Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants

Sourabh Palande; Joshua A. M. Kaste; Miles D. Roberts; Kenia Segura Abá; Carly Claucherty; Jamell Dacon; Rei Doko; Thilani B. Jayakody; Hannah R. Jeffery; Nathan Kelly; Andriana Manousidaki; Hannah M. Parks; Emily M. Roggenkamp; Ally M. Schumacher; Jiaxin Yang; Sarah Percival; Jeremy Pardo; Aman Y. Husbands; Arjun Krishnan; Beronda L Montgomery; Elizabeth Munch; Addie M. Thompson; Alejandra Rougon-Cardoso; Daniel H. Chitwood; Robert VanBuren

doi:10.1371/journal.pbio.3002397

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Peer-reviewed

Research Article

Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants

Sourabh Palande ,

Contributed equally to this work with: Sourabh Palande, Joshua A. M. Kaste, Miles D. Roberts, Kenia Segura Abá

Roles Conceptualization, Data curation, Formal analysis

Affiliation Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
⨯
Joshua A. M. Kaste ,

Contributed equally to this work with: Sourabh Palande, Joshua A. M. Kaste, Miles D. Roberts, Kenia Segura Abá

Roles Conceptualization, Data curation, Formal analysis, Writing – original draft

Affiliations Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America, Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America

https://orcid.org/0000-0003-1942-0315

⨯
Miles D. Roberts ,

Contributed equally to this work with: Sourabh Palande, Joshua A. M. Kaste, Miles D. Roberts, Kenia Segura Abá

Roles Conceptualization, Data curation, Formal analysis

Affiliation Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
⨯
Kenia Segura Abá ,

Contributed equally to this work with: Sourabh Palande, Joshua A. M. Kaste, Miles D. Roberts, Kenia Segura Abá

Roles Conceptualization, Data curation, Formal analysis

Affiliation Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
⨯
Carly Claucherty,

Roles Data curation, Formal analysis

Affiliation Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
⨯
Jamell Dacon,

Roles Conceptualization, Data curation

Affiliation Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America

https://orcid.org/0000-0002-6917-6835

⨯
Rei Doko,

Roles Data curation, Formal analysis

Affiliation Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
⨯
Thilani B. Jayakody,

Roles Data curation, Formal analysis

Affiliation Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
⨯
Hannah R. Jeffery,

Roles Data curation, Formal analysis

Affiliation Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
⨯
Nathan Kelly,

Roles Data curation, Formal analysis

Affiliation Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
⨯
Andriana Manousidaki,

Roles Data curation, Formal analysis

Affiliation Department of Statistics and Probability, Michigan State University, East Lansing, Michigan, United States of America
⨯
Hannah M. Parks,

Roles Data curation, Formal analysis

Affiliation Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America

https://orcid.org/0000-0002-9861-8049

⨯
Emily M. Roggenkamp,

Roles Data curation, Formal analysis

Affiliation Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
⨯
Ally M. Schumacher,

Roles Data curation, Formal analysis

Affiliation Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
⨯
Jiaxin Yang,

Roles Data curation, Formal analysis

Affiliation Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
⨯
Sarah Percival,

Roles Data curation, Formal analysis

Affiliation Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America

https://orcid.org/0000-0003-1024-4618

⨯
Jeremy Pardo,

Roles Data curation, Formal analysis, Software

Affiliation Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
⨯
Aman Y. Husbands,

Roles Conceptualization, Writing – review & editing

Affiliation Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
⨯
Arjun Krishnan,

Roles Conceptualization, Writing – review & editing

Affiliations Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America

https://orcid.org/0000-0002-7980-4110

⨯
Beronda L Montgomery,

Roles Conceptualization, Writing – review & editing

Affiliations Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America, Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America, MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
⨯
Elizabeth Munch,

Roles Conceptualization, Writing – review & editing

Affiliations Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America, Department of Mathematics, Michigan State University, East Lansing, Michigan, United States of America
⨯
Addie M. Thompson,

Roles Conceptualization, Writing – review & editing

Affiliations Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America, Plant Resilience Institute, Michigan State University, East Lansing, Michigan, United States of America
⨯
Alejandra Rougon-Cardoso,

Roles Conceptualization, Data curation, Formal analysis, Project administration, Writing – original draft, Writing – review & editing

Affiliations Laboratory of Agrigenomic Sciences, Universidad Nacional Autónoma de México, ENES-León, León, Mexico, Laboratorio Nacional Plantecc, ENES-León, León, Mexico

https://orcid.org/0000-0002-5273-5709

⨯
Daniel H. Chitwood ,

Roles Conceptualization, Data curation, Formal analysis, Project administration, Supervision, Visualization, Writing – original draft, Writing – review & editing

* E-mail: dhchitwood@gmail.com (DHC); bobvanburen@gmail.com (RV)

Affiliations Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America, Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America

https://orcid.org/0000-0003-4875-1447

⨯
[ ... ],
Robert VanBuren

Roles Conceptualization, Data curation, Formal analysis, Project administration, Supervision, Writing – original draft, Writing – review & editing

* E-mail: dhchitwood@gmail.com (DHC); bobvanburen@gmail.com (RV)

Affiliations Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America, Plant Resilience Institute, Michigan State University, East Lansing, Michigan, United States of America

https://orcid.org/0000-0003-2133-2760

⨯
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Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants

Sourabh Palande,
Joshua A. M. Kaste,
Miles D. Roberts,
Kenia Segura Abá,
Carly Claucherty,
Jamell Dacon,
Rei Doko,
Thilani B. Jayakody,
Hannah R. Jeffery,
Nathan Kelly

Published: December 5, 2023
https://doi.org/10.1371/journal.pbio.3002397

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Flowering plants
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