The first grape T2T reference genome has been published

The complete reference genome for genetics and plant breeding of grapevine (Vitis vinifera L.).

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Credit: Zhou laboratory

This article was originally posted on Horticultural 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 improvements over previous versions. The N50 contig length of PN_T2T was ~250 times that of 12X.v0 (25.93 Mb versus 102 kb), and all 9429 gaps in 12X.v0 were filled in the PN_T2T genome. Orientation errors in 12X.v0 were also corrected as inversions and translocations with respect to PN_T2T (Figure 1).

The authors found that the telomere repeat unit (TTTAGGG/CCCTAAA) was most abundant at both ends of each chromosome. Regarding the centromeric regions, the authors found that the 107-bp repeats were the most abundant unit in the whole genome, which had 182,620.5 (copies ≥ 2) repeats representing approximately 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 when exploring biological process (BP) related terms of these geniuses.

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

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

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

Introduction of Zhou’s laboratory

Professor Yongfeng Zhou’s research group focuses on crop population genomics and smart breeding, and carries out the following work: (1) harvest, conservation, evaluation and innovation of crop germplasm resources such as rice and grapes; (2) genetic basis of important agronomic traits; (3) machine learning and crop genome design for breeding. They conducted domesticated population genomics studies of crops such as rice and grapes, revealing the cost of domesticating crops, as well as adaptive variation, detrimental variation, and structural variation related to important agronomic traits. They also used genome editing technology (CRISPR-Cas9) to achieve functional genomic analysis and rapid molecular rearing. Prof. Zhou has published over 20 SCI papers such as Nature Plants, PNAS, Molecular Biology and Evolution as correspondent, first or correspondent authors in the past five years.

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References

Authors

Xiaoya Shi1, 2, #, Shu Cao2, 3, #Xu Wang2, 6, #Siyang Huang2, 4Yu Wang2, 5Zhongjie Liu2Wen Wen Liu2Xiangpeng Lung1Yanling Peng2Nan Wang2Yiwen Wang2Zhiyao Ma2Xiaodong Xu2Zhang fan2Hui Xue2HaixiaZhong7Yi Wang8Kekun Zhang9Amandine Velt10Komlan Avia10Daniela Holtgräwe11Jerome Grimplet12José Tomas Matus13Doreen Ware2.15 pm; Xiyu Wu7Haibo Wang16Chonghuai Liu17Yuling Fang9Camille Rustenholz10, *Zongming Cheng18, *Hua Xiao2, 7, *Yongfeng Zhou2, 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 of Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

3 Ministry of Education Horticultural Plant Biology Key Laboratory, 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 Horticultural Crops Institute, 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 Plant genetics and genomics, CeBiTec and Faculty of Biology, University of Bielefeld, 33615 Bielefeld, Germany

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

13 Institute of 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 (DW)

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/Horticultural Crops Biology and Breeding Key Laboratory (Utilization of Germplasm Resources), Ministry of Agriculture/Mineral Nutrition and Fertilizer Key Laboratory Efficient utilization of fruit tree deciduous, 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 Institute, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China

From Zhou laboratory

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


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