The first grape T2T reference genome was published

This article has been published on Horticulture Research with title: The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

This gap-free PN_T2T genome (494.87 Mb) has significant improvement compared to previous versions. The contig N50 length of PN_T2T was ~ 250 times higher than that of 12X.v0 (25.93 Mb versus 102 kb), and all the 9429 gaps in 12X.v0 were filled in PN_T2T genome. Orientation errors in 12X.v0 were also corrected such as inversions and translocations compared to PN_T2T (Figure 1).

The authors found the telomere repeat unit (TTTAGGG/CCCTAAA) was the most abundant in both ends of each chromosome. As to centromeric regions, the authors found 107 bp repeats were the most abundant unit in the whole genome, which had 182,620.5 (copies ≥ 2) repetitions accounted for about 3.95% of the genome. 343 genes were captured in the centromeres, and RNA modification, protein autophosphorylation, DNA integration, DNA recombination and photomorphogenesis appeared enriched while exploring biological process (BP)-related terms of these genes.

The authors found a total of 377 gene clusters in the grapevine reference genome, these duplications often involve local rearrangements and can extend into megabases with dozens to hundreds of genes involved. On chromosome 16 (23-27 Mb), there were 599 enriched domain genes; on chromosome 18 (25~36 Mb), there were 1237 genes enriched domains. Among them, many strongly enriched domains are part of plant disease resistance base (R base) domains, and these R genes and gene clusters in grapes highlight a tremendous opportunity for exploring plant defense mechanisms (Figure 2).

Although PN40024 genome is highly homozygous (99.8%), combined with the resequencing data of PN40024, the authors found nine hotspots of heterozygous SNPs on chromosomes. The results showed that the most significantly enriched terms were response to water deprivation, protein phosphorylation, cell division, response to oxidative stress and response to salt stress, which were closely associated with key physiological activities in plants.

Overall, the previous versions of the grapevine reference genome consisted of thousands of fragments with missing centromeres and telomeres, which limited the accessibility of the heredity of important agronomic traits in these regions. However, This gap-free reference genome, the first T2T reference genome for fruit trees., for the PN40024 provides important resources for grapevine genetics and breeding.

Introduction of Zhou’s Lab

Professor Yongfeng Zhou research group focuses on crop population genomics and intelligent breeding, and conducts the following work: (1) collection, preservation, evaluation, and innovation of crop germplasm resources such as rice and grape; (2) genetic basis of important agronomic traits; (3) machine learning and crop genome design for breeding. They have carried out domestication population genomics studies on crops such as rice and grape, revealing the domestication cost of crops, as well as adaptive variation, harmful variation, and structural variation related to important agronomic traits. They have also utilized genome editing technology (CRISPR-Cas9) to achieve functional genomics analysis and rapid molecular breeding. Prof. Zhou have published over 20 SCI papers such as Nature Plants, PNAS, Molecular Biology and Evolution as corresponding, first, or corresponding authors in recent five years.

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References

Authors

Xiaoya Shi^{1, 2, #,} Shuo Cao^{2, 3, #}, Xu Wang^{2, 6, #}, Siyang Huang^{2, 4}, Yue Wang^{2, 5}, Zhongjie Liu², Wenwen Liu², Xiangpeng Leng¹, Yanling Peng², Nan Wang², Yiwen Wang², Zhiyao Ma², Xiaodong Xu², Fan Zhang², Hui Xue², Haixia Zhong⁷, Yi Wang⁸, Kekun Zhang⁹, Amandine Velt¹⁰, Komlan Avia¹⁰, Daniela Holtgräwe¹¹, Jérôme Grimplet¹², José Tomás Matus¹³, Doreen Ware^14,15; Xinyu Wu⁷, Haibo Wang¹⁶, Chonghuai Liu¹⁷, Yuling Fang⁹, Camille Rustenholz^{10, *}, Zongming Cheng^{18, *}, Hua Xiao^{2, 7, *}, Yongfeng Zhou^{2, 19, *}

Affiliations

1 College of Horticulture, Qingdao Agricultural University, 266109, Qingdao, China

2 State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

3 Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, People’s Republic of China

4 Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, Guangxi, 530005 China

5 State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China

6 School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland

7 Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China

8 Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China

9 College of Enology, Northwest A&F University, Yangling 712100, China

10 SVQV, INRAE - University of Strasbourg, 68000 Colmar, France

11 Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany

12 Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain

13 Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain

14 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA; ware@cshl.edu (D.W.)

15 USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA

16 Fruit Research Institute,Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit Tree, Liaoning Province, Xingcheng, China

17 Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China

18 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China

19 State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China

About Zhou lab

Dr. Yongfeng Zhou, Dr. Hua Xiao, Professor Zongming Cheng, and Professor Camille Rustenholz are the co-corresponding authors of the paper. Dr. Yongfeng Zhou is the research professor in Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences. He obtained his PhD degree from the University of Oulu in 2014, and did a postdoc in University of California, Irvine from 2014 to 2020 working on population genomics of crop domestication and breeding. Now he is dedicated to crop population genomics and breeding by combining genomics, epigenomics, transcriptomics, phenomics, environmental variables and machine learning. As a first/corresponding author, he had published more than 20 papers in journals such as Nature Plants, PNAS, and MBE.