Zhangjun Fei
· Professor at the Boyce Thompson InstituteCornell University · Horticulture
Active 2004–2024
About
Zhangjun Fei is an adjunct professor at the School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, and a professor at the Boyce Thompson Institute. His research focuses on developing computational tools and resources to analyze and integrate large-scale 'omics' datasets, including genome, transcriptome, proteome, and metabolome data. His work aims to address the challenge of digesting massive amounts of biological information and using it in an intelligent and comprehensive manner, helping researchers understand how genes work together to comprise functioning cells and organisms. Dr. Fei's interests include computational analysis of large datasets and modeling regulatory networks.
Research topics
- Biology
- Genetics
- Botany
- Computational biology
- Evolutionary biology
- Computer Science
- Medicine
- Internal medicine
- Cell biology
- Ecology
- Horticulture
- Microbiology
- Biotechnology
- Agroforestry
- Immunology
- Biochemistry
- Endocrinology
- Food science
- Business
- Database
Selected publications
Nature Communications · 2023 · 130 citations
- Biology
- Botany
- Horticulture
Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.
Graph pangenome captures missing heritability and empowers tomato breeding
Nature · 2022 · 506 citations
- Biology
- Genetics
- Computational biology
. Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is largely due to resolving incomplete linkage disequilibrium through the inclusion of additional causal structural variants identified using the graph pangenome. Moreover, by resolving allelic and locus heterogeneity, structural variants improve the power to identify genetic factors underlying agronomically important traits leading to, for example, the identification of two new genes potentially contributing to soluble solid content. The newly identified structural variants will facilitate genetic improvement of tomato through both marker-assisted selection and genomic selection. Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.
CuGenDBv2: an updated database for cucurbit genomics
Nucleic Acids Research · 2022 · 130 citations
Senior authorCorresponding- Computer Science
- Biology
- Database
The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.
The Plant Cell · 2021 · 76 citations
- Biology
- Cell biology
- Botany
Flowers are the core reproductive structures and key distinguishing features of angiosperms. Flower opening to expose stamens and gynoecia is important in cases where pollinators much be attracted to promote cross-pollination, which can enhance reproductive success and species preservation. The floral opening process is accompanied by the coordinated movement of various floral organs, particularly petals. However, the mechanisms underlying petal movement and flower opening are not well understood. Here, we integrated anatomical, physiological, and molecular approaches to determine the petal movement regulatory network using rose (Rosa hybrida) as a model. We found that PETAL MOVEMENT-RELATED PROTEIN1 (RhPMP1), a homeodomain transcription factor (TF) gene, is a direct target of ETHYLENE INSENSITIVE3, a TF that functions downstream of ethylene signaling. RhPMP1 expression was upregulated by ethylene and specifically activated endoreduplication of parenchyma cells on the adaxial side of the petal (ADSP) base by inducing the expression of RhAPC3b, a gene encoding the core subunit of the Anaphase-Promoting Complex. Cell expansion of the parenchyma on the ADSP base was subsequently enhanced, thus resulting in asymmetric growth of the petal base, leading to the typical epinastic movement of petals and flower opening. These findings provide insights into the pathway regulating petal movement and associated flower-opening mechanisms.�.
Genetic Resources and Vulnerabilities of Major Cucurbit Crops
Genes · 2021 · 98 citations
Senior authorCorresponding- Biotechnology
- Biology
- Agroforestry
spp.). Centers of domestication in Africa, Asia, and the Americas were followed by distribution throughout the world and the evolution of secondary centers of diversity. Each of these crops is challenged by multiple fungal, oomycete, bacterial, and viral diseases and insects that vector disease and cause feeding damage. Cultivated varieties are constrained by market demands, the necessity for climatic adaptations, domestication bottlenecks, and in most cases, limited capacity for interspecific hybridization, creating narrow genetic bases for crop improvement. This analysis of crop vulnerabilities examines the four major cucurbit crops, their uses, challenges, and genetic resources. ex situ germplasm banks, the primary strategy to preserve genetic diversity, have been extensively utilized by cucurbit breeders, especially for resistances to biotic and abiotic stresses. Recent genomic efforts have documented genetic diversity, population structure, and genetic relationships among accessions within collections. Collection size and accessibility are impacted by historical collections, current ability to collect, and ability to store and maintain collections. The biology of cucurbits, with insect-pollinated, outcrossing plants, and large, spreading vines, pose additional challenges for regeneration and maintenance. Our ability to address ongoing and future cucurbit crop vulnerabilities will require a combination of investment, agricultural, and conservation policies, and technological advances to facilitate collection, preservation, and access to critical Cucurbitaceae diversity.
Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding
Nature Communications · 2020 · 156 citations
Senior authorCorresponding- Biology
- Genetics
- Botany
Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.
The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants
Cell · 2020 · 263 citations
- Biology
- Evolutionary biology
- Genetics
Cellular and Molecular Gastroenterology and Hepatology · 2020 · 100 citations
- Biology
- Microbiology
- Internal medicine
BACKGROUND & AIMS: The incidence of inflammatory bowel diseases has increased over the last half century, suggesting a role for dietary factors. Fructose consumption has increased in recent years. Recently, a high fructose diet (HFrD) was shown to enhance dextran sodium sulfate (DSS)-induced colitis in mice. The primary objectives of the current study were to elucidate the mechanism(s) underlying the pro-colitic effects of dietary fructose and to determine whether this effect occurs in both microbially driven and genetic models of colitis. METHODS: mice, respectively. RESULTS: mice and mice infected with C rodentium. CONCLUSIONS: Excess dietary fructose consumption has a pro-colitic effect that can be explained by changes in the composition, distribution, and metabolic function of resident enteric microbiota.
Nature Genetics · 2020 · 343 citations
Senior authorCorresponding- Biology
- Genetics
- Evolutionary biology
Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.
Horticulture Research · 2020 · 27 citations
- Biology
- Genetics
- Botany
genetic regulation advances our understanding of the 'foxy' aroma trait and makes it genetically trackable and amenable in grapevine breeding.
Recent grants
Frequent coauthors
- 330 shared
Yong Li
- 295 shared
Yi Zheng
Beijing University of Agriculture
- 251 shared
James J. Giovannoni
Robert W. Holley Center for Agriculture & Health
- 240 shared
Bin Wang
Soochow University
- 240 shared
Bin Wang
Qingdao University
- 193 shared
Ke Cao
University of New Brunswick
- 192 shared
Bin Wang
- 149 shared
Honghe Sun
Cornell University
Education
- 2003
Ph.D, Horticulture
Texas A&M University
- 1998
Master, Horticulture
China Agricultural University
- 1993
Bachelor, Horticulture
China Agricultural University
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