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.
Development of online databases to facilitate data distribution, analysis, mining and integration
- Tomato Functional Genomics Database
- Tomato Epigenome Database
- Cucurbit Genomics Database
- Kiwifruit Genome Database
- Whitefly Genomics Database
- Chinese Tomato Virome
- Pan-African Sweet Potato Virome
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.
- 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, co-led by Boyce Thompson Institute faculty member Zhangjun Fei, examined the genomes of peach’s wild relatives and landraces – varieties that have adapted over a […] Read more »
- 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 into S. lycopersicum – the modern cultivated tomato. Although today’s tomatoes are larger and easier to farm compared with their wild ancestor, they also are […] Read more »
- 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 one of our favorite and most valuable fruits: the domesticated apple (Malus domestica). Snack-packing travelers would pick apples at one spot, eat them and toss […] Read more »
- 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 & Chemical Biology, Dissertation title: “Development of click-chemistry based enrichment strategies to characterize ligand binding and metabolism” Jennifer Wilson, Heck lab, PhD in Plant Pathology, Thesis […] Read more »
- 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 had to develop structures to support themselves without the buoyancy provided by water. Researchers including BTI’s Zhangjun Fei found footprints of all these adaptations in […] Read more »
- 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 one of the world’s most popular fruits, second only to tomato – which many consider a vegetable. But there are six other wild species of […] Read more »
- 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 and disease resistance, were lost. Researchers from Boyce Thompson Institute and colleagues from partnering institutions have created a pan-genome that captures all of the genetic […] Read more »
- 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 evaluated on his achievements to date and the potential he possesses. Fei has made a name for himself as one of the world’s foremost experts […] Read more »
- 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 improved traits like increased disease resistance or higher yield, researchers first need a good way to keep track of the increasingly large amounts of resulting […] Read more »
- 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 endosymbiontsIn 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), of the fungus Diversispora epigaea (formerly known as Glomus versiforme) and its endosymbionts – beneficial bacteria that live inside its cells. D. epigaea is a […] Read more »
- 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 »
- 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 cropsIn 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 »
- 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 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 »
- 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 »
- The Fei lab releases VirusDetect, an automated bioinformatics pipeline that efficiently detects viruses and viroids from large-scale, small RNA datasets. Read more »
- Many BTI researchers will present their latest research at the 13th annual SolGenomics Conference, Sept. 12-16 in Davis, California. Read more »
- 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 »
- 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 »
- “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 »
- 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 »
- 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 »
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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