WELCOME TO THE THE KELLOGG LAB

Located at the Donald Danforth Plant Science Center

 

Our Research

Welcome to the Kellogg Lab at the Donald Danforth Plant Science Center. As you can see in the descriptions of projects below, the lab is a small business supported by grant funding, much of which represents federal tax dollars brought home to Missouri.  Like the other labs in the Center, we are an employer, a small business that keeps the economic engine of the city running. This is one part of the Center’s mission to “enhance the St. Louis region as a world center for plant science.”


“Feed the hungry and improve human health”


This is the central mission of the Center. We believe that food security is a human right, and that plant scientists have an obligation to contribute to feeding the growing global population. Cereal crops in the grass family - including rice, maize (corn), wheat, sorghum, barley, and oats - have fed civilizations for millennia, and are the center of our research.  These crops were selected by humans from an entire ecosystem of wild grasses, which dominate more than 25% of the land area of the earth. In our lab, we study how these wild plants grow, make seeds, and adapt to drought and floods. Another mission of the Center is to “preserve and renew the environment.” By studying cereal crops and their relatives in the grass family, we can then predict how wild species may adapt to a warmer, drier climate.


Our research in the Kellogg Lab, along with that of the Center’s many talented scientists, contributes to a bigger picture: increase our understanding of the underlying mechanisms of plants, so we can make more resilient crops, and protect and enhance one of Earth’s most precious resources – food.

 
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RESEARCH-PGR: PANAND: Harnessing convergence and constraint to predict adaptations to abiotic stress for maize and sorghum

NSF: IOS-PGRP, 2018-2022, https://panandropogoneae.com/

Increases in crop productivity will be crucial if we are to feed a growing world population and expanding adaptation of crops to a diverse range of environments would help immensely. However, to design crops to be adapted to a wider range of environments will require more knowledge on the genetic variation that produces phenotypic variation and adaptation. This project proposes to use nearly a thousand species, collectively representing over a billion years of evolutionary history, to understand the rules of convergence and constraint in the genomes with an aim to model fitness under drought and temperature stress. The sampling will focus on Andropogoneae, a tribe of grass that are among the most productive and water efficient plants, but for which breeding has taken advantage of variation in only a few species such as maize, sorghum, and sugarcane. By combining genomics, population genetics, and computational biology, DNA variants, genes, mechanisms, and pathways critical for performance and tolerance to heat and drought will be identified.

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Integration and modularity in grass diversification

NSF: DEB-Systematics and Biodiversity, 2019-2022

This project will incorporate the treasure trove of data the PANAND project will produce, and relate it to morphological studies of the Andropogoneae.

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Developing phenotypic and genomic tools to study salt tolerance in seashore paspalum (US Golf Association)

A collaboration with Ken Olsen, Washington University, and Ivan Baxter, DDPSC

Plants have a hard time growing in salty soil because the salt interferes with the uptake and movement of water.  This project investigates a highly salt tolerant grass, Seashore paspalum (Paspalum vaginatum), which is a turfgrass used for golf courses on salty sites such as coastal dunes. This project aims to determine the genetic basis of salt tolerance in seashore paspalum, using 1) new methods to measure the amount of salt in the plant (“ionomics”), 2) whole-genome sequencing (“genomics”) and 3) wild population samples, which may be even more salt tolerant.  Improving turfgrass to handle salt affected soils is a goal of the golf industry, and is also directly relevant to agriculture. The new methods used in this project will make salt tolerance measurements more precise, and this added precision will increase the efficiency of turfgrass breeding and research. Our use of whole genome data will provide genetic tools not commonly seen in breeding programs outside of the world’s staple food crops. The development of more robust turfgrass cultivars that require less fresh water and fewer chemical treatments is a critical step in increasing the environmental sustainability of the golf industry.

People

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Elizabeth Kellogg

Principal Investigator

Ph.D. Harvard University, USA.

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Yunqing Yu

Postdoctoral Associate

B.A.  in biology, Nankai University, China
Ph.D. in Plant Biology, Penn State, University, USA

"My PhD dissertation studied the functions of heterotrimeric G proteins in salinity tolerance and guard cell responses, using Arabidopsis as a model species. My current project focuses on abscission zone development in grasses. I am fascinated by the vast diversity of plants, and am interested in understanding the molecular mechanisms underlying plant developmental programs using comparative approaches."

Get in Touch
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Kurt Petersen

Postdoctoral Associate

"I am interested in the evolutionary history of morphological traits and understanding the adaptive advantages they provide. My PhD focused on the evolutionary history of heterospory in the land plants with a focus on the lycophytes and water ferns. My current work is looking at the evolutionary ecology and phylogenetic relationships of grasses in the Andropogoneae. The unique flowering structures of grasses are poorly understood from a macro ecology perspective and offer a wide variety of unexplored evolutionary questions."

Get in Touch
 
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Taylor AuBuchon-Elder

Senior Lab Technician

B.A. Biology, Minor Sustainability, Webster University, USA

Taylor has been researching the Andropogoneae grass clade as Dr. Kellogg’s technician for the past 4 years. She takes care of the live plant collections in their greenhouse as well as running experiments within the lab. Currently, she is managing field collections and germplasm care for the PANAND local adaptation project (NSF: IOS-PGRP, 2018-2022). Her interests include field botany, conservation science, restoration ecology, ethnobotany, and project management. She enjoys working collaboratively and providing mentorship to visiting undergraduate and high school students.

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David Goad

Graduate Student

B.S. in Biology, Valparaiso University, USA
PhD student at Washington University
Co-advised by Ken Olsen and Toby Kellogg

"I am interested in using population genomics and quantitative genetics to understand the evolution of interesting traits in wild species. For my thesis, I am investigating the evolution of salt-tolerance in the halophytic turf grass seashore paspalum by utilizing genome-wide SNP markers and tissue ion concentrations obtained from a diverse panel of turf cultivars and wild samples. In addition to my thesis project I am involved in mapping disease resistance QTLs in rice and using bioinformatics techniques to study the CLE gene family."

Get in Touch
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Patrick Minx

Technician

B.S. Forestry, Fisheries and Wildlife, University of Missouri Columbia

M.S. Biology, University of Missouri St. Louis

Pat joined the Kellogg Lab in August 2019 to work on the PANAND local adaptation project with Taylor and Toby. He brings extensive research experience with him from his work at the McDonnell Genome Institute at Washington University where he worked on the Human Genome Project. Now, he is applying his skills to plant research at the Danforth Center. His interests include herpetology and genomics.

 

Other Lab Associates

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Peter Stevens

B.A. Oxford University
Ph.D. University of Edinburgh

Peter's interests center on digesting information on seed and plant phylogeny, evolution and diversification as it appears, and making it readily available in the Angiosperm Phylogeny Website

 

Recent Publications

 

2020

Yu, Y., H. Hu, A. N. Doust, and E. A. Kellogg. 2020. Divergent gene expression networks underlie morphological diversity of abscission zone development in grasses (Poaceae).  New Phytologist 225: 1799-1815. doi.org/10.1111/nph.16087.


Bianconi, M. E., J. Hackel, M. S. Vorontsova, A. Alberti, W. Arthan, S. V. Burke, M. R. Duvall, E. A. Kellogg, S. Lavergne, M. R. McKain, A. Meunier, C. P. Osborne, P. Traiperm, P.-A. Christin, and G. Besnard.  2020. Continued adaptation of C4 photosynthesis after an initial burst of changes in the Andropogoneae grasses.  Systematic Biology 69: 445-461.

Yu, Y., P. Leyva, R. Tavares, and E. A. Kellogg.  2020. The anatomy of abscission zones in Poaceae changes rapidly in evolutionary time.  American Journal of Botany 107: 549-561.  doi.org/10.1002/ajb2.1454


Kellogg, E. A., J. R. Abbott, K. S. Bawa, K. N. Gandhi, B. R. Kailash, U. Babu Shrestha, and P. Raven.  2020. Checklist of the grasses of India.  Phytokeys: in press.


Li, M., M.-R. Shao, D. Zeng, T. Ju, E. A. Kellogg, and C. N. Topp.  2020. Comprehensive digital 3D phenotyping reveals continuous morphological

variation across genetically diverse sorghum inflorescences. New Phytologist: in press.

Yu, Y. (2020). Commentary: LACCASE2 negatively regulates lignin deposition of Arabidopsis roots. Plant Physiology 182 (3), 1190-1191

Yu, Y. (2020). Commentary: Paving the way for C4 evolution: study of C3-C4 intermediate species in grasses. Plant Physiology 182 (1), 453

2019

One Thousand Plant Transcriptomes Initiative.  2019.  One thousand plant transcriptomes and the phylogenomics of green plants.  Nature 574: 679-685.

Teisher, J. K., M. R. McKain, and B. A. Schaal, and E. A. Kellogg. 2019. Evolution of C4 photosynthesis in subfamily Micrairoideae (Poaceae). Systematic Botany 44: 32-40.  doi: 10.1600/036364419X697877 

Kumar, D., and E. A. Kellogg.  2019. Tansley Insight: Getting closer: vein density in C4 leaves. New Phytologist 221: 1260-1267.

Welker, C. A. D., M. R. McKain, M. S. Vorontsova, M. C. Peichoto, and E. A. Kellogg.  2019. Plastome phylogenomics of sugarcane and relatives confirms the segregation of the genus Tripidium (Poaceae-Andropogoneae). Taxon 68: 246-267. doi.org/10.1002/tax.12030 

Yu, Y., H. Hu, A. N. Doust, and E. A. Kellogg. 2019. Divergent gene expression networks underlie morphological diversity of abscission zone development in grasses (Poaceae).  New Phytologist: early view. doi.org/10.1111/nph.16087


Kellogg, E. A. 2019.  Different ways to be redundant.  Nature Genetics 51: 770-771. Doi: 10.1038/s41588-019-0406-y


Submitted: Huang, P., S. Mamidi, A. Healey, J. Grimwood, J. Jenkins, K. Barry, A. Sreedasyam, S. Shu, M. Feldman, J. Wu, Y. Yu, C. Chen, J. Johnson, H. Sakakibara, T. Kiba, T. Sakurai, D. Rokhsar, I. Baxter, J. Schmutz, T. P. Brutnell, E. A. Kellogg.  The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene. Submitted to Nature Biotechnology. Preprint at: https://www.biorxiv.org/content/10.1101/744557v1

2018

Yu, Y., and E. A. Kellogg.  2018. Inflorescence abscission zones in grasses: diversity and genetic regulation. Annual Plant Reviews 1: 1-35. doi: 10.1002/9781119312994.apr0619.


Zhu, C., J. Yang, M. C. Box, E. A. Kellogg, and A. L. Eveland.  A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics. Frontiers in Plant Science 9: 1309. doi: 10.3389/fpls.2018.01309.


McAllister, C., M. R. McKain, M. Li, B. Bookout, and E. A. Kellogg.  Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium. Philosophical Transactions of the Royal Society, Series B 374: 20170403.  


Teisher, J. K., M. R. McKain, and E A. Kellogg.  Evolution of C4 photosynthesis in the Micrairoideae (Poaceae). Systematic Botany 44: 32-40.  doi: 10.1600/036364419X697877. 


Welker, C. A. D., M. R. McKain, M. S. Vorontsova, M. C. Peichoto, and E. A. Kellogg.  Plastome phylogenomics of sugarcane and relatives confirms the segregation of the genus Tripidium (Poaceae-Andropogoneae). Taxon 68: 246-267. doi.org/10.1002/tax.12030


Kumar, D., and E. A. Kellogg.  Tansley Insight: Getting closer: vein density in C4 leaves.. New Phytologist 221: 1260-1267.

2017

Zhong, J., J. C. Preston, L. Hileman, and E. A. Kellogg.  Parallel losses of corolla bilateral symmetry correlate with distinct developmental genetic changes in the Lamiales.  Annals of Botany: in press

Huang, P. H. Jiang, K. Barry, J. Jenkins, J. Schmutz, M. S. Box, C. Zhu, E. A. Kellogg, and T. P. Brutnell.  2017.  The sparse panicle1 gene of Setaria viridis and maize is required for inflorescence branch development and root agravitropism. Nature Plants: 3: 17054.  DOI: 10.1038/nplants.2017.54 | www.nature.com/natureplants

Welker, C. A. D., T. T. de Souza-Chies, M. C. Peichoto, R. P. Oliveira, L. C. Carvalho, V. B. S. Mucillo, E. A. Kellogg, E. Kaitchuk-Santos. A new allopolyploid species of Saccharum (Poaceae - Andropogoneae) from South America, with notes on its cytogenetics. Systematic Botany: 42: 507-515. Doi.org/10.1600/036364417X696005

J. K. Teisher, M. R. McKain, B. A. Schaal and E. A. Kellogg..  Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn. Annals of Botany: in press. Doi.org/10.1093/aob/mcx058

Arthan, W., M. R. McKain, P. Traiperm, C. A. D. Welker, J. K. Teisher, and E. A. Kellogg.  Relationships of Southeast Asian Andropogoneae (Poaceae). Systematic Botany: 42: 418-431. Doi.org/10.1600/036364417X696023

Saeidi, S., M. R. McKain, and E. A. Kellogg.  High throughput DNA isolation and Illumina sequencing library construction for grasses from herbarium
specimens. JOVE (Journal of Visualized Experiments): in press.

Gehan, M. A., and E. A. Kellogg. 2017.  High-throughput phenotyping. American Journal of Botany doi:10.3732/ajb.1700044

2016

Kellogg, E. A. 2016.  Has the connection between polyploidy and diversification actually been tested?  Current Opinion in Plant Biology 30: 25-32. doi: 10.1016/j.pbi.2016.01.002

Kellogg, E. A. 2016.  Evolution of Setaria.  In A. Doust and X. Diao, eds. Genetics and genomics of Setaria. Springer. In press.

​S. Schröder, D. M. Eudy, D. Layton, E. A. Kellogg, B. A. Bahri, and K. M. Devos.  2016.  Genetic diversity and origin of North American green foxtail [Setaria viridis (L.) Beauv.] accessions. Genetic Resources and Crop Evolution. doi: 10.1007/s10722-016-0363-6

Welker, C. A. D., T. T. de Souza-Chies, H. M. Longhi-Wagner, M. C. Peichoto, M. R. McKain, E. A. Kellogg.  2016.  Phylogeny of Eriochrysis P. Beauv. (Poaceae – Andropogoneae) based on low-copy nuclear genes and complete plastome sequences: taxonomic implications and evidence of interspecific hybridization. Molecular Phylogenetics and Evolution 99: 155-167. 

Hodge, J. G., and E. A. Kellogg. 2016. Morphology and characterization of abscission zone development and domestication in Setaria viridis and Setaria italica. American Journal of of Botany. 103: 998-1005.  doi: 10.3732/ajb.1500499

Huang, P., A. J. Studer, J. Schnable, E. A. Kellogg, and T. P. Brutnell.  2016. Cross species selection scans identify components of C4 photosynthesis in the grasses. Journal of Experimental Botany.  doi:10.1093/jxb/erw256

Hackenberg, D., M. McKain, S. G. Lee, T. McCann, S. Schrier, J. M. Jez, E. Kellogg, and S. Pandey.  2016.  Gα:RGS protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants. New Phytologist: doi: 10.1111/nph.14180.

McKain, M. R., R. Hartsock, M. Wohl, and E. A. Kellogg.  2016. Verdant: Automated annotation, alignment, and phylogenetic analysis for whole chloroplast sequences. Bioinformatics 33: 130-132.  doi: 10.1093/bioinformatics/btw583

Studer, A. J., J. C. Schnable, S. Weissmann, A. R. Kolbe, M. R. McKain, Y. Shao, A. B. Cousins, E. A. Kellogg, T. P. Brutnell.  2016. The draft genome of Dichanthelium oligosanthes: A C3 panicoid grass species.  Genome Biology 17: 223. doi: 10.1186/s13059-016-1080-3.

Goad, D., C. Zhu, and E. A. Kellogg.  2016. Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function. New Phytologist: doi: 10.1111/nph.14348. 

2015

Grotewold, E., J. Chappell, and E. Kellogg.  2015.  Plant Genes, Genomes and Genetics.  Wiley-Blackwell 
ISBN: 978-1-119-99888-4.  

Kellogg, E. A.  2015.  Poaceae. In K. Kubtizki, ed., The Families and Genera of Vascular Plants.  Springer.  In press.

Zhong, J., and E. A. Kellogg.  2015. Duplication and expression of CYC2-like genes in the origin and maintenance of floral symmetry in Lamiales.  New Phytologist 205: 852-868.  doi 10.1111/nph.13104.
      
Welker, C. A. D., T. Teixeira de Souza-Chies, H. M. Longhi-Wagner, M. C. Peichoto, M. R. McKain, E. A. Kellogg.  2015. Phylogenetic analysis of Saccharum s.l. (Poaceae-Andropogoneae), with emphasis on the South American species.  American Journal of Botany 102: 248-263.  doi:10.3732/ajb.1400397

​Zhong, J., and E. A. Kellogg.  2015. Stepwise evolution of the expression pattern of corolla symmetry patterning genes CYC2-like and RAD-like in Lamiales.  American Journal of Botany 102: 1260-1267. doi: 10.3732/ajb.1500191
 
Welker, C. A. D., T. T. de Souza-Chies, H. M. Longhi-Wagner, M. C. Peichoto, M. R. McKain, E. A. Kellogg.  2016.  Phylogeny of Eriochrysis P. Beauv. (Poaceae – Andropogoneae) based on low-copy nuclear genes and complete plastome sequences: taxonomic implications and evidence of interspecific hybridization. Molecular Phylogenetics and Evolution.  In press.
 
 Kellogg, E. A.  2015.  Poaceae. In K. Kubtizki, ed., The Families and Genera of Vascular Plants.  Springer.
Grotewold, E., E. A. Kellogg, and J. Chappell,.  2015. Plant genes, genomes and genetics.  Wiley.
Judd, W. S., C. S. Campbell, E. A. Kellogg, P. F. Stevens, and M. J. Donoghue. 2015. Plant Systematics: A phylogenetic approach. 4th edition. Sinauer Associates: Sunderland, MA. 

Kellogg, E. A.  2015.  Brachypodium distachyon as a genetic model system.  Annual Review of Genetics 49: 1-20. 
 
Miller, A. J., A. Novy, J. Glover, J. E. Maul, P. Raven, and P. Wyse Jackson.  2015.  Plants, agriculture and the future of food: expanding the role of botanical gardens.  Nature Plants 1: 15078.

Kellogg, E. A.  2015.  Genome sequencing: Long reads for a short plant.  Nature Plants 1: 15169.  DOI: 10.1038/nplants.2015.169.

Outreach & Honors

 

2020

Toby was elected as a member of the National Academy of Sciences!

Toby spoke at Corteva Plant Breeding Symposium, Ithaca, NY, April 2020 (virtual) and at the Departmental seminar, University of Pennsylvania, Philadelphia, PA

Yunqing and Taylor judge science projects for Academy of Science St. Louis Science Fair

Taylor was selected for the Botanical Society of America Public Policy Award to attend Congressional Visits Day with the AIBS (postponed due to COVID-19)

We welcome our new postdoc, Kurt, to the Kellogg Lab!

2019

The St. Louis Post-Dispatch published a story on David’s Paspalum project, https://www.stltoday.com/business/local/missouri-researchers-study-golf-course-grass-to-address-agricultural-challenges/article_1ff3b7af-5f02-5b73-8461-0bb491273007.html

Toby participated in the Women in STEM panel, Washington University

Toby presented on the tallgrasses of the Missouri prairie, Webster Groves Nature Study Society

UMSL Daily, article on mentoring featured Toby,  https://blogs.umsl.edu/news/2018/12/03/crowell-nuraini/

Yunqing gave an oral presentation on her research " Diversity of abscission zone development and underlying transcriptomic regulation in grasses” at the pre-meeting of the 61st Annual 

Maize Genetics Conference. March


Yunqing volunteered for STEM day teaching “grocery store botany” at Meadows Elementary School, St. Louis. March


Yunqing volunteered at the MO Middle School Science Bowl Competition. March


A high school student Molly Li from STARs program and a REU Patricia Leyva joined the lab for their summer internship. They studied the genetic control and abscission zone diversity in grasses. 


Patricia Leyva presented a poster at the ASPB meeting on her REU project "Abscission Zone Anatomy of Grasses Changes Rapidly Through Evolutionary Time”

2018


  • Two high school students in the STARS (Students and Teachers as Research Scientists) program joined the lab for the summer mentored by Taylor, Rachel, and Mei. They studied meristem regulator genes and screened for mutants in Setaria viridis. They then presented their work at UMSL after 6 weeks of hard work!

  • Yunqing Yu joined the team of Associate Features Editors at Plant Physiology and published a commentary on ring chromosomes (doi.org/10.1104/pp.18.00083). March 2018

  • Yunqing Yu volunteered as a poster judge for the Missouri Tri-County Regional Science and Engineering Fair. March 2018

  • Yunqing Yu volunteered for the Raspberry Pi Jam event held at Donald Danforth Plant Science Center. January 2018

  • We are pleased to welcome our former intern and newest lab technician, Rachel Foister! She will be assisting Yunqing and Dhinesh in their research and gain experience for graduate school. This is another reason Danforth Center internships are so valuable; you may return as a future employee! If you'd like to learn more about the Center's undergraduate internship program, visit www.danforthcenter.org/education-outreach/research-internships

2017

  • Chuanmei Zhu was invited to talk at the Local Auxin Meeting in Tyson Research Center, MO on "Understanding the function of auxin influx carrier genes in grasses using Setaria as a model"

  • Chuanmei Zhu gave a talk at the Second International Setaria Genetics Conference and wrote a meeting report for this conference. Zhu C., Yang J., and Shyu C. (2017). "Setaria comes of age: meeting report on the second International Setaria Genetics Conference. Frontiers in Plant Science. 28.

  • E. A. Kellogg and Peter Stevens participated in STEM day at Jury Elementary School, Florissant, MO, March

  • E. A. Kellogg presented a seminar at the Max Planck Institute for Plant Breeding, Cologne, Germany, April

  • Olivia Crowell is joining the lab for summer as a STARS student; and Rachel Foister will be our REU intern

  • E. A. Kellogg and Michael McKain were featured in the Roots & Shoots Blog by the Donald Danforth Plant Science Center https://www.danforthcenter.org/news-media/roots-shoots-blog/blog-item/preserving-and-renewing-the-environment

  • E. A. Kellogg, Taylor AuBuchon, and Tina Zudock participated in the Girl Scouts of Eastern Missouri's and the Danforth Center's "Girls STEAM Ahead" program, which inspires girls in grades 2-12 to get involved in science, technology, engineering, art and math (STEAM).

  • E. A. Kellogg presented seminars at the University of Nebraska-Lincoln, Arnold Arboretum of Harvard University, the Boyce Thompson Institute in Ithaca, New York, and Washington University in St. Louis, Missouri

  • E. A. Kellogg gave a Science Day presentation to 2nd and 3rd graders, Jury Elementary School, Hazelwood, Missouri

  • Paper and poster contributions: St. Louis area Evolution, Ecology and Conservation Retreat, St. Louis University, 1 poster; Botanical Society of America, Forth Worth, Texas, 1 poster; Maize Genetics Meeting, St. Louis, Missouri, 4 posters; 

2016

  • E. A. Kellogg taught at the Cereal Genomics Workshop, Cold Spring Harbor Laboratory

  • E. A. Kellogg taught a workshop on grasses for high school teachers, Purdue University, IN

  • ​(June) Our REU summer interns and STARS students have arrived! Welcome Tina from WashU, Abigail from UMSL, Callista and Alex!

  • Chuanmei Zhu has joined the Kellogg Lab. Welcome!

  • Michael McKain was invited to talk in a seminar series at Michigan State University, Lansing, MI, on "Modern Consequences of Ancient Polyploidy: Comparative Phylogenomics of Maize Subgenomes," and at Kennesaw State University, Kennesaw, GA, on "Phylogenomics and Evolution of Ecologically Dominant Grasses."

  • E. A. Kellogg was selected by the American Association for the Advancement of Science (AAAS) to serve as chair-elect for the Biological Sciences Section ​

Tools

 
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Verdant

Verdant provides an easy-to-use environment for visualization, annotation, manipulation, alignment, and phylogenomic analysis of whole chloroplast genomes. Verdant is hosted by CyVerse and is built on a growing database of chloroplast genomes.

Includes a user friendly step-by-step tutorial

Visit this link to get started 

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Fast-Plast

Fast-Plast is a pipeline that leverages existing and novel programs to quickly assemble, orient, and verify whole chloroplast genome sequences. For most datasets with sufficient data, Fast-Plast is able to produce a full-length de novo chloroplast genome assembly in approximately 30 minutes with no user mediation.
Currently, Fast-Plast is written to accomodate Illumina data, though most data types could be used with a few changes.

Fast-Plast uses a de novo assembly approach by combining the de bruijn graph-based method of SPAdes with an iterative seed-based assembly implemented in afin to close gaps of contigs with low coverage. The pipeline then identifies regions from the quadripartite structure of the chloroplast genome, assigns identity, and orders them according to standard convention. A coverage analysis is then conducted to assess the quality of the final assembly.

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Primaclade

Primaclade is a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of PCR primers that will bind across the alignment. The Primaclade program iteratively runs the Primer3 application for each alignment sequence and collates the results. The user may adjust a number of parameters to improve and refine the results. These options include: 1) the maximum number of degenerate base pairs allowed, 2) the number of gapped lines in the alignment to ignore, 3) a region of the alignment to exclude for primer discovery, 4) the primer melting temperature and 5) the approximate GC content of the primer. Primaclade creates an HTML results page that recaps the original alignment, provides a consensus sequence and lists primers for each alignment area. In addition, the generated primers are color-coded to reflect the level of degeneracy in the primer.

Click here to go to the Primaclade website

Please note that the server that hosts Primaclade has no back-up power, so whenever the electricity flickers the server goes down.  If you are unable to access the site, please contact Elizabeth Kellogg, ekellogg@danforthcenter.org

 

Gallery

Life in the Kellogg Lab

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2017 Kellogg Lab

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Meeting with Andrew Doust and Hao Hu

Sorghum panicle collecting at Bradford Research Center, Columbia, Missouri

Field work with STARS students

Kellogg greenhouse
Kellogg greenhouse

Field work with STARS students

Summers with undergraduate REU interns

2016 Lab and summer interns

Shaw Nature Reserve Field Trip

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High school STARS students presenting their summer research at UMSL

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High school STARS students presenting their summer research at UMSL

 

Useful Links

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University of Missouri-St. Louis Biology Department

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American Society of Plant Taxonomists

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Botanical Society of America

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Society of Systematic Biologists

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Angiosperm Phylogeny Website

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Missouri Botanical Garden

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Donald Danforth Plant Science Center

 

Contact Us

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