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Luo W, Gonzalez E, Zarei A, Calleja S, Rozzi B, Demieville J, Li H, Truco MJ, Lavelle D, Michelmore R, Dyer JM, Jenks MA, Pauli D. Leaf cuticular wax composition of a genetically diverse collection of lettuce ( Lactuca sativa L.) cultivars evaluated under field conditions. Heliyon 2024; 10:e27226. [PMID: 38463774 PMCID: PMC10923717 DOI: 10.1016/j.heliyon.2024.e27226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/15/2023] [Accepted: 02/26/2024] [Indexed: 03/12/2024] Open
Abstract
Cuticular waxes of plants impart tolerance to many forms of environmental stress and help shed dangerous human pathogens on edible plant parts. Although the chemical composition of waxes on a wide variety of important crops has been described, a detailed wax compositional analysis has yet to be reported for lettuce (Lactuca sativa L.), one of the most widely consumed vegetables. We present herein the leaf wax content and composition of 12 genetically diverse lettuce cultivars sampled across five time points during their vegetative growth phase in the field. Mean total leaf wax amounts across all cultivars varied little over 28 days of vegetative growth, except for a notable decrease in total waxes following a major precipitation event, presumably due to wax degradation from wind and rain. All lettuce cultivars were found to contain a unique wax composition highly enriched in 22- and 24-carbon length 1-alcohols (docosanol and tetracosanol, respectively). In our report, the dominance of these shorter chain length 1-alcohols as wax constituents represents a relatively rare phenotype in plants. The ecological significance of these dominant and relatively short 1-alcohols is still unknown. Although waxes have been a target for improvement of various crops, no such work has been reported for lettuce. This study lays the groundwork for future research that aims to integrate cuticular wax characteristics of field grown plants into the larger context of lettuce breeding and cultivar development.
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Affiliation(s)
- Wenting Luo
- Departments of Mathematics and Biosystems Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - Emmanuel Gonzalez
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Ariyan Zarei
- Department of Computer Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Sebastian Calleja
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Bruno Rozzi
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jeffrey Demieville
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Haiquan Li
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - Maria-Jose Truco
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - Dean Lavelle
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - Richard Michelmore
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - John M. Dyer
- U.S. Department of Agriculture, Agricultural Research Service, Albany, CA, 94710, USA
| | - Matthew A. Jenks
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Duke Pauli
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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Vargas-Rojas L, Ting TC, Rainey KM, Reynolds M, Wang DR. AgTC and AgETL: open-source tools to enhance data collection and management for plant science research. FRONTIERS IN PLANT SCIENCE 2024; 15:1265073. [PMID: 38450403 PMCID: PMC10915008 DOI: 10.3389/fpls.2024.1265073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Advancements in phenotyping technology have enabled plant science researchers to gather large volumes of information from their experiments, especially those that evaluate multiple genotypes. To fully leverage these complex and often heterogeneous data sets (i.e. those that differ in format and structure), scientists must invest considerable time in data processing, and data management has emerged as a considerable barrier for downstream application. Here, we propose a pipeline to enhance data collection, processing, and management from plant science studies comprising of two newly developed open-source programs. The first, called AgTC, is a series of programming functions that generates comma-separated values file templates to collect data in a standard format using either a lab-based computer or a mobile device. The second series of functions, AgETL, executes steps for an Extract-Transform-Load (ETL) data integration process where data are extracted from heterogeneously formatted files, transformed to meet standard criteria, and loaded into a database. There, data are stored and can be accessed for data analysis-related processes, including dynamic data visualization through web-based tools. Both AgTC and AgETL are flexible for application across plant science experiments without programming knowledge on the part of the domain scientist, and their functions are executed on Jupyter Notebook, a browser-based interactive development environment. Additionally, all parameters are easily customized from central configuration files written in the human-readable YAML format. Using three experiments from research laboratories in university and non-government organization (NGO) settings as test cases, we demonstrate the utility of AgTC and AgETL to streamline critical steps from data collection to analysis in the plant sciences.
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Affiliation(s)
- Luis Vargas-Rojas
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - To-Chia Ting
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Katherine M. Rainey
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Matthew Reynolds
- Wheat Physiology Group, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Diane R. Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
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Swetnam TL, Antin PB, Bartelme R, Bucksch A, Camhy D, Chism G, Choi I, Cooksey AM, Cosi M, Cowen C, Culshaw-Maurer M, Davey R, Davey S, Devisetty U, Edgin T, Edmonds A, Fedorov D, Frady J, Fonner J, Gillan JK, Hossain I, Joyce B, Lang K, Lee T, Littin S, McEwen I, Merchant N, Micklos D, Nelson A, Ramsey A, Roberts S, Sarando P, Skidmore E, Song J, Sprinkle MM, Srinivasan S, Stanzione D, Strootman JD, Stryeck S, Tuteja R, Vaughn M, Wali M, Wall M, Walls R, Wang L, Wickizer T, Williams J, Wregglesworth J, Lyons E. CyVerse: Cyberinfrastructure for open science. PLoS Comput Biol 2024; 20:e1011270. [PMID: 38324613 PMCID: PMC10878509 DOI: 10.1371/journal.pcbi.1011270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 02/20/2024] [Accepted: 11/27/2023] [Indexed: 02/09/2024] Open
Abstract
CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.
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Affiliation(s)
- Tyson L. Swetnam
- The University of Arizona, Tucson, Arizona, United States of America
| | - Parker B. Antin
- The University of Arizona, Tucson, Arizona, United States of America
| | - Ryan Bartelme
- The University of Arizona, Tucson, Arizona, United States of America
- Pivot Bio, Berkeley, California, United States of America
| | - Alexander Bucksch
- The University of Arizona, Tucson, Arizona, United States of America
| | - David Camhy
- Graz University of Technology, Graz, Austria
| | - Greg Chism
- The University of Arizona, Tucson, Arizona, United States of America
| | - Illyoung Choi
- The University of Arizona, Tucson, Arizona, United States of America
| | - Amanda M. Cooksey
- The University of Arizona, Tucson, Arizona, United States of America
| | - Michele Cosi
- The University of Arizona, Tucson, Arizona, United States of America
| | - Cindy Cowen
- The University of Arizona, Tucson, Arizona, United States of America
| | - Michael Culshaw-Maurer
- The University of Arizona, Tucson, Arizona, United States of America
- The Carpentries, Oakland, California, United States of America
| | - Robert Davey
- The Carpentries, Oakland, California, United States of America
- Earlham Institute, Norwich, United Kingdom
| | - Sean Davey
- The University of Arizona, Tucson, Arizona, United States of America
| | - Upendra Devisetty
- The University of Arizona, Tucson, Arizona, United States of America
- Greenlight Biosciences, Durham North Carolina, United States of America
| | - Tony Edgin
- The University of Arizona, Tucson, Arizona, United States of America
| | - Andy Edmonds
- The University of Arizona, Tucson, Arizona, United States of America
| | - Dmitry Fedorov
- ViQI Inc. Santa Barbara, California, United States of America
| | - Jeremy Frady
- The University of Arizona, Tucson, Arizona, United States of America
| | - John Fonner
- Texas Advanced Computing Center, Austin Texas, United States of America
| | - Jeffrey K. Gillan
- The University of Arizona, Tucson, Arizona, United States of America
| | - Iqbal Hossain
- The University of Arizona, Tucson, Arizona, United States of America
| | - Blake Joyce
- The University of Arizona, Tucson, Arizona, United States of America
| | | | - Tina Lee
- The University of Arizona, Tucson, Arizona, United States of America
| | - Shelley Littin
- The University of Arizona, Tucson, Arizona, United States of America
| | - Ian McEwen
- The University of Arizona, Tucson, Arizona, United States of America
| | - Nirav Merchant
- The University of Arizona, Tucson, Arizona, United States of America
| | - David Micklos
- DNA Learning Center, Cold Spring Harbor Laboratory, Long Island New York, United States of America
| | - Andrew Nelson
- Boyce Thompson Institute, Ithaca, New York, United States of America
| | - Ashley Ramsey
- The University of Arizona, Tucson, Arizona, United States of America
| | - Sarah Roberts
- The University of Arizona, Tucson, Arizona, United States of America
| | - Paul Sarando
- The University of Arizona, Tucson, Arizona, United States of America
| | - Edwin Skidmore
- The University of Arizona, Tucson, Arizona, United States of America
| | - Jawon Song
- Texas Advanced Computing Center, Austin Texas, United States of America
| | | | - Sriram Srinivasan
- The University of Arizona, Tucson, Arizona, United States of America
| | - Dan Stanzione
- Texas Advanced Computing Center, Austin Texas, United States of America
| | | | - Sarah Stryeck
- Graz University of Technology, Graz, Austria
- Know Center GmbH, Graz, Austria
| | - Reetu Tuteja
- The University of Arizona, Tucson, Arizona, United States of America
- Greenlight Biosciences, Durham North Carolina, United States of America
| | - Matthew Vaughn
- Texas Advanced Computing Center, Austin Texas, United States of America
| | - Mojib Wali
- Graz University of Technology, Graz, Austria
| | - Mariah Wall
- The University of Arizona, Tucson, Arizona, United States of America
| | - Ramona Walls
- The University of Arizona, Tucson, Arizona, United States of America
- Critical Path Institute, Tucson, Arizona, United States of America
| | - Liya Wang
- DNA Learning Center, Cold Spring Harbor Laboratory, Long Island New York, United States of America
| | - Todd Wickizer
- The University of Arizona, Tucson, Arizona, United States of America
| | - Jason Williams
- DNA Learning Center, Cold Spring Harbor Laboratory, Long Island New York, United States of America
| | | | - Eric Lyons
- The University of Arizona, Tucson, Arizona, United States of America
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