Science
Associate Conservation Genomics Scientist
Curriculum Vitae:
Teaching and Research Affiliations:

Teaching and Research Affiliations:
Adjunct Professor, Biological Sciences, Northwestern University

Selected Professional Associations:

Professional Associations:
Botanical Society of America

Research Interests:

-    Comparative and evolutionary genomics
-    Plant adaptation to biotic and abiotic pressures
-    Bioinformatic tool development for plants
-    Conservation of imperiled plant species 
-    Use of native plants in landscaping and agriculture
-    Connecting people to nature through Community Science

Statement:

My research investigates genomic aspects of plant evolution and adaptation, leveraging my expertise in the analysis of large data sets comprising complex molecular information from individuals, populations, or lineages of plants. I work toward understanding how changing distributions and phenotypes within and between populations contribute to landscape-level ecological patterns and processes, across space and time. I am particularly interested in native plants, their conservation, and how they can be implemented into landscapes to positively impact human well-being and health.

Current Projects:

Adaptation to temperature extremes. Temperature is one of the greatest drivers of plant diversification, with adaptation to both hot and cold extremes resulting in the colonization of new niche space and the emergence of rapid radiations across plant lineages. I am exploring the phenotypic and genotypic correlates of cold tolerance in Asimina triloba (common pawpaw) and how cold adaptation has evolved in the Annonaceae and impacted species distributions. While the family comprises mostly tropical species, the genus Asimina is able to grow over a range of USDA hardiness zones (zones 5-9). I am leading a project to develop genomics resources for A. triloba and explore genetic diversity in Asimina. Collaborators and I are sampling A. triloba populations from the extremes and midpoint of its native range to identify signatures of local adaptation. This project is integrally tied with traditional knowledge of local Native American communities given the importance of pawpaw plantations to pre-colonial managed forests and landscapes.

Systematics and conservation of North American Aconitum. I lead a collaborative effort to understand how species distributions are changing in response to climate change in North American Aconitum species. Through this project, I am resolving the phylogeny of the genus in North America and determining whether Aconitum noveboracense, a federally listed endangered species, is genetically distinct from its close relatives. I am also interested in the mechanisms allowing the closely related western Aconitum species to thrive while A. noveboracense is only found in four states as a glacial relict with rapidly declining populations. I am using the results of genomic sequencing approaches from field-collected and herbarium samples to develop an improved conservation plan based on the distribution of diversity in the subpopulations of A. noveboracense and to project future distributions under different climate scenarios.

American Beech Conservation. American beech (Fagus grandifolia) is a keystone tree species in North American forest ecosystems, currently being devastated by beech bark disease (BBD). I am developing genomic tools for woodlot management that can identify trees that are resistant to BBD and use them in a genetic improvement program to help maintain this tree as an iconic species in the American landscape. We are setting trials for woodlot management and conducting long-term monitoring to assess whether a marker-assisted propagation approach improves woodlot health and maintains a diversity of flora and fauna.

Structural Variation in Calochortus spp. Calochortus (Liliaceae) is a large genus (75 spp.) of bulbous herbs with flowers of kaleidoscopic variety and exquisite complexity. Calochortus has undergone striking radiations in flower morphology, habitat, and substrate preference, and most taxa have narrow ranges. We are using long-read sequencing to identify structural variants (SVs), including copy number variants, to explore their involvement in the bases of floral trait evolution, adaptation, and ecological distribution in Calochortus. Structural variants have been implicated as drivers of ecological and evolutionary processes in many systems. We are identifying structural variants between Calochortus spp. and assessing their implications in adaptive evolution and species diversification through transcriptomic and functional approaches. We will predict the population-level presence of these SVs using selective nanopore sequencing allowing us to determine the prevalence of identified SVs, if they may be fixed in the population/species, and form testable hypotheses about their evolutionary significance.

Other Interests:

I am interested in nativars and how planting these varieties may impact ecosystem services. I would like to explore the genomic basis of ecologically successful nativars and work with breeders to provide varieties to the public.

We are becoming increasingly aware of how biodiversity impacts human wellbeing. I am interested in using tools like hyperspectral imaging to gauge biodiversity and working with social scientists to assess its impact on human health.

Additionally, I would like to explore how artificial intelligence might be used to incorporate pollinator, locality, phenotype, and genomics data - including data from historical collections - to understand plant adaptation and inform conservation genomics.

Selected Publications:

G. Y. De La Cerda, J. B. Landis, E. Eifler, A. I. Hernandez, FW Li, J. Zhang, C. M. Tribble, N. Karimi, P. Chan, T. Givnish, S. R. Strickler, C. D. Specht. Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales. Applications in Plant Sciences. 2023 May 1:e11524.

A. F. Powell, J. Zhang, D. Hauser, J. A. Vilela, A. Hu, D. J. Gates, L. A. Mueller, F.-W. Li, S. R. Strickler, S. D. Smith, Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae. Plant Genome, e20223 (2022).

A. F. Powell, A. Feder, J. Li, M. H.-W. Schmidt, L. Courtney, S. Alseekh, E. M. Jobson, A. Vogel, Y. Xu, D. Lyon, K. Dumschott, M. McHale, R. Sulpice, K. Bao, R. Lal, A. Duhan, A. Hallab, A. K. Denton, M. E. Bolger, A. R. Fernie, S. R. Hind, L. A. Mueller, G. B. Martin, Z. Fei, C. Martin, J. J. Giovannoni, S. R. Strickler, B. Usadel, A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. Plant J. (2022), doi:10.1111/tpj.15770.

G. Moghe, S. Strickler, metaPathwayMap: A tool to predict metabolic pathway neighborhoods from structural classes of untargeted metabolomics peaks. bioRxiv (2022), p. 2022.03.15.484337.

J. H. Boyle, S. Strickler, A. Twyford, A. Ricono, A. Powell, J. Zhang, H. Xu, H. J. Dalgleish, G. Jander, A. A. Agrawal, J. R. Puzey, Temporal matches and mismatches between monarch butterfly and milkweed population changes over the past 12,000 years. bioRxiv (2022), p. 2022.02.25.481796.

G. Torres-Silva, L. N. F. Correia, D. S. Batista, A. D. Koehler, S. V. Resende, E. Romanel, D. Cassol, A. M. R. Almeida, S. R. Strickler, C. D. Specht, W. C. Otoni, Transcriptome Analysis of Melocactus glaucescens (Cactaceae) Reveals Metabolic Changes During in vitro Shoot Organogenesis Induction. Front. Plant Sci. 12, 697556 (2021).

G. Torres-Silva, L. N. F. Correia, A. D. Koehler, D. S. Batista, D. V. Faria, S. V. Resende, S. R. Strickler, J. Fouracre, E. Romanel, C. D. Specht, W. C. Otoni, Expression of Melocactus glaucescens SERK1 sheds new light on the mechanism of areolar activation in cacti. Plant Cell Tissue Organ Cult. (2021), doi:10.1007/s11240-021-02137-9.

X. Wang, L. Gao, C. Jiao, S. Stravoravdis, P. S. Hosmani, S. Saha, J. Zhang, S. Mainiero, S. R. Strickler, C. Catala, G. B. Martin, L. A. Mueller, J. Vrebalov, J. J. Giovannoni, S. Wu, Z. Fei, Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nat. Commun. 11, 5817 (2020).

E.-H. Thioune, S. Strickler, T. Gallagher, A. Charpagne, P. Decombes, B. Osborne, J. McCarthy, Temperature Impacts the Response of Coffea canephora to Decreasing Soil Water Availability. Trop. Plant Biol. 13, 236–250 (2020).

V. Y. Baba, A. F. Powell, S. T. Ivamoto-Suzuki, L. F. P. Pereira, A. L. L. Vanzela, R. M. Giacomin, S. R. Strickler, L. A. Mueller, R. Rodrigues, L. S. A. Gonçalves, Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages. Sci. Rep. 10, 12048 (2020).

J. S. Ramsey, E. L. Chin, J. D. Chavez, S. Saha, D. Mischuk, J. Mahoney, J. Mohr, F. M. Robison, E. Mitrovic, Y. Xu, S. R. Strickler, N. Fernandez, X. Zhong, M. Polek, K. E. Godfrey, J. J. Giovannoni, L. A. Mueller, C. M. Slupsky, J. E. Bruce, M. Heck, Longitudinal Transcriptomic, Proteomic, and Metabolomic Analysis of Citrus limon Response to Graft Inoculation by Candidatus Liberibacter asiaticus. J. Proteome Res. 19, 2247–2263 (2020).

T. Züst, S. R. Strickler, A. F. Powell, M. E. Mabry, H. An, M. Mirzaei, T. York, C. K. Holland, P. Kumar, M. Erb, G. Petschenka, J.-M. Gómez, F. Perfectti, C. Müller, J. C. Pires, L. A. Mueller, G. Jander, Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae). Elife. 9 (2020), doi:10.7554/eLife.51712.

S. S.-E.-A. Zaidi, R. Z. Naqvi, M. Asif, S. Strickler, S. Shakir, M. Shafiq, A. M. Khan, I. Amin, B. Mishra, M. S. Mukhtar, B. E. Scheffler, J. A. Scheffler, L. A. Mueller, S. Mansoor, Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum). Plant Biotechnol. J. 18, 691–706 (2020).

C. Mazo-Molina, S. Mainiero, B. J. Haefner, R. Bednarek, J. Zhang, A. Feder, K. Shi, S. R. Strickler, G. B. Martin, Ptr1 evolved convergently with RPS2 and Mr5 to mediate recognition of AvrRpt2 in diverse solanaceous species. Plant J. 103, 1433–1445 (2020).

D. V. Lantican, S. R. Strickler, A. O. Canama, R. R. Gardoce, L. A. Mueller, H. F. Galvez, De Novo Genome Sequence Assembly of Dwarf Coconut (Cocos nucifera L. “Catigan Green Dwarf”) Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species. G3 . 9, 2377–2393 (2019).

R. Roberts, S. Mainiero, A. F. Powell, A. E. Liu, K. Shi, S. R. Hind, S. R. Strickler, A. Collmer, G. B. Martin, Natural variation for unusual host responses and flagellin-mediated immunity against Pseudomonas syringae in genetically diverse tomato accessions. New Phytol. (2019), doi:10.1111/nph.15788.

I. Gonda, H. Ashrafi, D. A. Lyon, S. R. Strickler, A. M. Hulse-Kemp, Q. Ma, H. Sun, K. Stoffel, A. F. Powell, S. Futrell, T. W. Thannhauser, Z. Fei, A. E. Van Deynze, L. A. Mueller, J. J. Giovannoni, M. R. Foolad, Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection. Plant Genome. 12 (2019), doi:10.3835/plantgenome2018.02.0010.

V. Tzin, Y. Hojo, S. R. Strickler, L. J. Bartsch, C. M. Archer, K. R. Ahern, S. Zhou, S. A. Christensen, I. Galis, L. A. Mueller, G. Jander, Rapid defense responses in maize leaves induced by Spodoptera exigua caterpillar feeding. J. Exp. Bot. 68, 4709–4723 (2017).

L. E. Wyatt, S. R. Strickler, L. A. Mueller, M. Mazourek, Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin. Hortic Res. 3, 16045 (2016).

B. Castandet, A. M. Hotto, S. R. Strickler, D. B. Stern, ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress. G3 . 6, 2817–2827 (2016).

S. R. Hind, S. R. Strickler, P. C. Boyle, D. M. Dunham, Z. Bao, I. M. O’Doherty, J. A. Baccile, J. S. Hoki, E. G. Viox, C. R. Clarke, B. A. Vinatzer, F. C. Schroeder, G. B. Martin, Tomato receptor FLAGELLIN-SENSING 3 binds flgII-28 and activates the plant immune system. Nat Plants. 2, 16128 (2016).

D. J. Gates, S. R. Strickler, L. A. Mueller, B. J. S. C. Olson, S. D. Smith, Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae. J. Mol. Evol. 83, 26–37 (2016).
J. Yan, T. Aboshi, M. Teraishi, S. R. Strickler, J. E. Spindel, C.-W. Tung, R. Takata, F. Matsumoto, Y. Maesaka, S. R. McCouch, Y. Okumoto, N. Mori, G. Jander, The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice. Plant Cell. 27, 1265–1278 (2015).

S. R. Strickler, A. Bombarely, J. D. Munkvold, T. York, N. Menda, G. B. Martin, L. A. Mueller, Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives. PeerJ. 3, e793 (2015).

L. E. Wyatt, S. R. Strickler, L. A. Mueller, M. Mazourek, An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita. Hortic Res. 2, 14070 (2015).

Z. Bao, F. Meng, S. R. Strickler, D. M. Dunham, K. R. Munkvold, G. B. Martin, Identification of a Candidate Gene in Solanum habrochaites for Resistance to a Race 1 Strain of Pseudomonas syringae pv. tomato. Plant Genome. 8 (2015), doi:10.3835/plantgenome2015.02.0006.

C. Perrois, S. R. Strickler, G. Mathieu, M. Lepelley, L. Bedon, S. Michaux, J. Husson, L. Mueller, I. Privat, Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta). Planta. 241, 179–191 (2015).

N. Menda, S. R. Strickler, J. D. Edwards, A. Bombarely, D. M. Dunham, G. B. Martin, L. Mejia, S. F. Hutton, M. J. Havey, D. P. Maxwell, L. A. Mueller, Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. BMC Plant Biol. 14, 287 (2014).

J. A. Labate, L. D. Robertson, S. R. Strickler, L. A. Mueller, Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex. Genome. 57, 169–180 (2014).
S. R. Strickler, T. Tantikanjana, J. B. Nasrallah, Regulation of the S-locus receptor kinase and self-incompatibility in Arabidopsis thaliana. G3 . 3, 315–322 (2013).

S. R. Strickler, A. Bombarely, L. A. Mueller, Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am. J. Bot. 99, 257–266 (2012).