Zhangjun Fei

Research Overview

The development of high throughput technologies has given rise to a wealth of information at system level including genome, transcriptome, proteome and metabolome. However, it remains a major challenge to digest the massive amounts of information and use it in an intelligent and comprehensive manner. To address this question, Dr. Fei’s group has focused on developing computational tools and resources to analyze and integrate large scale “omics” datasets,” which help researchers to understand how genes work together to comprise functioning cells and organisms.

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Development of online databases to facilitate data distribution, analysis, mining and integration

Development of computational tools for omics data analysis

Plant MetGenMAP – a web-based tool for comprehensive mining and integration of gene expression and metabolite changes in the context of biochemical pathways.
iAssembler – A de novo assembly package for transcriptome sequences generated using 454 or Sanger platforms
iTAK – A package to identify and classify plant transcription factors and protein kinases.
VirusDetect – An automated pipeline for efficient virus discovery using deep sequencing of small RNAs.

Application of NGS technologies and bioinformatics in crop improvement

During the past several years, significant progresses have been made regarding the DNA sequencing technologies. As a result, several next-generation sequencing (NGS) platforms, such Illumina HiSeq, have received wide applications due to their high throughput and low cost. We are interested in using NGS technologies to investigate genomes, epigenomes and transcriptomes of several economically important crops including tomato, cucurbits, sweetpotato, and fruit tree crops, to facilitate the understanding of the evolution and regulatory networks of important agronomical traits. We are also using NGS technologies to perform large-scale virus survey for crops like sweet potato and tomato, in an effort to understand global virus diversity, distribution and evolution in important food crops.

Inferring gene regulatory networks

Living cells are the product of gene expression programs involving regulated transcription of thousands of genes. How a collection of transcriptional regulatory factors associates with genes during specific biological processes or under specific environmental conditions can be described as a gene regulatory network. We are interested in developing new algorithms to infer gene regulatory networks by integrating datasets from various different sources, including gene expression data, metabolomics data, promoter sequences, and microRNA information.

Lab Members

: Honghe Sun

: Jiantao Zhao

: Xuebo Zhao

: Zhe Zhou

In the News

Study Reveals Role of Allele Dosage in Improving Sweetpotato Traits
December 12th, 2024
Sweetpotatoes are an agricultural powerhouse that feeds millions globally. However, their complex genetics make it challenging for breeders to understand and improve traits like yield, disease resistance, and nutritional content. […] Read more »
Study Finds Genetic Mechanisms Behind High-Yield Apple Trees
November 25th, 2024
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Unlocking the Genetic Mysteries of Modern Roses
October 14th, 2024
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Across Oceans and Millennia: Decoding the Origin and History of the Bottle Gourd
March 20th, 2024
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Unlocking the Genetic Code of Peppers: New Study Reveals Insights into Domestication and Diversity
September 14th, 2023
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More News

Behind the Rind: New Genomic Insights into Watermelon Evolution, Quality, and Resilience
August 11th, 2023
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Watermelon Wonders: The Surprising Science Behind Your Favorite Summer Fruit
August 3rd, 2023
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BTI Welcomes 2023 High School Research Experience & Workforce Advantage Students
July 17th, 2023
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BTI Welcomes 2023 Undergraduate Student Researchers
June 12th, 2023
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Controlling insect pests by targeting genes acquired from other species
January 30th, 2023
Killing crop-damaging insects by targeting genes essential to their survival is a promising approach to pest control. Because essential genes are often conserved across multiple insect species, the challenge is […] Read more »
Wild tomato genome will benefit domesticated cousins
June 24th, 2022
Wild relatives of crops are becoming increasingly valuable to plant researchers and breeders. During the process of domestication, crops tend to lose many genes, but wild relatives often retain genes […] Read more »
BTI Welcomes Summer Student Interns
June 8th, 2022
On May 31, Boyce Thompson Institute welcomed 41 of the country’s brightest undergraduate students from universities around the country to experience the life of a researcher for 10 weeks. Ten […] Read more »
Genetic discoveries could improve spinach’s disease resistance and palatability
December 22nd, 2021
Most of us are familiar with “spinach teeth,” the harmless but gritty-chalky mouthfeel caused by the vegetable. A team of researchers from Boyce Thompson Institute (BTI) and six Chinese universities […] Read more »
Gene discovery may help peaches tolerate climate stress
March 9th, 2021
A BTI-led team has identified genes enabling peaches and their wild relatives to tolerate stressful conditions – findings that could help the domesticated peach adapt to climate change. The study, […] Read more »
Tomato’s Wild Ancestor Is a Genomic Reservoir for Plant Breeders
December 1st, 2020
Thousands of years ago, people in the region now known as South America began domesticating Solanum pimpinellifolium, a weedy plant with small, intensely flavored fruit. Over time, the plant evolved […] Read more »
Silk Road Contains Genomic Resources for Improving Apples
November 2nd, 2020
The fabled Silk Road – the 4,000-mile stretch between China and Western Europe where trade flourished from the second century B.C. to the 14th century A.D. – is responsible for […] Read more »
Congratulations Spring 2020 Graduates!
June 15th, 2020
We are pleased to announce that six BTI researchers received their degrees from Cornell University this spring. Congratulations to our newest alumni: Jason Hoki, Schroeder lab, PhD in Chemistry & […] Read more »
Algal genome provides insights into first land plants
May 21st, 2020
In order to shift from water to land – a transition that still puzzles scientists – plants had to protect themselves from drying out and from ultraviolet (UV) radiation, and they […] Read more »
Harvesting Genes to Improve Watermelons
November 1st, 2019
When many people think of watermelon, they likely think of Citrullus lanatus, the cultivated watermelon with sweet, juicy red fruit enjoyed around the world as a dessert. Indeed, watermelon is […] Read more »
BTI Welcomes Summer Student Interns
June 18th, 2019
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BTI Scientists Create New Genomic Resource for Improving Tomatoes
May 13th, 2019
Tomato breeders have traditionally emphasized traits that improve production, like larger fruits and more fruits per plant. As a result, some traits that improved other important qualities, such as flavor […] Read more »
BTI Promotes Faculty Member Fei
April 5th, 2019
David Stern, president of the Boyce Thompson Institute (BTI), is delighted to announce that faculty member Zhangjun Fei has been promoted to Full Professor on February 27, 2019. Fei was […] Read more »
New CRISPR database to catalyze collaborations
January 30th, 2019
Recently developed gene editing tools like CRISPR/Cas enable scientists to figure out the functions of myriad plant genes. While these studies could eventually lead to the creation of crops with […] Read more »
Orange is the new white: New sweetpotato data is something to be thankful for
November 2nd, 2018
The genome sequences of I. trifida and I. triloba can be used as robust references to facilitate sweetpotato breeding. The genomic resources developed in this study set the stage for increased rates of genetic gains for key traits such as yield, resistance to disease, and high beta-carotene. Read more »
Back to our roots: Insights from genomes of a plant-associated fungus and its bacterial endosymbionts
October 25th, 2018
In an article published this month in the journal New Phytologist, researchers at the Boyce Thompson Institute and the National Center for Genome Resources describe the genome sequences (DNA sequences), […] Read more »
Pear genomes show evidence of independent domestication in Asia and Europe
July 5th, 2018
Researchers from the Boyce Thompson Institute (BTI) and partnering institutions in China, the U.S., and New Zealand, report their findings on the domestication of the pear in Genome Biology. Read more »
New ‘Tomato Expression Atlas’ dives deep into the fruit’s flesh
February 5th, 2018
Researchers at BTI, Cornell and USDA published a spatiotemporal map of gene expression across all tissues and developmental stages of the tomato fruit – the genetic information underlying how a fruit changes from inside to out as it ripens. Their data is available in the new Tomato Expression Atlas (TEA). Read more »
Bottle gourd genome provides insight on evolutionary history and genetic relationships of cucurbit crops
November 30th, 2017
In their findings, researchers compared the sequenced bottle gourd genome to those of other cucurbit species, allowing them to reconstruct the ancient genomic history of the Cucurbitaceae family. Read more »
Pumpkin genomes sequenced revealing uncommon evolutionary history
October 29th, 2017
For some, pumpkins conjure carved Halloween decorations, but for many people around the world, these gourds provide nutrition. Scientists at Boyce Thompson Institute (BTI) and the National Engineering Research Center for Vegetables in Beijing have sequenced the genomes of two important pumpkin species, Cucurbita maxima and Cucurbita moschata. Read more »
New genomic insights reveal a surprising two-way journey for apple on the Silk Road
August 15th, 2017
New research out of Boyce Thompson Institute reveals surprising insights into the genetic exchange along the Silk Road that brought us the modern apple. Read more »
Newly-published spinach genome will make more than Popeye stronger
May 24th, 2017
Today in Nature Communications, researchers from BTI and the Shanghai Normal University report a new draft genome of Spinacia oleracea, better known as spinach. Additionally, the authors have sequenced the transcriptomes (all the RNA) of 120 cultivated and wild spinach plants, which has allowed them to identify which genetic changes have occurred due to domestication. Read more »
VirusDetect: a new pipeline for virus identification
November 28th, 2016
The Fei lab releases VirusDetect, an automated bioinformatics pipeline that efficiently detects viruses and viroids from large-scale, small RNA datasets. Read more »
SolGenomics Meeting Has Newest Advances in Nightshades
September 8th, 2016
Many BTI researchers will present their latest research at the 13th annual SolGenomics Conference, Sept. 12-16 in Davis, California. Read more »
The Watermelon’s Past, Present, and Future
June 1st, 2016
Watermelons have changed from a small, bitter fruit that grows wild in Africa to the most popular fruit in the world. What's next for watermelons? Read more »
BTI Scientists Envision the “Future of Food”
November 15th, 2015
What will your dinner plate look like in 2050? With discoveries from the Boyce Thompson Institute, future crops may have more nutrients and greater resistance to insects, drought and disease. Read more »
$6.5 Million Grant May Lead to Disease-Resistant Cucurbits
October 13th, 2015
A consortium of 20 researchers is using advanced genomic techniques to accelerate the development of disease-resistant varieties of cucurbit crops. BTI Associate Professor Zhangjun Fei will lead the bioinformatics and genomics part of the initiative. Read more »
From Flower to Fruit: Study Reveals Details of Tomato Formation
August 14th, 2015
BTI Researchers pinpointed which genes are important at different stages of tomato fruit development by monitoring how gene expression changed in the first four days after a flower becomes pollinated. Read more »
Student Symposium Caps Off 2015 Summer Intern Program
August 13th, 2015
“My experience was really valuable...It confirmed the fact that I want to do science...science doesn’t work a lot of the time...it’s having the motivation and determination to tackle problems that you’re always going to come across.” Juan G Read more »
BTI Welcomes New Crop of Summer Interns
May 26th, 2015
BTI welcomes 20 college-level interns for 10 weeks of research in Plant Genome Research Program, the Bioinformatics Program or the Bioenergy Education Program. Read more »
Extra DNA Creates Cucumber with All-Female Flowers
May 22nd, 2015
Researchers discover the genetics behind high-yield cucumbers that bear all-female flowers by screening 115 genome sequences to find large chromosomal variations. Read more »
Scientists Work Together to Develop Global Distribution Map of Tomato Virus
November 23rd, 2012
Boyce Thompson Institute Scientist Zhangjun Fei has teamed up with scientists from across the country to generate a comprehensive global virus distribution map for tomatoes. Read more »

Intern Projects

The development of high throughput technologies has given rise to a wealth of information at system level including genome, transcriptome, proteome and metabolome. However, it remains a major challenge to digest the massive amounts of information and use it in an intelligent and comprehensive manner. To address this question, Dr. Fei’s group has focused on developing computational tools and resources to analyze and integrate large scale “omics” datasets”, which help researchers to understand how genes work together to comprise functioning cells and organisms.

Internship Program | Projects & Faculty | Apply for an Internship

Publications

A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication

2023.

Wu, S., Sun, H., Gao, L., Branham, S., McGregor, C., Renner, S.S., Xu, Y., Kousik, C., Wechter, W.P., Levi, A,. Fei, Zhangjun

Plant Biotechnology Journal.

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Starch deficiency in tomato causes transcriptional reprogramming that modulates fruit development, metabolism and stress responses

2023.

Nicolas, P., Pattison, R.J., Zheng, Y., Lapidot-Cohen, T., Brotman, Y., Osorio, S., Fernie, A.R., Fei, Zhangjun, Catala, Carmen.

Journal of Experimental Botany.

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Transcriptomic and metabolic profiling of watermelon uncovers the role of salicylic acid and flavonoids in the resistance to cucumber green mottle mosaic virus

2023.

Liu, M., Kang, B., Wu, H., Aranda, M.A., Peng, B., Liu, L., Fei, Zhangjun, Hong, N., Gu, Q.

Journal of Experimental Botany.

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Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

2023.

Li, N., He, Q.,Wang, J., Wang, B., Zhao, J., Huang, S., Yang, T., Tang, Y., Yang, S., Aisimutuola, P., Xu, R., Hu, J., Jia, C., Ma, K., Li, Z., Jiang, F., Gao, J., Lan, H., Zhou, Y., Zhang, X., Huang, S., Fei, Zhangjun, Wang, H., Li, H., Yu, Q.

Nature Genetics.

55

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852–860

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Genomic analyses reveal dead-end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation

2023.

Yu, X., Qin, M., Qu, M., Jiang, Q., Guo, S., Chen, Z., Shen, Y., Fu, G., Fei, Zhangjun, Huang, H., Gao, L., Yao, X.

The Plant Journal.

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SnRK1 kinase-mediated phosphorylation of transcription factor bZIP39 regulates sorbitol metabolism in apple

2023.

Meng, D., Cao, H., Yang, Q., Zhang, M., Borejsza-Wysocka, E., Wang, H., Dandekar, A.M., Fei, Zhangjun, Cheng. L.

Plant Physiology.

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The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis.

2023.

Lou, H., Song, L., Li, X., Zi, H., Chen, W., Gao, Y., Zheng, S., Fei, Zhangjun, Sun, X., Wu, J.

Nat Commun..

14

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1315

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Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections

2023.

Hernandez, C.O., Labate, J., Reitsma, K., Fabrizio, J., Bao, K., Fei, Zhangjun, Grumet, R., Mazourek, M.

Frontiers in Plant Science.

14

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Loss of OPT3 function decreases phloem copper levels and impairs crosstalk between copper and iron homeostasis and shoot-to-root signaling in Arabidopsis thaliana

2023.

Chia, J.C., Yan, J., Rahmati Ishka, M., Faulkner, M.M., Simons, E., Huang, R., Smieska, L., Woll, A., Tappero, R., Kiss, A., Jiao, C., Fei, Zhangjun, Kochian, L.V., Walker, E., Piñeros, M., Vatamaniuk, O.K.

Plant Cell.

35

:

2157–2185

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Horizontally transferred genes as RNA interference targets for aphid and whitefly control

2022.

Feng, H., Chen, W., Hussain, S., Shakir, S., Tzin, V., Adegbayi, F., Ugine, T., Fei, Zhangjun, Jander, Georg

Plant Biotechnol J..

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Domestication and selection footprints in Persian walnuts (Juglans regia)

2022.

Luo, X., Zhou, H., Cao, D., Yan, F., Chen, P., Wang, J., Woeste, K., Chen, X., Fei, Zhangjun, An, H., Malvolti, M., Ma, K., Liu, C., Ebrahimi, A., Qiao, C., Ye, H., Li, M., Lu, Z., Xu, J., Cao, S., Zhao, P.

PLoS Genet..

18

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e1010513

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Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence.

2022.

Tu, X., Ren, S., Shen, W., Li, J., Li, Y., Li, C., Li, Y., Zong, Z., Xie, W., Grierson, D., Fei, Zhangjun, Giovannoni, James J., Li, P., Zhong, S.

Nat Commun..

13

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7632

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CuGenDBv2: an updated database for cucurbit genomics.

2022.

Yu, J., Wu, S., Sun, H., Wang, X., Tang, X., Guo, S., Zhang, Z., Huang, S., Xu, Y., Weng, Y., Mazourek, M., McGregor, C., Renner, S.S., Branham, S., Kousik, C., Wechter, W.P., Levi, A., Grumet, R., Zheng, Y., Fei, Zhangjun

Nucleic Acids Res..

51

:

D1457–D1464

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Loss of function of the bHLH transcription factor Nrd1 in tomato enhances resistance to Pseudomonas syringae

2022.

Zhang, N., Hecht, C., Sun, X., Fei, Zhangjun, Martin, Gregory B.

Plant Physiol..

190

:

1334–1348

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Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress.

2022.

Nicolas, P., Shinozaki, Y., Powell, A., Philippe, G., Snyder, S.I., Bao, K., Zheng, Y., Xu, Y., Courtney, L., Vrebalov, J., Casteel, C.L., Mueller, Lukas A., Fei, Zhangjun, Giovannoni, James J., Rose, J.K.C., Catalá, Carmen

Plant Physiol..

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Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors

2022.

Chen, M., Guo, L., Ramakrishnan, M., Fei, Zhangjun., Vinod, K.K., Ding, Y., Jiao, C., Gao, Z., Zha, R., Wang, C., Gao, Z., Yu, F., Ren, G., Wei, Q.

The Plant Cell.

34

:

3577–3610

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Cellular differentiation, hormonal gradient, and molecular alternation between the division zone and the elongation zone of bamboo internodes

2022.

Guo, L., Wang, C., Chen, J., Ju, Y., Yu, F., Jiao, C., Fei, Zhangjun, Ding, Y., Wei, Q.

Physiologia Plantarum.

174

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e13744

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An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion

2022.

Ban, S., El-Sharkawy, I., Zhao, J., Fei, Zhangjun, Xu, K.

The Plant Journal.

111

:

1609–1625

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Genome Sequencing of up to 6,000-Year-Old Citrullus Seeds Reveals Use of a Bitter-Fleshed Species Prior to Watermelon Domestication

2022.

Pérez-Escobar, O.A., Tusso, S., Przelomska, N.A.S., Wu, S., Ryan, P., Nesbitt, M., Silber, M.V., Preick, M., Fei, Zhangjun, Hofreiter, M., Chomicki, G., Renner, S.S.

Molecular Biology and Evolution.

39

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Long-Term Lacticaseibacillus rhamnosus GG Storage at Ambient Temperature in Vegetable Oil: Viability and Functional Assessments

2022.

Davachi, S.M., Dogan, B., Khazdooz, L., Zhang, S., Khojastegi, A., Fei, Zhangjun, Sun, H., Meletharayil, G., Kapoor, R., Simpson, K.W., Abbaspourrad, A.

Journal of Agricultural and Food Chemistry.

70

:

9399–9411

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