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Pearce DL, Edson JE, Jennelle CS, Walter WD. Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels. Sci Rep 2024; 14:11340. [PMID: 38760358 PMCID: PMC11101418 DOI: 10.1038/s41598-024-56128-9] [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: 11/01/2023] [Accepted: 03/01/2024] [Indexed: 05/19/2024] Open
Abstract
Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method; however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the different DNA requirements between microsatellites and SNPs, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed high- or medium-density SNP panels. We found seven sample categories that met the DNA requirements for use in all three panels, and one sample category that did not meet any of the three panels requirements; however, DNA integrity was highly variable and not all sample categories that met panel DNA requirements could be considered high quality DNA. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates (tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction) could influence DNA yield.
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Affiliation(s)
- David L Pearce
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
- Department of Rangeland, Wildlife and Fisheries Management, Texas A&M University, College Station, TX, 77843, USA
| | - Jessie E Edson
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
| | - Chris S Jennelle
- Minnesota Department of Natural Resources, 5463 West Broadway Ave., Forest Lake, MN, 55025, USA
- Minnesota Department of Natural Resources, Division of Ecological and Water Resources, Nongame Wildlife Program, St Paul, MN, 55155, USA
| | - W David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 403 Forest Resources Building, University Park, PA, 16802, USA.
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Quatela AS, Cangren P, Jafari F, Michel T, de Boer HJ, Oxelman B. Retrieval of long DNA reads from herbarium specimens. AOB PLANTS 2023; 15:plad074. [PMID: 38130422 PMCID: PMC10735254 DOI: 10.1093/aobpla/plad074] [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: 12/01/2022] [Accepted: 11/06/2023] [Indexed: 12/23/2023]
Abstract
High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.
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Affiliation(s)
- Anne-Sophie Quatela
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
| | - Farzaneh Jafari
- Department of Biology, Faculty of Basic Sciences, Lorestan University, P.O. BOX 6815144316, Khorramabad, Iran
- Department of Plant Science, Center of Excellence in Phylogeny of Living Organisms, School of Biology, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
| | - Thibauld Michel
- Tropical Diversity Research Department, Royal Botanic Garden of Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LRUK
| | - Hugo J de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
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Hay NM, Windham MD, Mandáková T, Lysak MA, Hendriks KP, Mummenhoff K, Lens F, Pryer KM, Bailey CD. A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets. AMERICAN JOURNAL OF BOTANY 2023; 110:e16226. [PMID: 37561651 DOI: 10.1002/ajb2.16226] [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: 03/14/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
PREMISE Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae. METHODS To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low-copy nuclear genes using both supermatrix and species coalescence methods. RESULTS Our analyses resulted in a well-resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes. CONCLUSIONS This study presents the first broadly sampled, well-resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system.
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Affiliation(s)
- Nikolai M Hay
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Michael D Windham
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kasper P Hendriks
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
| | - Frederic Lens
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
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Martina M, Acquadro A, Portis E, Barchi L, Lanteri S. Diversity analyses in two ornamental and large-genome Ranunculaceae species based on a low-cost Klenow NGS-based protocol. FRONTIERS IN PLANT SCIENCE 2023; 14:1187205. [PMID: 37360724 PMCID: PMC10289064 DOI: 10.3389/fpls.2023.1187205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Persian buttercup (Ranunculus asiaticus L.) and poppy anemone (Anemone coronaria L.) are ornamental, outcrossing, perennial species belonging to the Ranunculaceae family, characterized by large and highly repetitive genomes. We applied K-seq protocol in both species to generate high-throughput sequencing data and produce a large number of genetic polymorphisms. The technique entails the application of Klenow polymerase-based PCR using short primers designed by analyzing k-mer sets in the genome sequence. To date the genome sequence of both species has not been released, thus we designed primer sets based on the reference the genome sequence of the related species Aquilegia oxysepala var. kansuensis (Brühl). A whole of 11,542 SNPs were selected for assessing genetic diversity of eighteen commercial varieties of R. asiaticus, while 1,752 SNPs for assessing genetic diversity in six cultivars of A. coronaria. UPGMA dendrograms were constructed and in R. asiaticus integrated in with PCA analysis. This study reports the first molecular fingerprinting within Persian buttercup, while the results obtained in poppy anemone were compared with a previously published SSR-based fingerprinting, proving K-seq to be an efficient protocol for the genotyping of complex genetic backgrounds.
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McAssey EV, Downs C, Yorkston M, Morden C, Heyduk K. A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11527. [PMID: 37342160 PMCID: PMC10278930 DOI: 10.1002/aps3.11527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 06/22/2023]
Abstract
Premise The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library. Methods Plants collected for the Hawaiian Plant DNA Library were simultaneously accessioned as herbarium specimens at the time of collection, from 1994-2019. Paired samples were sequenced using short-read sequencing and assessed for chloroplast assembly and nuclear gene recovery. Results Herbarium specimen-derived DNA was statistically more fragmented than freezer-stored DNA derived from fresh tissue, leading to poorer chloroplast assembly and overall lower coverage. The number of nuclear targets recovered varied mostly by total sequencing reads per library and age of specimen, but not by storage method (herbarium or long-term freezer). Although there was evidence of DNA damage in the samples, there was no evidence that it was related to the length of time in storage, whether frozen or as herbarium specimens. Discussion DNA extracted from herbarium tissues will continue to be invaluable, despite being highly fragmented and degraded. Rare floras would benefit from both traditional herbarium storage methods and extracted DNA freezer banks.
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Affiliation(s)
- Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Cassidy Downs
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Mitsuko Yorkston
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Clifford Morden
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
| | - Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHawaiʻiUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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Rushworth CA, Wagner MR, Mitchell-Olds T, Anderson JT. The Boechera model system for evolutionary ecology. AMERICAN JOURNAL OF BOTANY 2022; 109:1939-1961. [PMID: 36371714 DOI: 10.1002/ajb2.16090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.
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Affiliation(s)
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
| | | | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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Rosche C, Baasch A, Runge K, Brade P, Träger S, Parisod C, Hensen I. Tracking population genetic signatures of local extinction with herbarium specimens. ANNALS OF BOTANY 2022; 129:857-868. [PMID: 35670810 PMCID: PMC9292615 DOI: 10.1093/aob/mcac061] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness, which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. METHODS We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as a surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. KEY RESULTS Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both the spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as a powerful predictor of functional connectivity which may promote decision-making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. CONCLUSIONS Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex situ population and a germination trial underlines the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.
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Affiliation(s)
- Christoph Rosche
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Große Steinstraße 79/80, 06108 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Annett Baasch
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg (Saale), Germany
| | - Karen Runge
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg (Saale), Germany
| | - Philipp Brade
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg (Saale), Germany
| | - Sabrina Träger
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Große Steinstraße 79/80, 06108 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Christian Parisod
- University of Fribourg, Department of Biology, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Isabell Hensen
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Große Steinstraße 79/80, 06108 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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A RADseq Phylogeny of Barleria (Acanthaceae) Resolves Fine-Scale Relationships. Mol Phylogenet Evol 2022; 169:107428. [DOI: 10.1016/j.ympev.2022.107428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 12/29/2021] [Accepted: 01/14/2022] [Indexed: 11/20/2022]
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Kämper W, Ogbourne SM, Hawkes D, Trueman SJ. SNP markers reveal relationships between fruit paternity, fruit quality and distance from a cross-pollen source in avocado orchards. Sci Rep 2021; 11:20043. [PMID: 34625603 PMCID: PMC8501009 DOI: 10.1038/s41598-021-99394-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/07/2021] [Indexed: 11/26/2022] Open
Abstract
Cross-pollination can improve fruit yield, fruit size and nutritional quality of many food crops. However, we rarely understand what proportions of the crop result from self- or cross-pollination, how cross-pollination affects crop quality, and how far pollen is transported by pollinators. Management strategies to improve pollination services are consequently not optimal for many crops. We utilised a series of SNP markers, unique for each cultivar of avocado, to quantify proportions of self- and cross-paternity in fruit of Hass avocado at increasing distances from cross-pollen sources. We assessed whether distance from a cross-pollen source determined the proportions of self-pollinated and cross-pollinated fruit, and evaluated how self- and cross-paternity affected fruit size and nutritional quality. Avocado fruit production resulted from both self- and cross-pollination in cultivar Hass in Queensland, Australia. Cross-pollination levels decreased with increasing distance from a cross-pollen source, from 63% in the row adjacent to another cultivar to 25% in the middle of a single-cultivar block, suggesting that pollen transport was limited across orchard rows. Limited pollen transport did not affect fruit size or quality in Hass avocados as xenia effects of a Shepard polliniser on size and nutritional quality were minor.
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Affiliation(s)
- Wiebke Kämper
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Nathan, QLD, Australia.
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr-University Bochum, Bochum, Germany.
| | - Steven M Ogbourne
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, Australia
| | - David Hawkes
- Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, Brisbane, QLD, Australia
| | - Stephen J Trueman
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Nathan, QLD, Australia
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Slimp M, Williams LD, Hale H, Johnson MG. On the potential of Angiosperms353 for population genomic studies. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311419. [PMID: 34336401 PMCID: PMC8312745 DOI: 10.1002/aps3.11419] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 05/11/2023]
Abstract
PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)-typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics. DISCUSSION Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens.
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Affiliation(s)
- Madeline Slimp
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Lindsay D. Williams
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Haley Hale
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
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Albani Rocchetti G, Armstrong CG, Abeli T, Orsenigo S, Jasper C, Joly S, Bruneau A, Zytaruk M, Vamosi JC. Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species. THE NEW PHYTOLOGIST 2021; 230:433-450. [PMID: 33280123 DOI: 10.1111/nph.17133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 05/29/2023]
Abstract
Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.
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Affiliation(s)
| | | | - Thomas Abeli
- Department of Science, University Roma Tre, Viale G. Marconi 446, Roma, 00154, Italy
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Caroline Jasper
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Simon Joly
- Montreal Botanical Garden, Montréal, QC, H1X 2B2, Canada
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Maria Zytaruk
- Department of English, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Martina M, Tikunov Y, Portis E, Bovy AG. The Genetic Basis of Tomato Aroma. Genes (Basel) 2021; 12:genes12020226. [PMID: 33557308 PMCID: PMC7915847 DOI: 10.3390/genes12020226] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as "sweet", "smoky", or "fruity" aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and 5ifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.
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Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
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Folk RA, Kates HR, LaFrance R, Soltis DE, Soltis PS, Guralnick RP. High-throughput methods for efficiently building massive phylogenies from natural history collections. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11410. [PMID: 33680581 PMCID: PMC7910806 DOI: 10.1002/aps3.11410] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/20/2020] [Indexed: 05/10/2023]
Abstract
PREMISE Large phylogenetic data sets have often been restricted to small numbers of loci from GenBank, and a vetted sampling-to-sequencing phylogenomic protocol scaling to thousands of species is not yet available. Here, we report a high-throughput collections-based approach that empowers researchers to explore more branches of the tree of life with numerous loci. METHODS We developed an integrated Specimen-to-Laboratory Information Management System (SLIMS), connecting sampling and wet lab efforts with progress tracking at each stage. Using unique identifiers encoded in QR codes and a taxonomic database, a research team can sample herbarium specimens, efficiently record the sampling event, and capture specimen images. After sampling in herbaria, images are uploaded to a citizen science platform for metadata generation, and tissue samples are moved through a simple, high-throughput, plate-based herbarium DNA extraction and sequencing protocol. RESULTS We applied this sampling-to-sequencing workflow to ~15,000 species, producing for the first time a data set with ~50% taxonomic representation of the "nitrogen-fixing clade" of angiosperms. DISCUSSION The approach we present is appropriate at any taxonomic scale and is extensible to other collection types. The widespread use of large-scale sampling strategies repositions herbaria as accessible but largely untapped resources for broad taxonomic sampling with thousands of species.
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Affiliation(s)
- Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippiUSA
| | - Heather R. Kates
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Raphael LaFrance
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
- Genetics InstituteUniversity of FloridaGainesvilleFloridaUSA
- Biodiversity InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
- Genetics InstituteUniversity of FloridaGainesvilleFloridaUSA
- Biodiversity InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Robert P. Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
- Biodiversity InstituteUniversity of FloridaGainesvilleFloridaUSA
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15
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Dean GH, Muriithi AN, Culley TM. Conducting botanical research with limited resources: Low‐cost methods in the plant sciences. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11341. [PMCID: PMC7186899 DOI: 10.1002/aps3.11341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 06/12/2023]
Affiliation(s)
- Gillian H. Dean
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverV6T 1Z4Canada
| | - Alice N. Muriithi
- School of Agricultural and Food SciencesJaramogi Oginga Odinga University of Science and TechnologyBox 210-40601BondoKenya
| | - Theresa M. Culley
- Department of Biological SciencesUniversity of Cincinnati614 Rieveschl HallCincinnatiOhio45221‐0006USA
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Jordon‐Thaden IE, Beck JB, Rushworth CA, Windham MD, Diaz N, Cantley JT, Martine CT, Rothfels CJ. A basic ddRADseq two-enzyme protocol performs well with herbarium and silica-dried tissues across four genera. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11344. [PMID: 32351803 PMCID: PMC7186894 DOI: 10.1002/aps3.11344] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/28/2020] [Indexed: 05/25/2023]
Abstract
PREMISE The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double-digest restriction site-associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica-dried and herbarium tissue. METHODS DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed. RESULTS Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples. DISCUSSION These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on-site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium-based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.
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Affiliation(s)
- Ingrid E. Jordon‐Thaden
- University Herbaria and Department of Integrative BiologyUniversity of California Berkeley3040 Valley Life Sciences BuildingBerkeleyCalifornia94720USA
- Present address:
Department of BotanyUniversity of Wisconsin430 Lincoln DriveMadisonWisconsin53706USA
| | - James B. Beck
- Department of Biological SciencesWichita State University1845 FairmountWichitaKansas67260USA
- Botanical Research Institute of Texas1700 University DriveFort WorthTexas76107USA
| | - Catherine A. Rushworth
- Department of Evolution and Ecology and Center for Population BiologyUniversity of California DavisOne Shields AvenueDavisCalifornia95616USA
- Department of Plant and Microbial BiologyUniversity of Minnesota1500 Gortner AvenueSt. PaulMinnesota55108USA
| | - Michael D. Windham
- Department of BiologyDuke University130 Science DriveDurhamNorth Carolina27708USA
| | - Nicolas Diaz
- Department of BiologyBucknell University1 Dent DriveLewisburgPennsylvania17837USA
- Present address:
Biology DepartmentPortland State University1719 SW 10th AvenuePortlandOregon97201USA
| | - Jason T. Cantley
- Department of BiologyBucknell University1 Dent DriveLewisburgPennsylvania17837USA
- Present address:
Department of BiologySan Francisco State University1600 Holloway AvenueSan FranciscoCalifornia94132USA
| | | | - Carl J. Rothfels
- University Herbaria and Department of Integrative BiologyUniversity of California Berkeley3040 Valley Life Sciences BuildingBerkeleyCalifornia94720USA
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