ArticleNature genetics2023
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species.
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Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 159 papers.
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159citing papers in PubMed
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159 citing papers in PubMed.
- Unlocking the future of crop improvement with crop wild relatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Establishment of an efficient and PAM-relaxed LbCas12a genome editing tool in plants.The New phytologist · 2026Article
- Multi-variant GWAS and genomic prediction dissect the genetic architecture underlying tomato fruit weight.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Graph-based pangenomics reveals the genetic basis of agronomic traits in tomato fruits.Horticulture research · 2026Article
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
- Cross incompatibility restricting genome exchange and diversification of primary gene pool in plants: challenges and opportunities.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Integrating deep learning and pangenomics to recover missing heritability from wild structural variations.BMC genomics · 2026Review
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- Genomics Approach Links ROS-Scavenging to Enhanced Lateral Root Development Under Salt Stress in Tomato.Plant, cell & environment · 2026Article
- Article
- Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.BMC genomics · 2026Article
- Graph-based pan-genome reveals structural variations associated with agronomic traits in mung bean.Nature genetics · 2026Article
- Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.Horticulture research · 2026Article
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- Genomic analysis of 3,330 accessions provides insights into the evolutionary history and self-incompatibility locus of the Brassica A genome.Nature genetics · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Metabolomic and transcriptomic analyses reveal grafting-regulated nutritional and flavor metabolites in tomato.BMC plant biology · 2026Article
- Genome-wide association studies in horticultural crops: decoding genetic diversity for precision breeding.Horticulture research · 2026Article
99 more citing papers are in PubMed but not listed here.
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Authors and funding
25 authors.
Ning Li *The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Qiang He *Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.ORCID http://orcid.org/0000-0003-3356-2125
Juan WangThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Baike WangThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Jiantao ZhaoShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.ORCID http://orcid.org/0000-0002-5140-8220
Shaoyong HuangThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Tao YangThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Yaping TangThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Shengbao YangThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Patiguli AisimutuolaThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Ruiqiang XuThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Jiahui HuThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Chunping JiaThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Kai MaThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
Zhiqiang LiAdsen Biotechnology Co., Ltd., Urumqi, China.
Fangling JiangCollege of Horticulture, Nanjing Agricultural University, Nanjing, China.
Jie GaoCollege of Horticulture, Xinjiang Agricultural University, Urumqi, China.
Haiyan LanCollege of Life Science and Technology, Xinjiang University, Urumqi, China.
Yongfeng ZhouShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.ORCID http://orcid.org/0000-0003-0780-2973
Xinyan ZhangShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Sanwen HuangShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.ORCID http://orcid.org/0000-0002-8547-5309
Zhangjun FeiBoyce Thompson Institute, Cornell University, Ithaca, NY, USA.ORCID http://orcid.org/0000-0001-9684-1450
Huan WangBiotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China. wanghuan@caas.cn.ORCID http://orcid.org/0000-0003-3836-0741
Hongbo LiShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. lihongbo_solab@163.com.ORCID http://orcid.org/0000-0003-1579-4600
Qinghui YuThe State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China. yuqinghui@xaas.ac.cn.ORCID http://orcid.org/0000-0002-9342-5301
Funding
No grant is acknowledged in the PubMed record.
Abstract
Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.
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SolanumSolanum lycopersicumGenome, PlantGenome-Wide Association StudyGenomicsPlant Breeding
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