Children of the Sorghum
The Murphy Research Group at Centenary College of Louisiana
Our Research
"This fall, we're doing crop-fit :) "
As the world population increases, increasing food and energy demands need to be met. While technological advances from all branches of science are required to meet these needs, plant biology plays a special role in providing crops as a source for both food and fuel. The economic balance between food and fuel crops is a delicate one, therefore efforts have been taken to maintain this balance. Part of these efforts include finding optimal sources for bioenergy feedstocks that do not interfere with crops grown for food...and we're placing our bets on Sorghum bicolor!
"Our model organism can beat up your model organism."
Sorghum is one of the top five economically important food and feed crops grown worldwide, and recently, sorghum has generated interest as an energy crop, as its drought tolerance and relatively low nitrogen requirements allow it to grow on marginal lands that are unsuitable for food crops such as corn or sugarcane.
Our job is to, through breeding, germplasm screens, genetic techniques, and informatics, optimize those traits involved with the efficient production of biomass, with special emphasis on maturation time. Take a look below to see how each of us is working to achieve that goal!
The Children
Rebecca Murphy (she/her)
I obtained my Ph.D. in Biochemistry from Texas A&M University in August of 2012, where my dissertation work focused on the improvement of agriculturally important crop species. Ten days later I was in front of my first class as an assistant professor of biology at Centenary College of Louisiana. There I teach Cell Biology and Molecular Genetics, in addition to several other upper level courses. The best part, however, is getting our students involved and interested in plant biology, which we do in collaboration with the University of Arizona, Boyce Thompson Institute, Texas A&M, Ceres, Inc., and DuPont Pioneer.
Our primary research goals include understanding the molecular basis of flowering time in Sorghum bicolor, which we do using physiological studies, genomics, gene expression techniques, and other molecular approaches. We are also employing bioinformatics techniques to understand RNA diversity in the context of flowering, as well as in other developmental stages and in response to stress.
Current Students
2022 LIVE-for-Plants applications will open soon!
Graduates
Isabella Kreko
c/o 2020
Long non-coding RNAs (lncRNAs) are an abundant and functionally diverse class within eukaryotic transcriptomes. LncRNA identification and functional characterization lags behind similar efforts in protein-coding genes and microRNAs, particularly in non-model plant species. Here we describe efforts to identify and annotate lncRNAs in grape (Vitis vinifera), an important agronomic plant species. As part of the lincRNA identification and validation exercise (LIVE-for-Plants) summer research program, we processed over 2,379 experiments representing >3 terabases of publicly generated RNA-seq data from the NCBI SRA database. We processed these data using a computational pipeline consisting of RMTA and Evolinc. From these data we identified 22,255 lncRNAs that passed a stringent set of expression and sequence-level features. These lncRNAs were further examined for expression, tissue specificity, and sequence conservation relative to other species within the rosid lineage. We determined that most lncRNAs showed a higher degree of tissue specificity relative to protein-coding genes and that higher expression correlated with lower tissue specificity. We are in the process of using these data to annotate identified lncRNAs based on tissue of expression, breadth of expression, and whether the lncRNAs are differentially expressed in response to biotic stress.
See my poster: LIVE-for-Plants: identification and validation of long non-coding RNAs from grape (Vitis vinifera) RNA-seq data
Bella is currently in her first year of graduate school.
Lauren McHan
c/o 2020
Last summer, I completed an REU with Dr. Andrew Nelson and Dr. Rebecca Murphy under the LIVE for Plants program at the University of Arizona in Tucson, Arizona. This research consisted of developing RMTA which allows for read mapping and transcript assembly research. This was published in Frontiers in Genetics. Specifically I focused on Solanum lycopersicum (tomatoes). I analyzed over 5,600 GB of data from the tomato transcriptome and identified novel long intergenic noncoding RNAs (lincRNAs). With this research, I have continued at Centenary College of Louisiana to verify the expression of lincRNAs potentially involved in the role of red light in resistance against Pseudomonas syringae in tomatoes. I will be presenting my research at the Tri Beta Regional Conference as well as at the 2020 American Society of Plant Biologists Worldwide Summit.
See my poster: LIVE-for-Plants: identification and validation of long non-coding RNAs
within Solanum lycopersicum from over 4,500 public experiments
Lauren is currently in her first year of PA school.
Alexandra Naron
c/o 2020
Long non-coding RNAs (lncRNAs) are an abundant and functionally diverse class within eukaryotic transcriptomes. LncRNA identification and functional characterization lags behind similar efforts in proteins and microRNAs, even in model systems. Here we present efforts to use our RMTA and Evolinc computational pipeline to document and annotate Medicago lncRNAs from ~ 4 Terabases (TB) of RNA-seq data. These 4 TB of RNA-seq data represent all of the 1,330 RNA-seq experiments available on the NCBI SRA for Medicago. As part of the NSF-funded lincRNA identification and validation exercise (LIVE) for Plants, identified lncRNAs were annotated based on expression, tissues specificity, and sequence conservation across the legume family. The goal is to provide the plant community with an updated genome annotation for Medicago that more accurately reflects the transcribed genes in its genome. As Medicago is an excellent system for studying transcriptional responses to plant-microbe interactions, we focused on a subset of RNA-seq data to help us identify lncRNAs that may influence this interaction. We specifically examined Medicago lncRNAs differentially expressed in plants infected by the soil-born pathogen R. solani. We identified 14 lncRNAs whose expression was specifically altered under pathogen attack but not under any other tested conditions, raising the possibility that they might serve as biomarkers for plants infected by this significant pathogen. In sum, we have developed an extensive dataset of lncRNAs for Medicago, and highlighted several that specifically respond to pathogen attack.
See my poster: LIVE-for-Plants: identifying Long Non-Coding RNAs in Medicago truncatula using publicly available RNAseq data
Alex is currently in her first year of graduate school.
Rebekah Frazier
c/o 2018
I'm interested in flowering time in corn and in figuring out how it became relatively insensitive to photoperiod during domestication! To do this I am comparing genes discovered in the sorghum flowering pathway to those that have been identified in maize, and looking for allelic differences in a wide variety of maize genotypes.
I'm also interested in outreach and love to teach kids about the organelles in plant cells!
See my poster: Shedding Light on Floral Regulation in Maize
Rebekah is currently in her fourth year of medical school.
Melissa Traver
c/o 2017
The focus of my research is to understand the interactions between the protein Constans and various photoperiod responsive promoters using ChIP-seq techniques. I am also interested in the expression analysis of Nuclear Factor Y family genes to determine when these proteins might be expressed in development or throughout the course of the day. Additionally, my research has been funded in part by the Summer Undergraduate Research Fellowship from the American Society of Plant Biologists and an NSF REU!
See my poster: Analysis of Concurrently Expressed CCT‐domain Proteins During the Floral
Transition in Sorghum bicolor
The Role of Protein Interactions in the Control of Photoperiodic Flowering in Sorghum bicolor
Melissa is in her fifth year of graduate school studying plant biology at Rice University.
Manon Doucet, M.D.
c/o 2017
I look at the interactions between various proteins involved in flowering, including Constans, PRR37, Ghd7, and various Nuclear factor Y family proteins. These proteins are hypothesized to interact in various ways on the promoters of certain genes involved with photoperiod response to activate downstream transcription of florigen mRNA.
Hint: Yes, PRR37 does have something to do with it ;)
See my poster: Shining Light on the Role of Conserved CCT‐domain Proteins in Flowering in Sorghum bicolor
Manon is a practicing M.D. in her first year of residency.
Chris Cates, CRT
c/o 2016
My project involves the identification of genes involved with flowering by exploiting phenotypic differences in maturation time in sorghum populations. High-throughput genotyping of these populations via the Illumina-Hi Seq allows us to compare phenotype to genotype and locate genes using map-based cloning techniques to find genes underlying flowering QTL.
See my poster: Identification of Novel Genes Controlling Flowering Time in Sorghum bicolor
Chris is now a practicing respiratory therapist.
Morgan (Navalance) ELLEDGE, PA
c/0 2016
My work is focused on pinpointing the developmental time at which sorghum moves from juvenile to adult stage and becomes competent to flower, and understanding the regulation of flowering genes at that transition.
This is achieved using qRT-PCR to analyze the expression of genes known to be involved in flowering, such as PRR37, Ghd7, Ehd1, and others.
I also study the relationship of these genes to the circadian clock, as expression is evaluated under circadian cycling conditions.
See my poster: Examination of Genes Controlling Flowering Time During Leaf Development in Sorghum bicolor
Morgan is currently a practicing physician's assistant.
Andrea (Lemus) Brumley, M.D.
c/o 2015
In order to understand the control of flowering time in sorghum, I specifically am curious about the florigen "switch" that triggers flowering to begin. In Arabidopsis, there are only a couple of members of this FT-like family that play a main role in the transition, but in sorghum this family has expanded to include more than 20 members!
To get a better understanding about the FT-like proteins in sorghum that are truly involved in reproductive growth, I study the expression of multiple members of this family to determine whether 1) they are expressed in the correct location, 2) at the correct developmental point, and 3) whether they respond to floral inductive stimuli.
See my poster: Florigen Makes the Whorl Go Round: A Survey of the FT‐like PEBP family in Sorghum bicolor
Andrea is currently a practicing M.D. in a surgery residency.
Publications
Jolene Ramsey, Brenley McIntosh, Daniel Renfro, Suzanne A. Aleksander, Sandra LaBonte, Curtis Ross, Adrienne E. Zweifel, Nathan Liles, Shabnam Farrar, Jason J. Gill, Ivan Erill, Sarah Ades, Tanya Z. Berardini, Jennifer A. Bennett, Siobhan Brady, Robert Britton, Seth Carbon, Steven M. Caruso, Dave Clements, Ritu Dalia, Meredith Defelice, Erin L. Doyle, Iddo Friedberg, Susan M. R. Gurney, Lee Hughes, Allison Johnson, Jason M. Kowalski, Donghui Li, Ruth C. Lovering, Tamara L. Mans, Fiona McCarthy, Sean D. Moore, Rebecca Murphy, Timothy D. Paustian, Sarah Perdue, Celeste N. Peterson, Birgit M. Prüß, Margaret S. Saha, Robert R. Sheehy, John T. Tansey, Louise Temple, Alexander William Thorman, Saul Trevino, Amy Cheng Vollmer, Virginia Walbot, Joanne Willey, Deborah A. Siegele, James C. Hu. Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). (2021). PLoS Comput Biol 17(10): e1009463.
Peri, S., Roberts, S., Kreko, I.R., McHan, L.B., Naron, A.M., Ram, A., Murphy, R.L. Lyons, E., Gregory, B.D., Devisetty, U.K., Nelson, A.D.L. RMTA: A scalable and high-throughput workflow for the processing and analysis of RNA-seq data. 2020. Frontiers in Genetics, Bioinformatics and Computational Biology.
Rebecca L. Murphy, Olga Danilevskaya, Graziana Taramino, and John Mullet.
“Over-expression of sorghum flowering genes alter maturation time in maize” In preparation.
Murphy, R.L., Rodriguez, J., and Ticich, T., Introduction to Systems Biology Using Cell Illustrator. Proceedings of the 2015 Association for Biology Laboratory Education Meeting, Vol. 37. Boston University, MA. (Accepted 2016).
Yang, S., , Morishige, D.T., Klein, P.E., Rooney, W.L., and Mullet, J.E.Sorghum Phytochrome B Inhibits Flowering in Long Days by Activating Expression of SbPRR37 and SbGHD7, Repressors of SbEHD1, SbCN8 and SbCN12. (2014) PLoS ONE 9(8): e105352. doi:10.1371/journal.pone.0105352
Murphy, R.L., Morishige, D.T., Brady, J.A., Rooney, W.L., Miller, F.R., Klein, P.E., and Mullet, J.E. Ghd7 (Ma6) Represses Sorghum Flowering in Long Days: Ghd7 Alleles Enhance Biomass Accumulation and Grain Production. (2014) The Plant Genome. 7: doi:10.3835/plantgenome2013.11.0040
Mullet, J.E., Rooney, W.L., Klein, P.E., Morishige, D., , and Brady, J.A. (2010). Discovery and Utilization of Sorghum Genes (/). US. Pub. No.: US 2012/0024065 A1. Filed Jul. 21, 2009.Issue date: Jan. 28, 2010.
Murphy, R.L., Klein, R.R., Morishige, D.T., Brady, J.A., Rooney, W.L., Miller, F.R., Dugas, D.V., Klein, P.E., and Mullet, J.E. (2011). Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum. Proc. Natl. Acad. Sci. USA. 108, 16469-16474
Funding:
National Science Foundation Award Number 2023310.
PI: Andrew Nelson. Co-PIs: Brian Gregory, Eric Lyons, Rebecca Murphy.
“TRTech-PGR: Identification and characterization of stress-responsive and evolutionary conserved epitranscriptome modification sites in plant transcriptomes.” August 2020 - August 2024
National Science Foundation RO1758532 PI: Andrew Nelson. Co-PIs: Upendra Devisetty, Rebecca Murphy. “MINE-PGR: Mining public RNA-seq data to identify and annotate long non-coding RNAs in fifteen diverse angiosperms." August 2018 - August 2020.
Presentations
"MINE the Gap: lncRNA Identification as Bridge between Computational and Bench Approaches in the Undergraduate Classroom"
Murphy, R.L., Nelson, A.D.L.
2020 Plant and Animal Genome Conference (San Diego, CA)
“An Ear-ie Coincidence: Conserved Pathways Regulate Photoperiodic Flowering in Maize and Sorghum”
Murphy, R.L., Stephenson, L., Danilevskaya, O., Frazier, R., Mullet, J., Taramino, G.
2019 Centenary College 27th Annual Student Research Forum.
"The Identification of Maturity Loci Sheds Light on Photoperiodic Flowering in Sorghum"
Rebecca L. Murphy
2016 ARKLATEX.ICC Research Forum, received best presentation award.
“Introduction to systems biology using Cell Illustrator” Workshop
Rebecca L. Murphy, Juan Rodriguez, and Tom Ticich
Association for Biology Laboratory Education annual meeting 2015 (Boston, MA)
“Coincident light and clock regulation of psuedoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum”
Murphy, R.L., Klein, R.R., Morishige, D.T., Brady, J.A., Rooney, W.L., Miller, F.R., Dugas, D.V., Klein, P.E., and Mullet, J.E
2011 American Society of Plant Biologists Annual Meeting (Minneapolis, MN)
“Characterization of Maturity Genes Controlling Flowering in Response to Photoperiod in Sorghum bicolor”
Murphy, R.L., Klein, R.R., Morishige, D.T., Brady, J.A., Rooney, W.L., Miller, F.R., Dugas, D.V., Klein, P.E., and Mullet, J.E
2012 American Society of Plant Biologists Annual Meeting (Austin, TX), minisymposium on circadian rhythms
“What a Coincidence! Identification of sheds light on photoperiodic flowering in sorghum”
Rebecca L. Murphy, Daryl T. Morishige, John E. Mullet
Student Research week, Texas A&M University
Student Presentations
“LIVE-for-Plants: Identification and validation of long non-coding RNAs from grape (Vitis vinifera) RNA-seq data”
Kreko, I.R., Murphy, R.L., Nelson, A.D.L.
Plant Biology Worldwide Summit 2020 (Virtual)
“LIVE-for-Plants: Identification and validation of long non-coding RNAs within Solanum lycopersicum from over 4,500 public experiments”
McHan, L., Murphy, R.L., Nelson, A.D.L.
Plant Biology Worldwide Summit 2020 (Virtual)
“LIVE-for-Plants: Identification and validation of long non-coding RNAs in Medicago truncatula using publicly available RNAseq data”
Naron, A., Murphy, R.L., Nelson, A.D.L.
Plant Biology Worldwide Summit 2020 (Virtual)
"Shedding Light on Floral Regulation in Maize"
Frazier, R.D., Morishige D.T., Mullet, J.E., Murphy, R.L.
American Society of Plant Biologists Annual Meeting 2017 (Honolulu, HI)
“The Role of Protein Interactions in the Control of Photoperiodic Flowering in Sorghum bicolor”
Traver, M.S, Morishige, D.T, Mullet, J.M, Murphy, R.L.
American Society of Plant Biologists Annual Meeting 2016 (Austin, TX)
“Shining Light on the Role of Conserved CCT – domain Proteins in Flowering in Sorghum bicolor”
Doucet, M., Morishige, D.T, Mullet, J.M, Murphy, R.L.
2016 Centenary College 25th Annual Student Research Forum; received 1st place.
“Analysis of Concurrently Expressed CCT-domain Proteins During the Floral Transition in Sorghum bicolor”
Traver, M.S, Morishige, D.T, Mullet, J.M, Murphy, R.L.
2016 Centenary College 25th Annual Student Research Forum; received 2nd place.
“Shining Light on the Role of Conserved CCT-domain Proteins in Flowering in Sorghum bicolor”
Doucet, M., Morishige, D.T, Mullet, J.M, Murphy, R.L.
American Society of Plant Biologists Annual Meeting 2015 (Minneapolis, MN)
“Analysis of Concurrently Expressed CCT-domain Proteins During the Floral Transition in Sorghum bicolor”
Traver, M., Lemus, A., Navalance, M.A., Morishige, D.T, Mullet, J.M, Murphy, R.L.
American Society of Plant Biologists Annual Meeting 2015 (Minneapolis, MN)
“Identification of Novel Genes Controlling Flowering Time in Sorghum bicolor”
Cates, C.A., Navalance, M.A., Morishige, D.T., Mullet, J.M., Murphy, R.L.
Centenary College 24th Annual Student Research Forum; received 1st place.
“Examination of Genes Controlling Flowering Time During Leaf Development in Sorghum bicolor”
Navalance, M.A., Cates, C.A., Morishige, D.T, Mullet, J.M, Murphy, R.L.
Centenary College 24th Annual Student Research Forum; received 1st place.
“Examination of Genes Controlling Flowering Time During Leaf Development in Sorghum bicolor”
Navalance, M.A., Cates, C.A., Morishige, D.T, Mullet, J.M, Murphy, R.L.
2014 American Society of Plant Biologists Annual Meeting (Portland, OR)
“Identification of Novel Genes Controlling Flowering Time in Sorghum bicolor”
Cates, C.A., Navalance, M.A., Morishige, D.T., Mullet, J.M., Murphy, R.L.
2014 American Society of Plant Biologists Annual Meeting (Portland, OR)
“Florigen Makes the Whorl Go Round:A Survey of the FT-like PEBP family in Sorghum bicolor”
Andrea Lemus, Daryl T. Morishige, John E. Mullet, Rebecca L. Murphy
Centenary College 23rd Annual Student Research Forum; received 3rd place.
“Florigen Makes the Whorl Go Round:A Survey of the FT-like PEBP family in Sorghum bicolor”
Lemus, A., Morishige, D.T., Mullet, J.E., Murphy, R.L.
2013 Biology Enthusiasts Association of Students at Tulane (BEAST) Undergraduate Research Symposium (New Orleans, LA)
“Florigen Makes the Whorl Go Round:A Survey of the FT-like PEBP family in Sorghum bicolor”
Lemus, A., Morishige, D.T., Mullet, J.E., Murphy, R.L. 2013 American Society of Plant Biologists Annual Meeting (Providence, RI)
“Functional Annotation of Ebola and Marburg Virus Proteins via Community Assessment of Community Annotation with Ontologies”
Lindsey Fileccia, Rebecca Murphy.
Centenary College 22nd Annual Student Research Forum; received 3rd place.