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Applications in Plant Sciences

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https://www.readbyqxmd.com/read/29732268/practical-considerations-for-plant-phylogenomics
#1
REVIEW
Michael R McKain, Matthew G Johnson, Simon Uribe-Convers, Deren Eaton, Ya Yang
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome-scale data from diverse lineages. The development of high-throughput sequencing and long-read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732267/chromploid-an-r-package-for-chromosome-number-evolution-across-the-plant-tree-of-life
#2
Rosana Zenil-Ferguson, J Gordon Burleigh, José Miguel Ponciano
Premise of the Study: Polyploidy has profound evolutionary consequences for land plants. Despite the availability of large phylogenetic and chromosomal data sets, estimating the rates of polyploidy and chromosomal evolution across the tree of life remains a challenging, computationally complex problem. We introduce the R package chromploid, which allows scientists to perform inference of chromosomal evolution rates across large phylogenetic trees. Methods and Results: chromploid is an open-source package in the R environment that calculates the likelihood function of models of chromosome evolution...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732266/targeting-legume-loci-a-comparison-of-three-methods-for-target-enrichment-bait-design-in-leguminosae-phylogenomics
#3
Mohammad Vatanparast, Adrian Powell, Jeff J Doyle, Ashley N Egan
Premise of the Study: The development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts. Methods: Using 30 transcriptomes, we compared Hyb-Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation- and coalescent-based methods...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732265/extraction-of-phenotypic-traits-from-taxonomic-descriptions-for-the-tree-of-life-using-natural-language-processing
#4
Lorena Endara, Hong Cui, J Gordon Burleigh
Premise of the Study: Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732264/algorithms-and-strategies-in-short-read-shotgun-metagenomic-reconstruction-of-plant-communities
#5
Robert S Harbert
Premise of the Study: DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants. Methods: To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732263/a-protocol-for-high-throughput-untargeted-forest-community-metabolomics-using-mass-spectrometry-molecular-networks
#6
Brian E Sedio, Cristopher A Boya P, Juan Camilo Rojas Echeverri
Premise of the Study: We describe a field collection, sample processing, and ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) instrumental and bioinformatics method developed for untargeted metabolomics of plant tissue and suitable for molecular networking applications. Methods and Results: A total of 613 leaf samples from 204 tree species was collected in the field and analyzed using UHPLC-MS/MS. Matching of molecular fragmentation spectra generated over 125,000 consensus spectra representing unique molecular structures, 26,410 of which were linked to at least one structurally similar compound...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732262/comparison-of-taxon-specific-versus-general-locus-sets-for-targeted-sequence-capture-in-plant-phylogenomics
#7
John H Chau, Wolfgang A Rahfeldt, Richard G Olmstead
Premise of the Study: Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and have orthologs in large clades of plants. Methods: We identify and compare a taxon-specific locus set and three general locus sets (conserved ortholog set [COSII], shared single-copy nuclear [APVO SSC] genes, and pentatricopeptide repeat [PPR] genes) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732261/raspberry-pi-powered-imaging-for-plant-phenotyping
#8
Jose C Tovar, J Steen Hoyer, Andy Lin, Allison Tielking, Steven T Callen, S Elizabeth Castillo, Michael Miller, Monica Tessman, Noah Fahlgren, James C Carrington, Dmitri A Nusinow, Malia A Gehan
Premise of the Study: Image-based phenomics is a powerful approach to capture and quantify plant diversity. However, commercial platforms that make consistent image acquisition easy are often cost-prohibitive. To make high-throughput phenotyping methods more accessible, low-cost microcomputers and cameras can be used to acquire plant image data. Methods and Results: We used low-cost Raspberry Pi computers and cameras to manage and capture plant image data. Detailed here are three different applications of Raspberry Pi-controlled imaging platforms for seed and shoot imaging...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732260/a-guide-to-sequence-your-favorite-plant-genomes
#9
REVIEW
Fay-Wei Li, Alex Harkess
With the rapid development of sequencing technology and the plummeting cost, assembling whole genomes from non-model plants will soon become routine for plant systematists and evolutionary biologists. Here we summarize and compare several of the latest genome sequencing and assembly approaches, offering a practical guide on how to approach a genome project. We also highlight certain precautions that need to be taken before investing time and money into a genome project.
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732259/species-distribution-modeling-based-on-the-automated-identification-of-citizen-observations
#10
Christophe Botella, Alexis Joly, Pierre Bonnet, Pascal Monestiez, François Munoz
Premise of the Study: A species distribution model computed with automatically identified plant observations was developed and evaluated to contribute to future ecological studies. Methods: We used deep learning techniques to automatically identify opportunistic plant observations made by citizens through a popular mobile application. We compared species distribution modeling of invasive alien plants based on these data to inventories made by experts. Results: The trained models have a reasonable predictive effectiveness for some species, but they are biased by the massive presence of cultivated specimens...
February 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732258/use-of-globally-unique-identifiers-guids-to-link-herbarium-specimen-records-to-physical-specimens
#11
REVIEW
Gil Nelson, Patrick Sweeney, Edward Gilbert
With the advent of the U.S. National Science Foundation's Advancing Digitization of Biodiversity Collections program and related worldwide digitization initiatives, the rate of herbarium specimen digitization in the United States has expanded exponentially. As the number of electronic herbarium records proliferates, the importance of linking these records to the physical specimens they represent as well as to related records from other sources will intensify. Although a rich and diverse literature has developed over the past decade that addresses the use of specimen identifiers for facilitating linking across the internet, few implementable guidelines or recommended practices for herbaria have been advanced...
February 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732257/the-australasian-virtual-herbarium-tracking-data-usage-and-benefits-for-biological-collections
#12
David J Cantrill
Premise of the Study: Globally, natural history collections are focused on digitizing specimens and information and making these data accessible. Usage information on National Herbarium of Victoria data made available through the Atlas of Living Australia and The Australasian Virtual Herbarium (AVH) is analyzed to understand how and by whom herbarium data are being used. Methods: Since 2010, AVH data usage information has been gathered from users and supplied to data custodians as a spreadsheet that includes number of download events, number of records downloaded, and user reasons for downloading data in predefined categories...
February 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732256/a-workflow-and-protocol-describing-the-field-to-digitization-process-for-new-project-based-fossil-leaf-collections
#13
Dori L Contreras
Premise of the Study: This article provides a workflow and protocol for paleobotanical researchers that integrates project-based fossil leaf specimen and data collection with curation and digitization. The methods aim to facilitate efficient digitization of new collections by researchers during the course of their study and promote public databasing of new specimen and project data. Methods and Results: The workflow was developed and refined to facilitate a project reconstructing an extensive fossil forest from leaf impressions/compressions...
February 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732255/herbarium-data-global-biodiversity-and-societal-botanical-needs-for-novel-research
#14
REVIEW
Shelley A James, Pamela S Soltis, Lee Belbin, Arthur D Chapman, Gil Nelson, Deborah L Paul, Matthew Collins
Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change...
February 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732254/using-citizen-science-to-bridge-taxonomic-discovery-with-education-and-outreach
#15
Matt von Konrat, Thomas Campbell, Ben Carter, Matthew Greif, Mike Bryson, Juan Larraín, Laura Trouille, Steve Cohen, Eve Gaus, Ayesha Qazi, Eric Ribbens, Tatyana Livshultz, Taylor J Walker, Tomomi Suwa, Taylor Peterson, Yarency Rodriguez, Caitlin Vaughn, Christina Yang, Selma Aburahmeh, Brian Carstensen, Peter de Lange, Charlie Delavoi, Kalman Strauss, Justyna Drag, Blanka Aguero, Chris Snyder, Joann Martinec, Arfon Smith
Premise of the Study: Biological collections are uniquely poised to inform the stewardship of life on Earth in a time of cataclysmic biodiversity loss. Efforts to fully leverage collections are impeded by a lack of trained taxonomists and a lack of interest and engagement by the public. We provide a model of a crowd-sourced data collection project that produces quality taxonomic data sets and empowers citizen scientists through real contributions to science. Entitled MicroPlants, the project is a collaboration between taxonomists, citizen science experts, and teachers and students from universities and K-12...
February 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732253/digitization-protocol-for-scoring-reproductive-phenology-from-herbarium-specimens-of-seed-plants
#16
Jennifer M Yost, Patrick W Sweeney, Ed Gilbert, Gil Nelson, Robert Guralnick, Amanda S Gallinat, Elizabeth R Ellwood, Natalie Rossington, Charles G Willis, Stanley D Blum, Ramona L Walls, Elspeth M Haston, Michael W Denslow, Constantin M Zohner, Ashley B Morris, Brian J Stucky, J Richard Carter, David G Baxter, Kjell Bolmgren, Ellen G Denny, Ellen Dean, Katelin D Pearson, Charles C Davis, Brent D Mishler, Pamela S Soltis, Susan J Mazer
Premise of the Study: Herbarium specimens provide a robust record of historical plant phenology (the timing of seasonal events such as flowering or fruiting). However, the difficulty of aggregating phenological data from specimens arises from a lack of standardized scoring methods and definitions for phenological states across the collections community. Methods and Results: To address this problem, we report on a consensus reached by an iDigBio working group of curators, researchers, and data standards experts regarding an efficient scoring protocol and a data-sharing protocol for reproductive traits available from herbarium specimens of seed plants...
February 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732252/the-macrofungi-collection-consortium
#17
Barbara M Thiers, Roy E Halling
Premise of the Study: The Macrofungi Collection Consortium (MaCC) is a digitization project funded by the National Science Foundation's Advancing Digitization of Biodiversity Collections program. The main scientific objective of the MaCC project was to provide baseline data for determining the extent and distribution of macrofungal diversity. Methods and Results: Between 2012 and 2017, 39 participating institutions digitized approximately 1,250,000 specimens of macrofungi from U...
February 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732251/pollen-sleuthing-for-terrestrial-plant-surveys-locating-plant-populations-by-exploiting-pollen-movement
#18
Lesley G Campbell, Stephanie J Melles, Eric Vaz, Rebecca J Parker, Kevin S Burgess
Premise of the Study: We present an innovative technique for sampling, identifying, and locating plant populations that release pollen, without extensive ground surveys. This method (1) samples pollen at random locations within the target species' habitat, (2) detects species' presence using morphological pollen analysis, and (3) uses kriging to predict likely locations of populations to focus future search efforts. Methods: To demonstrate, we applied the pollen sleuthing system to search for artificially constructed populations of Brassica rapa in an old field...
January 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732249/editorial-the-beginning-of-a-new-partnership
#19
EDITORIAL
Pamela K Diggle, Theresa M Culley
No abstract text is available yet for this article.
January 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29732248/microsatellite-markers-for-study-of-the-invasive-species-rumex-alpinus-polygonaceae
#20
Mária Šurinová, Andrea Jarošová, Zuzana Münzbergová
Premise of the Study: Polymorphic microsatellite markers were developed to study genetic diversity, population structure, and dispersal strategies of the highly invasive species Rumex alpinus (Polygonaceae). Methods and Results: Fifteen polymorphic microsatellite loci were developed using a 454 sequencing approach and used to genotype 72 individuals from six populations in Austria and France. All markers were polymorphic in at least one investigated population, and the number of alleles ranged from one to four alleles per locus...
January 2018: Applications in Plant Sciences
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