the Royal Belgian Academy of Sciences. Dr Ma Aichu and researcher Yu Congwen from Pingdingshan Academy of Agricultural Sciences also participated in the research. This work also includes collaborators from Umemo University in Sweden, Laval University in Canada, University of British Columbia, Ghent University, Pretoria University and Nanjing Agricultural University. This research is supported by projects such as tackling key scientific and technological problems in Henan Province and starting fund for high-level talents in Pingdingshan University.

Haplotype separation and nomenclature of diploid ginger and its unique synthesis pathway of gingerol

This work is led by Chongqing University of Arts and Sciences, and completed by Yangtze University, Southwest University and Huada Gene. Professor, Associate Professor Wu Lin, Associate Professor Dong Lighting, Professor Jiang and Dr. Jiang Sanjie are the first authors, and Professor Xia Qingyou, Dr. Jian Jianbo and Associate Professor Zou Yong are the corresponding authors. Li, a researcher of Jinan Second Academy of Agricultural Sciences, and Li Qingzhi, a senior engineer, participated in the research. This study was supported by the major project of Ginger Genome of Chongqing University of Arts and Sciences and the Natural Science Foundation of Chongqing.

Article link:

Genome assembly and allele-specific expression of haplotype analysis of cultivated ginger

/articles/s 4 1438-02 1-00599-8

Genome analysis of diploid ginger haplotype and its unique pathway of gingerol biosynthesis

/articles/s 4 1438-02 1-00627-7