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Stettinius A, Holmes H, Zhang Q, Mehochko I, Winters M, Hutchison R, Maxwell A, Holliday J, Vlaisavljevich E. DNA release from plant tissue using focused ultrasound extraction (FUSE). APPLICATIONS IN PLANT SCIENCES 2023; 11:e11510. [PMID: 36818781 PMCID: PMC9934592 DOI: 10.1002/aps3.11510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 06/18/2023]
Abstract
PREMISE Sample preparation in genomics is a critical step that is often overlooked in molecular workflows and impacts the success of downstream genetic applications. This study explores the use of a recently developed focused ultrasound extraction (FUSE) technique to enable the rapid release of DNA from plant tissues for genetic analysis. METHODS FUSE generates a dense acoustic cavitation bubble cloud that pulverizes targeted tissue into acellular debris. This technique was applied to leaf samples of American chestnut (Castanea dentata), tulip poplar (Liriodendron tulipifera), red maple (Acer rubrum), and chestnut oak (Quercus montana). RESULTS We observed that FUSE can extract high quantities of DNA in 9-15 min, compared to the 30 min required for control DNA extraction methods. FUSE extracted DNA quantities of 24.33 ± 6.51 ng/mg and 35.32 ± 9.21 ng/mg from American chestnut and red maple, respectively, while control methods yielded 6.22 ± 0.87 ng/mg and 11.51 ± 1.95 ng/mg, respectively. The quality of the DNA released by FUSE allowed for successful amplification and next-generation sequencing. DISCUSSION These results indicate that FUSE can improve DNA extraction efficiency for leaf tissues. Continued development of this technology aims to adapt to field-deployable systems to increase the cataloging of genetic biodiversity, particularly in low-resource biodiversity hotspots.
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Affiliation(s)
- Alexia Stettinius
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Hal Holmes
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
- Conservation X LabsSeattleWashingtonUSA
| | - Qian Zhang
- Department of Forest Resources and Environmental ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Isabelle Mehochko
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | | | - Ruby Hutchison
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Adam Maxwell
- Department of UrologyUniversity of WashingtonSeattleWashingtonUSA
| | - Jason Holliday
- Department of Forest Resources and Environmental ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Eli Vlaisavljevich
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
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Finch KN, Jones FA, Cronn RC. Cryptic species diversity in a widespread neotropical tree genus: The case of Cedrela odorata. AMERICAN JOURNAL OF BOTANY 2022; 109:1622-1640. [PMID: 36098061 PMCID: PMC9827871 DOI: 10.1002/ajb2.16064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Reconciling the use of taxonomy to partition morphological variation and describe genetic divergence within and among closely related species is a persistent challenge in phylogenetics. We reconstructed phylogenetic relationships among Cedrela odorata (Meliaceae) and five closely allied species to test the genetic basis for the current model of species delimitation in this economically valuable and threatened genus. METHODS We prepared a nuclear species tree with the program SNPhylo and 16,000 single-nucleotide polymorphisms from 168 Cedrela specimens. Based on clades present and ancestral patterns ADMIXTURE, we designed nine species delimitation models and compared each model to current taxonomy with Bayes factor delimitation. Timing of major lineage divergences was estimated with the program SNAPP. RESULTS The resulting analysis revealed that modern C. odorata evolved from two genetically distinct ancestral sources. All species delimitation models tested better fit the data than the model representing current taxonomic delimitation. Models with the greatest marginal likelihoods separated Mesoamerican C. odorata and South American C. odorata into two species and lumped C. angustifolia and C. montana as a single species. We estimated that Cedrela diversified in South America within the last 19 million years following one or more dispersal events from Mesoamerican lineages. CONCLUSIONS Our analyses show that the present taxonomic understanding within the genus obscures divergent lineages in C. odorata due in part to morphological differentiation and taxonomic distinctions that are not predictably associated with genetic divergence. A more accurate application of taxonomy to C. odorata and related species may aid in its conservation, management, and restoration efforts.
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Affiliation(s)
- Kristen N. Finch
- Department of Botany and Plant PathologyOregon State University2082 Cordley Hall, 2701 SW Campus WayCorvallisOR97331USA
| | - F. Andrew Jones
- Department of Botany and Plant PathologyOregon State University2082 Cordley Hall, 2701 SW Campus WayCorvallisOR97331USA
- Smithsonian Tropical Research InstituteBalboa, AnconRepublic of Panama
| | - Richard C. Cronn
- USFS PNW Research Station3200 SW Jefferson WayCorvallisOR97331USA
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Vasquez-Ruiz V, Ramírez-Cisneros MÁ, Rios MY. Triterpenes and limonoids of Cedrela: Distribution, biosynthesis, and 1 H and 13 C NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:275-358. [PMID: 34730255 DOI: 10.1002/mrc.5229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Cedrela genus, a member of the Meliaceae family, presents both chemical characteristics associated with and those that distinguish it from the rest of its members. The presence of triterpenes and limonoids is the characteristic of the Meliaceae family, but the class and type of these chemical constituents are distinctive for each genus. Cedrela includes cycloartane, ursane, oleanane, tirucallane, butyrospermane, and apotirucallane triterpenes, and its limonoids belongs to six class and nine types, known as class Ia-type havanensines, class Ib-type delevoyin, class II-type gedunin, class IIIb-type andirobin, class IIIg-type mexicanolide, class IVa-type evoludone, class Va-type obacunol, class V-type limonin, and class VIII. Each of these structural arrangements includes specific traits, defined by their biosynthetic origin, which can be established by means of structural elucidation techniques, particularly 1 H and 13 C NMR, which assisted by 2D NMR techniques, allowing to deduce their structures unequivocally. The constant presence of these skeletal arrangements in Cedrela ensures that they are its chemophenetic markers and their recurrence is an important criterion for their identity. This review is a compilation of the occurrence of triterpenes and limonoids in Cedrela genus, detailing their biosynthetic association and collecting and organizing their NMR data, with the purpose of facilitating its location, analysis, and use in the phytochemical study of species from this genus.
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Affiliation(s)
- Vianey Vasquez-Ruiz
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - M Ángeles Ramírez-Cisneros
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Maria Yolanda Rios
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
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Valderrama E, Sass C, Pinilla-Vargas M, Skinner D, Maas PJM, Maas-van de Kamer H, Landis JB, Guan CJ, Specht CD. Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L. FRONTIERS IN PLANT SCIENCE 2020; 11:1195. [PMID: 32922414 PMCID: PMC7456938 DOI: 10.3389/fpls.2020.01195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/23/2020] [Indexed: 06/01/2023]
Abstract
The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L. (c. 57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical Costus species using a targeted enrichment approach. Baits were designed to capture conserved elements' variable at the species level using available genomic sequences of Costus species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.
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Affiliation(s)
- Eugenio Valderrama
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Chodon Sass
- The University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Maria Pinilla-Vargas
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | | | - Paul J. M. Maas
- Section Botany, Naturalis Biodiversity Center, Leiden, Netherlands
| | | | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Clarice J. Guan
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Chelsea D. Specht
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
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Predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01282-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Shee ZQ, Frodin DG, Cámara-Leret R, Pokorny L. Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. FRONTIERS IN PLANT SCIENCE 2020; 11:258. [PMID: 32265950 PMCID: PMC7099051 DOI: 10.3389/fpls.2020.00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/19/2020] [Indexed: 05/19/2023]
Abstract
With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia - the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands - represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.
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Affiliation(s)
- Zhi Qiang Shee
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Singapore Botanic Gardens, Singapore, Singapore
| | | | - Rodrigo Cámara-Leret
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Madrid, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
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Finch KN, Jones FA, Cronn RC. Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives. BMC Genomics 2019; 20:58. [PMID: 30658593 PMCID: PMC6339301 DOI: 10.1186/s12864-018-5382-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tree species in the genus Cedrela P. Browne are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several 'omic resources including a leaf transcriptome, organelle genome (cpDNA), and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin and enable future research on this widespread Neotropical tree genus. RESULTS We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaf tissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptome for C. odorata, and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript models successfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probes worked effectively for five Cedrela species, with each species showing similar mean on-target sequence yield and depth. The probes showed greater enrichment efficiency for Cedrela species relative to the other three distantly related Meliaceae species. We provide a set of candidate SNPs for species identification of four of the Cedrela species included in this analysis, and present draft chloroplast genomes for multiple individuals of eight species from four genera in the Meliaceae. CONCLUSIONS Deforestation and illegal logging threaten forest biodiversity globally, and wood screening tools offer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources described here provide the foundation required to develop genetic screening methods for Cedrela species identification and source validation. Due to their transferability across the genus and family as well as demonstrated applicability for both fresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studies examining the ecology and evolutionary history of Cedrela and related species in the Meliaceae.
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Affiliation(s)
- Kristen N. Finch
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - F. Andrew Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Richard C. Cronn
- USDA Forest Service Pacific Northwest Research Station, Corvallis, Oregon 97331 USA
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