Lopez, Carlos Rodriguez

Environmental Epigenetics and Genetics Group – LCC Cluster

PI Dr. Carlos Lopez Rodriguez

**Project 1. Influence of vegetative propagation on methylome rejuvenation and its effect on gene expression in Vitis vinifera cv. Cabernet Sauvignon**

Epigenetic priming has been proposed as a system to produce locally adapted cultivars. This is especially significant for vegetatively propagated perennial woody crops with protracted breeding programs. For this to be effective, vegetative propagating methodologies must allow the maintenance of epigenetic memory. Unfortunately, the mechanisms regulating epigenetic memory maintenance in perennials are not well understood. Our previous work suggests that vegetative propagation of grapevine using callused cuttings results in the rejuvenation of the methylome of the propagules which leads to a partial erasing of environmentally induced and age acquired epigenetic memory in the propagules. To understand the mechanism controlling this loss of epigenetic memory, we are using a multi-omics approach which includes: RNA-Sequencing, Small RNA Sequencing, whole genome re-sequencing, whole genome bisulphite sequencing and ChiP sequencing.

Students:

Harshraj Shinde, Horticulture, Post-doc, LCC Resources, MCC Resources 04/13/2022

Tajbir Raihan, Horticulture, Graduate, LCC Resources, MCC Resources 04/13/2022

Lakshay Anand, Horticulture, Graduate, Bioinformatician, LCC Resources, MCC Resources 04/13/2022

Jin W Tan, Horticulture, Graduate, LCC Resources, MCC Resources 04/13/2022

Benjamin P Clements, Ctr for Enhancement of Learning & Teaching, Undergrad, MCC Resources 04/13/2022

Alex Stewart, Visiting Scholar, MCC Resources 04/13/2022

Dr. Roberta Magnani, Horticulture, Added on MCC resources 11/22/2022

Mckenna J Walker, Horticulture, Added on MCC resources 11/22/2022

Jackson P Montgomery, Horticulture, Added on MCC resources 11/22/2022

Software:

Salmon160

Hisat221

htseq0124

mirdeep2

bcftools

samtools

bowtie

fastqc

adaptorremoval

viennarna2415

star275c

tophat211

gff3toolkit

trimmomatic

r

wgcna

samtools

sabre1000

tpmcalculator

Project 2. Identification of plant epigenetic loci contributing to the assembly of microbial communities in soybean

Breeding programs have traditionally tapped into the species genetic diversity for the identification of alleles capable of conferring beneficial traits to the crop of interest. This approach considers the crop as a single species. However, in nature, plants cohabit with diverse microbes (collectively termed the plant microbiota). The genome-genome interactions in the host-microbiota assemblage (the holobiont), are considered a central tenet for plant development and health. Unravelling the molecular mechanisms that enable plants to regulate the assembly of beneficial root microbiotas is paramount for future breeding programs aimed to improve and sustain crop quality and productivity. Although, very little is known about the molecular mechanisms regulating the assembly of plant microbiota, multiple studies have pointed at the importance of epigenetic mechanisms regulating the cross-talk between the host and its associated microbiota. We hypothesize that the stochastic perturbation of DNA methylation in a population will uniquely alter the ability of each plant to direct its microbiota assembly. The overall goal of this project is to identify genes involved in the regulation of plant–microbiota interactions. To achieve this, we will capitalize on a soybean epimutant population generated in house, to carry out an epigenome-wide association study linking novel epialleles to soil metabolome and root microbiome datasets.

Students:

Lakshay Anand, Horticulture, Graduate Bioinformatician, LCC Resources

Benjamin P Clements, Undergraduate, LCC Resources

Software:

Salmon160

Hisat221

htseq0124

mirdeep2

bcftools

samtools

bowtie

fastqc

adaptorremoval

viennarna2415

star275c

tophat211

gff3toolkit

trimmomatic

r

wgcna

samtools

sabre1000

tpmcalculator

Project 3. Characterization of the gut microbiome of cane toad populations showing different invasive behaviours using a hybrid assembly approach

Gut bacterial communities influence, and are influenced by, the behaviour and ecology of their hosts. Those interactions have been studied primarily in humans and model organisms, but we need field research to understand the relationship between an organism’s gut bacteria and its ecological challenges, such as those imposed by rapid range expansion (as in invasive species) and the presence of host-manipulating parasites. Cane toads (Rhinella marina) provide an excellent model system in this respect, because the species’ ongoing colonization of Australia has enforced major changes in phenotypic traits (including behaviour), and lungworm parasites (Rhabdias pseudosphaerocephala) modify host gut function in ways that enhance the viability of lungworm larvae. Here we are characterizing the gut microbiome of six cane toad populations presenting different invasive behaviours using a hybrid metagenome assembly approach with long-read Oxford nanopore and short-read Illumina sequencing datasets.

Students:

Alex Stewart, Undergraduate, LCC Resources

Software:

Salmon160

Hisat221

htseq0124

mirdeep2

bcftools

samtools

bowtie

fastqc

adaptorremoval

viennarna2415

star275c

tophat211

gff3toolkit

trimmomatic

r

wgcna

samtools

sabre1000

tpmcalculator

Project 4. Development of data analysis tools to study quality and terroir in grapevines

Vitis vinifera (grapevine) is one of the most important fruit crops, both for fresh consumption and wine and spirit production. The term terroir is frequently used in viticulture and the wine industry to relate wine sensory attributes to its geographic origin. Although, V. vinifera can be cultivated in a wide range of environments, differences in growing conditions have a significant impact on fruit traits that ultimately affect wine quality. Understanding how fruit quality and yield are controlled at a molecular level in grapevine in response to environmental cues has been a major driver of research. Advances in the area of genomics, epigenomics, transcriptomics, proteomics and metabolomics, have significantly increased our knowledge on the abiotic regulation of yield and quality in many crop species, including V. vinifera. The integrated analysis of multiple ‘omics’ can give us the opportunity to better understand how plants modulate their response to different environments. However, ‘omics’ technologies provide a large amount of biological data and its interpretation is not always straightforward, especially when different ‘omic’ results are combined.

Students:

Lakshay Anand, Horticulture, Graduate Bioinformatician, LCC Resources

Software:

Salmon160

Hisat221

htseq0124

mirdeep2

bcftools

samtools

bowtie

fastqc

adaptorremoval

viennarna2415

star275c

tophat211

gff3toolkit

trimmomatic

r

wgcna

samtools

sabre1000

tpmcalculator

Publications:

Breen, J., Mur, A. J., Sivakumaran, A., Akinyemi, A., Wilkinson, M. J., Rodriguez Lopez, C. M. (2022). Botrytis cinerea loss and restoration of virulence during in vitro culture follows flux in global DNA methylation, International Journal of Molecular Sciences. JIF: 5.923
Anand, L., Rodriguez Lopez, C. M. (2022). ChromoMap: An R package for Interactive Visualization of Multi-Omic Data and Annotation of Chromosomes, BMC Bioinformatics. JIF: 3.169.
Fabres, P. J., Anand, L., Sai, N., Pederson, S., Zheng, F., ^ Stewart, A. A., ^ Clements, B., Lampugnani, E. R., Breen, J., Gilliham, M., Tricker, P., Rodríguez López, C. M., David, R. (2021). Tissue and regional expression patterns of dicistronic tRNA–mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants, Horticulture Research, 8(1).
Raihan, T., Geneve, R. L., Perry, S. E., Rodriguez Lopez, C. M. (2021). The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator, Epigenomes.
Berbel-Filho, W. M., Tatarenkov, A., Pacheco, G., Espírito-Santo, H. M.V., Lira, M. G., de Leaniz, C. G., Avise, J. C., Lima, S. M.Q., Rodriguez Lopez, C. M., Consuegra, S. (2021). Against the odds: Hybrid zones between mangrove killifish species with different mating systems, Genes, 12(10).
Dini, P., Kalbfleisch, T. S., Uribe-Salazar, J. M., Carossino, M., Ali, H. E., Loux, S. C., Esteller-Vico, A., Norris, J. K., Anand, L., Scoggin, K. E., Rodriguez Lopez, C. M., Breen, J., Bailey, E. F., Daels, P., Ball, B. A. (2021). Parental bias in expression and interaction of genes in the equine placenta., Proceedings of the National Academy of Sciences of the United States of America, 118(16).
Zhou, J., Cavagnaro, T. R., De Bei, R., Nelson, T. M., Stephen, J. R., Metcalfe, A., Gilliham, M., Breen, J., Collins, C., Rodriguez Lopez, C. M. (2021). Wine Terroir and the Soil Bacteria: An Amplicon Sequencing–Based Assessment of the Barossa Valley and Its Sub-Regions, Frontiers in Microbiology, 11.
Tesfamicael, K., Gebre, E., March, T., Sznajder, B., Mather, D., Rodriguez Lopez, C. M. (2020). Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset, Horticulture Research.
Konate, M., Wilkinson, M. J., Taylor, J., Scott, E., Berger, B., Rodriguez Lopez, C. M. (2020). Greenhouse Spatial Effects Detected in the Barley (Hordeum vulgare L.) Epigenome Underlie Stochasticity of DNA Methylation, Frontiers in Plant Science.
Babalola, O. O., Alawiye, T. T., Rodriguez Lopez, C. M., Ayangbenro, A. S. (2020). Shotgun metagenomic sequencing data of sunflower rhizosphere microbial community in South Africa, Data in Brief, v. 31, 105831.
Zhou, J., Nelson, T. M., Rodriguez Lopez, C. M., Sarma, R. R., Zhou, S. J., Rollins, L. A. (2020). A comparison of nonlethal sampling methods for amphibian gut microbiome analyses, Molecular Ecology Resources, 20(4), 844-855.
Corbin, K. R., ^ Bolt, B., Rodriguez Lopez, C. M. (2020). Breeding for beneficial microbial communities using epigenomics, Frontiers in Microbiology, 11, 937.
Akankunda, T., To, H., Rodriguez Lopez, C. M., Leijs, R., Hogendoorn, K. (2020). A method to generate multilocus barcodes of pinned insect specimens using MiSeq, Molecular Ecology Resources, 20(3), 692-705.
Konate, M., Wilkinson, M. J., Taylor, J., Berger, B., Scott, E., Rodriguez Lopez, C. M. (2019). Detection of differentially methylated markers induced by mild salt stress in barley using the methylation sensitive amplified polymorphism (MSAP), Science and technology review. Social sciences series / General Delegation for Scientific and Technical Research, 38(1), 51-67.
Akomeah, B., Quain, M. D., Ramesh, S. A., Anand, L., Rodriguez Lopez, C. M. (2019). Common garden experiment reveals altered nutritional values and DNA methylation profiles in three micropropagated elite Ghanaian sweet potato genotypes, PlosOne.
Konate, M., Wilkinson, M. J., Mayne, B. T., Pederson, S. M., Scott, E. S., Berger, B., Rodriguez Lopez, C. M. (2018). Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare), Epigenomes, 2(2).
Mayne, B. T., Leemaqz, S. Y., Buckberry, S., Roberts, C. T., Rodriguez Lopez, C. M., Bianco-Miotto, T., Breen, J. (2018). msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data, Scientific Reports, 8.

Grants:

Improving Phosphorus Recovery in Aquaponic Systems Through Environmental Manipulation of the Plant Rhizosphere Microbiota. $750,000NIFA-AFRI. 2021-2025. Co-PIs: Rodriguez Lopez C., M., Coyne M., S., Hager, J.
Implications of epigenetic rejuvenation during vegetative propagation for the production of locally adapted perennial crop cultivars. $500,000. NFA-AFRI. 2019-2022. PI: Rodriguez Lopez C., Co-PIs: Perry, S., Geneve, R., Wheeler, J.
The impact of gut microbiota on the Australian cane toad invasion. $12,000. Holsworth Wildlife Research Endowment. 2019-2021. PI: Rollins L., co-PI. Rodriguez Lopez C., Jia Zou
Adding value to Kentucky wines: Bioprospecting for novel yeast. $57,959. USDA: Specialty Crop Block Grant Program. 2020–2023. PI: Carlos Rodriguez Lopez, Co-PIs: Kendall Corbin, Jeff Wheeler
Investigating how storage conditions affect the microbial safety of soft winter wheat. $21,600. 2021-2022. Siemer Milling Company. PI: Kendall Corbin, Co-PI: Carlos Rodriguez Lopez
A pilot study for the identification of genome locations associated to soil microbiome assembly for a more sustainable agriculture. $7,264. 2020–2021. Food Connection. PI: Carlos Rodriguez Lopez, Co-PIs: Kendall Corbin and Bridget Bolt
Developing a genomic toolkit to harness bacterial cellulose biosynthesis for energy applications. $51,854. 2020–2021. UK Energy Research Priority Partnership Seed Grant. PI:Kendall Corbin, Co-PIs: Chen, J., Miller, A.-F., Rodriguez Lopez C.
NRN-LCEE Proposal Writing Fellowship at Swansea University (Wales, United Kingdom) January-March2018 ($15,500). Sole PI: Carlos Rodriguez Lopez
University of Adelaide Beacon Research FellowshipUniversity of Adelaide (Adelaide, Australia) 2017 ($96,000). Sole PI: Carlos Rodriguez Lopez