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Ruan Z, Jiao J, Zhao J, Liu J, Liang C, Yang X, Sun Y, Tang G, Li P. Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash. BMC Genomics 2024; 25:502. [PMID: 38773367 PMCID: PMC11110190 DOI: 10.1186/s12864-024-10424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker. RESULTS In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family. CONCLUSION This study sheds light on the genetic basis of F. zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.
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Affiliation(s)
- Zhao Ruan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiahui Jiao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junchi Zhao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiaxue Liu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chaoqiong Liang
- Shaanxi Academy of Forestry, Xi'an, Shaanxi, 710082, People's Republic of China
| | - Xia Yang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yan Sun
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peiqin Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Pant P, Kaur J. Control of Sclerotinia sclerotiorum via an RNA interference (RNAi)-mediated targeting of SsPac1 and SsSmk1. PLANTA 2024; 259:153. [PMID: 38744752 DOI: 10.1007/s00425-024-04430-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
MAIN CONCLUSION The study evaluates the potential of Spray-Induced Gene Silencing and Host-Induced Gene Silencing for sustainable crop protection against the broad-spectrum necrotrophic fungus Sclerotinia sclerotiorum. Sclerotinia sclerotiorum (Lib.) de Bary, an aggressive ascomycete fungus causes white rot or cottony rot on a broad range of crops including Brassica juncea. The lack of sustainable control measures has necessitated biotechnological interventions such as RNA interference (RNAi) for effective pathogen control. Here we adopted two RNAi-based strategies-Spray-Induced Gene Silencing (SIGS) and Host-Induced Gene Silencing (HIGS) to control S. sclerotiorum. SIGS was successful in controlling white rot on Nicotiana benthamiana and B. juncea by targeting SsPac1, a pH-responsive transcription factor and SsSmk1, a MAP kinase involved in fungal development and pathogenesis. Topical application of dsRNA targeting SsPac1 and SsSmk1 delayed infection initiation and progression on B. juncea. Further, altered hyphal morphology and reduced radial growth were also observed following dsRNA application. We also explored the impact of stable dsRNA expression in A. thaliana against S. sclerotiorum. In this report, we highlight the utility of RNAi as a biofungicide and a tool for preliminary functional genomics.
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Affiliation(s)
- Pratibha Pant
- Department of Genetics, University of Delhi, South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Jagreet Kaur
- Department of Genetics, University of Delhi, South Campus, Benito Juarez Marg, New Delhi, 110021, India.
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Azizi A, Del Río Mendoza LE. Effective Control of Sclerotinia Stem Rot in Canola Plants Through Application of Exogenous Hairpin RNA of Multiple Sclerotinia sclerotiorum Genes. PHYTOPATHOLOGY 2024; 114:1000-1010. [PMID: 38506733 DOI: 10.1094/phyto-10-23-0395-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Sclerotinia stem rot is a globally destructive plant disease caused by Sclerotinia sclerotiorum. Current management of Sclerotinia stem rot primarily relies on chemical fungicides and crop rotation, raising environmental concerns. In this study, we developed an eco-friendly RNA bio-fungicide targeting S. sclerotiorum. Six S. sclerotiorum genes were selected for double-stranded RNA (dsRNA) synthesis. Four genes, a chitin-binding domain, mitogen-activated protein kinase, oxaloacetate acetylhydrolase, and abhydrolase-3, were combined to express hairpin RNA in Escherichia coli HT115. The effect of application of total RNA extracted from E. coli HT115 expressing hairpin RNA on disease progressive and necrosis lesions was evaluated. Gene expression analysis using real-time PCR showed silencing of the target genes using 5 ng/µl of dsRNA in a fungal liquid culture. A detached leaf assay and greenhouse application of dsRNA on canola stem and leaves showed variation in the reduction of necrosis symptoms by dsRNA of different genes, with abhydrolase-3 being the most effective. The dsRNA from a combination of four genes reduced disease severity significantly (P = 0.01). Plants sprayed with hairpin RNA from four genes had lesions that were almost 30% smaller than those of plants treated with abhydrolase-3 alone, in lab and greenhouse assays. The results of this study highlight the potential of RNA interference to manage diseases caused by S. sclerotiorum; however, additional research is necessary to optimize its efficacy.
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Affiliation(s)
- Abdolbaset Azizi
- Department of Plant Pathology, North Dakota State University, ND, U.S.A
- Department of Plant Protection, University of Kurdistan, Sanandaj, Iran
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Tian L, Li J, Xu Y, Qiu Y, Zhang Y, Li X. A MAP kinase cascade broadly regulates the lifestyle of Sclerotinia sclerotiorum and can be targeted by HIGS for disease control. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:324-344. [PMID: 38149487 DOI: 10.1111/tpj.16606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/15/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023]
Abstract
Sclerotinia sclerotiorum causes white mold or stem rot in a wide range of economically important plants, bringing significant yield losses worldwide. Control of this pathogen is difficult as its resting structure sclerotia can survive in soil for years, and no Resistance genes have been identified in S. sclerotiorum hosts. Host-induced gene silencing (HIGS) has shown promising effects in controlling many fungal pathogens, including S. sclerotiorum. However, better molecular genetic understanding of signaling pathways involved in its development and pathogenicity is needed to provide effective HIGS gene targets. Here, by employing a forward genetic screen, we characterized an evolutionarily conserved mitogen-activated protein kinase (MAPK) cascade in S. sclerotiorum, consisting of SsSte50-SsSte11-SsSte7-Smk1, which controls mycelial growth, sclerotia development, compound appressoria formation, virulence, and hyphal fusion. Moreover, disruption of the putative downstream transcription factor SsSte12 led to normal sclerotia but deformed appressoria and attenuated host penetration, as well as impaired apothecia formation, suggestive of diverged regulation downstream of the MAPK cascade. Most importantly, targeting SsSte50 using host-expressed double-stranded RNA resulted in largely reduced virulence of S. sclerotiorum on both Nicotiana benthamiana leaves and transgenic Arabidopsis thaliana plants. Therefore, this MAPK signaling cascade is generally needed for its growth, development, and pathogenesis and can serve as ideal HIGS targets for mitigating economic damages caused by S. sclerotiorum infection.
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Affiliation(s)
- Lei Tian
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Josh Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Yan Xu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Yilan Qiu
- Department of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yuelin Zhang
- College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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Xu Y, Tan J, Lu J, Zhang Y, Li X. RAS signalling genes can be used as host-induced gene silencing targets to control fungal diseases caused by Sclerotinia sclerotiorum and Botrytis cinerea. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:262-277. [PMID: 37845842 PMCID: PMC10754012 DOI: 10.1111/pbi.14184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 08/27/2023] [Accepted: 09/02/2023] [Indexed: 10/18/2023]
Abstract
Sclerotinia sclerotiorum causes white mold (also called stem rot, Sclerotinia blight, etc.) in many economically important plants. It is a notorious soilborne fungal pathogen due to its wide host range and ability to survive in soil for long periods of time as sclerotia. Although host-induced gene silencing (HIGS) was recently demonstrated to be an effective method for controlling white mold, limited gene targets are available. Here, using a forward genetics approach, we identified a RAS-GTPase activating protein, SsGAP1, which plays essential roles in sclerotia formation, compound appressoria production and virulence. In parallel, as revealed by our knockout analysis, the SsGAP1 ortholog in Botrytis cinerea, BcGAP1, plays similar roles in fungal development and virulence. By knocking down SsRAS1 and SsRAS2, we also revealed that both SsRAS1 and SsRAS2 are required for vegetative growth, sclerotia development, compound appressoria production and virulence in S. sclerotiorum. Due to the major roles these RAS signalling components play in Sclerotiniaceae biology, they can be used as HIGS targets to control diseases caused by both S. sclerotiorum and B. cinerea. Indeed, when we introduced HIGS constructs targeting SsGAP1, SsRAS1 and SsRAS2 in Nicotiana benthamiana and Arabidopsis thaliana, we observed reduced virulence. Taken together, our forward genetics gene discovery pipeline in S. sclerotiorum is highly effective in identifying novel HIGS targets to control S. sclerotiorum and B. cinerea.
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Affiliation(s)
- Yan Xu
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Jinyi Tan
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Junxing Lu
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- College of Life ScienceChongqing Normal UniversityChongqingChina
| | - Yuelin Zhang
- Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Xin Li
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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Luciano-Rosario D, Peng H, Gaskins VL, Fonseca JM, Keller NP, Jurick WM. Mining the Penicillium expansum Genome for Virulence Genes: A Functional-Based Approach to Discover Novel Loci Mediating Blue Mold Decay of Apple Fruit. J Fungi (Basel) 2023; 9:1066. [PMID: 37998873 PMCID: PMC10672711 DOI: 10.3390/jof9111066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/25/2023] Open
Abstract
Blue mold, a postharvest disease of pome fruits, is caused by the filamentous fungus Penicillium expansum. In addition to the economic losses caused by P. expansum, food safety can be compromised, as this pathogen is mycotoxigenic. In this study, forward and reverse genetic approaches were used to identify genes involved in blue mold infection in apple fruits. For this, we generated a random T-DNA insertional mutant library. A total of 448 transformants were generated and screened for the reduced decay phenotype on apples. Of these mutants, six (T-193, T-275, T-434, T-588, T-625, and T-711) were selected for continued studies and five unique genes were identified of interest. In addition, two deletion mutants (Δt-625 and Δt-588) and a knockdown strain (t-434KD) were generated for three loci. Data show that the ∆t-588 mutant phenocopied the T-DNA insertion mutant and had virulence penalties during apple fruit decay. We hypothesize that this locus encodes a glyoxalase due to bioinformatic predictions, thus contributing to reduced colony diameter when grown in methylglyoxal (MG). This work presents novel members of signaling networks and additional genetic factors that regulate fungal virulence in the blue mold fungus during apple fruit decay.
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Affiliation(s)
| | - Hui Peng
- Everglades Research and Education Center, Horticultural Sciences Department, University of Florida, Belle Glade, FL 33430, USA;
| | - Verneta L. Gaskins
- Food Quality Laboratory, USDA-ARS, Beltsville, MD 20705, USA; (V.L.G.); (J.M.F.)
| | - Jorge M. Fonseca
- Food Quality Laboratory, USDA-ARS, Beltsville, MD 20705, USA; (V.L.G.); (J.M.F.)
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA;
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA
| | - Wayne M. Jurick
- Food Quality Laboratory, USDA-ARS, Beltsville, MD 20705, USA; (V.L.G.); (J.M.F.)
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Qin L, Nong J, Cui K, Tang X, Gong X, Xia Y, Xu Y, Qiu Y, Li X, Xia S. SsCak1 Regulates Growth and Pathogenicity in Sclerotinia sclerotiorum. Int J Mol Sci 2023; 24:12610. [PMID: 37628791 PMCID: PMC10454577 DOI: 10.3390/ijms241612610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Sclerotinia sclerotiorum is a devastating fungal pathogen that causes severe crop losses worldwide. It is of vital importance to understand its pathogenic mechanism for disease control. Through a forward genetic screen combined with next-generation sequencing, a putative protein kinase, SsCak1, was found to be involved in the growth and pathogenicity of S. sclerotiorum. Knockout and complementation experiments confirmed that deletions in SsCak1 caused defects in mycelium and sclerotia development, as well as appressoria formation and host penetration, leading to complete loss of virulence. These findings suggest that SsCak1 is essential for the growth, development, and pathogenicity of S. sclerotiorum. Therefore, SsCak1 could serve as a potential target for the control of S. sclerotiorum infection through host-induced gene silencing (HIGS), which could increase crop resistance to the pathogen.
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Affiliation(s)
- Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Jieying Nong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Kan Cui
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China;
| | - Xianyu Tang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Xin Gong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Yunong Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
| | - Yan Xu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yilan Qiu
- Department of Life Science, Hunan Normal University, Changsha 410081, China;
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (L.Q.); (J.N.); (X.T.); (X.G.); (Y.X.)
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Walker PL, Ziegler DJ, Giesbrecht S, McLoughlin A, Wan J, Khan D, Hoi V, Whyard S, Belmonte MF. Control of white mold (Sclerotinia sclerotiorum) through plant-mediated RNA interference. Sci Rep 2023; 13:6477. [PMID: 37081036 PMCID: PMC10119085 DOI: 10.1038/s41598-023-33335-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/11/2023] [Indexed: 04/22/2023] Open
Abstract
The causative agent of white mold, Sclerotinia sclerotiorum, is capable of infecting over 600 plant species and is responsible for significant crop losses across the globe. Control is currently dependent on broad-spectrum chemical agents that can negatively impact the agroecological environment, presenting a need to develop alternative control measures. In this study, we developed transgenic Arabidopsis thaliana (AT1703) expressing hairpin (hp)RNA to silence S. sclerotiorum ABHYDROLASE-3 and slow infection through host induced gene silencing (HIGS). Leaf infection assays show reduced S. sclerotiorum lesion size, fungal load, and ABHYDROLASE-3 transcript abundance in AT1703 compared to wild-type Col-0. To better understand how HIGS influences host-pathogen interactions, we performed global RNA sequencing on AT1703 and wild-type Col-0 directly at the site of S. sclerotiorum infection. RNA sequencing data reveals enrichment of the salicylic acid (SA)-mediated systemic acquired resistance (SAR) pathway, as well as transcription factors predicted to regulate plant immunity. Using RT-qPCR, we identified predicted interacting partners of ABHYDROLASE-3 in the polyamine synthesis pathway of S. sclerotiorum that demonstrate co-reduction with ABHYDROLASE-3 transcript levels during infection. Together, these results demonstrate the utility of HIGS technology in slowing S. sclerotiorum infection and provide insight into the role of ABHYDROLASE-3 in the A. thaliana-S. sclerotiorum pathosystem.
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Affiliation(s)
- Philip L Walker
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Dylan J Ziegler
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Shayna Giesbrecht
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Austein McLoughlin
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Joey Wan
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Deirdre Khan
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Vanessa Hoi
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Steve Whyard
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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