Weed removal in agriculture is typically achieved using herbicides. The use of autonomous robots to reduce weeds is a promising alternative solution, although their implementation requires the precise detection and identification of crops and weeds to allow an efficient action.

Trichomes are hair‐like appendages extending from the plant epidermis. They serve many important biotic roles, including interference with herbivore movement. Characterizing the number, density, and distribution of trichomes can provide valuable insights on plant response to insect infestation and define the extent of plant defense capability. Automated trichome counting would speed up this research

Advancements in machine learning and the rise of accessible “big data” provide an important opportunity to improve trait‐based plant identification. Here, we applied decision‐tree induction to a subset of data from the TRY plant trait database to (1) assess the potential of decision trees for plant identification and (2) determine informative traits for distinguishing taxa.

High‐resolution cameras are very helpful for plant phenotyping as their images enable tasks such as target vs. background discrimination and the measurement and analysis of fine above‐ground plant attributes. However, the acquisition of high‐resolution images of plant roots is more challenging than above‐ground data collection. An effective super‐resolution (SR) algorithm is therefore needed for overcoming

Statistical methods used by most morphologists to validate species boundaries (such as principal component analysis [PCA] and non‐metric multidimensional scaling [nMDS]) are limiting because these methods are mostly used as visualization methods, and because the groups are identified by taxonomists (i.e., supervised), adding human bias. Here, we use a spectral clustering algorithm for the unsupervised

The automated recognition of Latin scientific names within vernacular text has many applications, including text mining, search indexing, and automated specimen‐label processing. Most published solutions are computationally inefficient, incapable of running within a web browser, and focus on texts in English, thus omitting a substantial portion of biodiversity literature.

Recent advances in sequencing and informatic technologies have led to a deluge of publicly available genomic data. While it is now relatively easy to sequence, assemble, and identify genic regions in diploid plant genomes, functional annotation of these genes is still a challenge. Over the past decade, there has been a steady increase in studies utilizing machine learning algorithms for various aspects

X‐ray microcomputed tomography (microCT) can be used to measure 3D leaf internal anatomy, providing a holistic view of tissue organization. Previously, the substantial time needed for segmenting multiple tissues limited this technique to small data sets, restricting its utility for phenotyping experiments and limiting our confidence in the inferences of these studies due to low replication numbers

In our paper, “Maximizing human effort for analyzing scientific images: A case study using digitized herbarium sheets,” Figure 2 was published without the legend. We apologize for the error. The published article (full‐text and PDF) has been corrected. Figure 2 Open in figure viewerPowerPoint Predicted accuracy of in‐person volunteers (A) and Notes from Nature volunteers (B) given the plant genus and

Seed germination over time is characterized by a sigmoid curve, called a germination curve, in which the percentage (or absolute number) of seeds that have completed germination is plotted against time. A number of individual coefficients have been developed to characterize this germination curve. However, as germination is considered to be a qualitative developmental response of an individual seed

Machine learning approaches are affecting all aspects of modern society, from autocorrect applications on cell phones to self‐driving cars to facial recognition, personalized medicine, and precision agriculture. Although machine learning has a long history, drastic improvements in these application areas recently have been driven by improvements to computational infrastructure; increased computing

Herbarium specimens represent an outstanding source of material with which to study plant phenological changes in response to climate change. The fine‐scale phenological annotation of such specimens is nevertheless highly time consuming and requires substantial human investment and expertise, which are difficult to rapidly mobilize.

Digitization and imaging of herbarium specimens provides essential historical phenotypic and phenological information about plants. However, the full use of these resources requires high‐quality human annotations for downstream use. Here we provide guidance on the design and implementation of image annotation projects for botanical research.

Digitized images of herbarium specimens are highly diverse with many potential sources of visual noise and bias. The systematic removal of noise and minimization of bias must be achieved in order to generate biological insights based on the plants rather than the digitization and mounting practices involved. Here, we develop a workflow and data set of high‐resolution image masks to segment plant tissues

Despite the economic significance of insect damage to plants (i.e., herbivory), long‐term data documenting changes in herbivory are limited. Millions of pressed plant specimens are now available online and can be used to collect big data on plant–insect interactions during the Anthropocene.

Equisetum is a distinctive vascular plant genus with 15 extant species worldwide. Species identification is complicated by morphological plasticity and frequent hybridization events, leading to a disproportionately high number of misidentified specimens. These may be correctly identified by applying appropriate computer vision tools.

The generation of morphological data in evolutionary, taxonomic, and ecological studies of plants using herbarium material has traditionally been a labor‐intensive task. Recent progress in machine learning using deep artificial neural networks (deep learning) for image classification and object detection has facilitated the establishment of a pipeline for the automatic recognition and extraction of

Plant biodiversity is threatened, yet many species remain undescribed. It is estimated that >50% of undescribed species have already been collected and are awaiting discovery in herbaria. Robust automatic species identification algorithms using machine learning could accelerate species discovery.

Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure leaves from digitized herbarium specimens or leaf images using an ensemble of machine learning algorithms.

Premise Nuclear microsatellite markers were developed for Linum bienne, the sister species of the crop L. usitatissimum, to provide molecular genetic tools for the investigation of L. bienne genetic diversity and structure. Methods and Results Fifty microsatellite loci were identified in L. bienne by means of genome skimming, and 44 loci successfully amplified. Of these, 16 loci evenly spread across

Premise Young plant roots share a common architecture: a central vascular cylinder surrounded by enveloping cylinders of ground and dermal tissue produced by an apical promeristem. Roots with closed apical organization can be studied to explore how ontogeny is managed. The analysis of transverse and longitudinal sections has been the most useful approach for this, but suffers from limitations. We developed

Premise Atractylodes japonica (Asteraceae) is endemic to East Asia, where its rhizomes are used in traditional medicine. To investigate the genetic diversity of this species, we developed polymorphic microsatellite markers. Methods and Results We obtained a total of 175,825 simple sequence repeat (SSR) loci using the Illumina HiSeq 2500 system. Eighteen polymorphic SSR primer pairs were selected to

Premise Camellia reticulata, which is native to southwestern China, is an economically important plant belonging to the family Theaceae. We developed expressed sequence tag-simple sequence repeat (EST-SSR) markers for C. reticulata, which can be used to investigate its genetic diversity, population structure, and evolutionary history. Methods and Results We detected 4780 SSRs in C. reticulata from

Premise Physiological processes may vary within leaf laminae; however, the accompanying heterogeneity in leaf venation is rarely investigated because its quantification can be time consuming. Here we introduce accelerated protocols using existing software to increase sample throughput and ask whether laminae venation varies among three crop types and four subspecies of Brassica rapa. Methods FAA (formaldehyde

Premise Putatively single-copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment

Premise We present a low-cost, battery-operated, portable pump, "FloPump," which allows regulated air sampling for the study of volatile organic compounds (VOCs). VOCs are routinely investigated in applications such as atmospheric chemistry, agriculture, and fragrance biology. Methods and Results We compared the performance of FloPump with the Supelco pump in collecting VOCs using two test samples:

Plant ecologists in the Anthropocene are tasked with documenting, interpreting, and predicting how plants respond to environmental change. Phenology, the timing of seasonal biological events including leaf-out, flowering, fruiting, and leaf senescence, is among the most visible and oft-recorded facets of plant ecology. Climate-driven shifts in plant phenology can alter reproductive success, interspecific

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

Premise In the ferns, cell size has been explored with spores, which are largely uniform within species, produced in abundance, and durable. However, spore size and shape have been variously defined, and the relationship of these traits to genome size has not been well established. Here, we explore the variation in fern spore size and shape by ploidy level and genome size. Methods Measurements of spore

Premise Seed oil is an economically important trait in Brassica oilseed crops. A novel method was developed to isolate Arabidopsis thaliana seeds with altered oil content. Methods and Results In A. thaliana, seed oil content is correlated with seed density, with high-oil seeds being less dense than wild type and tending to float in solution, and low-oil seeds being denser and tending to sink. In contrast

Premise We developed a novel low-cost method to visually phenotype belowground structures in the plant rhizosphere. We devised the method introduced here to address the difficulties encountered growing plants in seed germination pouches for long-term experiments and the high cost of other mini-rhizotron alternatives. Methods and Results The method described here took inspiration from homemade ant farms

Premise Over 3000 species of plants and animals release toxic hydrogen cyanide (HCN) gas when their tissues are crushed. To investigate the role of cyanogenesis in Passiflora-herbivore interactions, we developed an inexpensive, rapid, sensitive method for measuring HCN emissions from crushed tissues. Methods The method includes crushed tissue confinement in a closed chamber, where cyanogenesis reactions

Premise A portable, simple, yet efficient method was developed for the rapid extraction of xylem sap from the stems and petioles of tomato plants for diagnostic and quantification assays of the xylem-colonizing wilt bacterium Ralstonia solanacearum. Methods and Results Xylem saps were extracted from tomato stem sections using negative pressure generated from handheld needleless syringes. The samples

High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies

The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which can be inflated when using off-the-shelf kits or reagents not

Premise Drought-induced tree mortality is an emergent threat to forests worldwide, particularly to large trees. Drought-manipulation experiments involving throughfall exclusion (TFE) tend to focus on large plots that can be expensive to establish and maintain and may be unsuitable for large trees or indigenous forests. We set out to establish a relatively inexpensive TFE method in a natural forest

Premise A set of polymorphic nuclear microsatellite loci was developed and tested for use in population genetic analyses of Anthericum ramosum (Agavaceae) and related species. Methods and Results Sequences of 110 primers were extracted in silico from Illumina MiSeq genome skimming data. The degree of polymorphism of 19 loci was tested in four A. ramosum populations collected in Central and Eastern

Premise Flowers of the Apocynaceae (milkweed family) have complex structures and pollination mechanisms. Pollen removal and deposition in Angadenia, Pentalinon, and Echites are similar, with anthers releasing pollen onto the sterile style head. The mid-style head excretes a glue that coats the mouthparts of vistors to aid in the transfer of pollen. Subsequent probes may deposit pollen on the receptive

Premise The Climate Reconstruction Analysis using Coexistence Likelihood Estimation (CRACLE) method utilizes a robust set of modeling tools for estimating climate and paleoclimate from vegetation using large repositories of biodiversity data and open access R software. Methods Here, we implement a new R package for the estimation of climate from extant and fossil vegetation. The 'cRacle' package implements

Premise Ferula sadleriana (Apiaceae) is a polycarpic, perennial herb with a very limited range and small populations. It is listed as "endangered" on the IUCN Red List of Threatened Species. Microsatellite markers can contribute to conservation efforts by allowing the study of the genetic structure of its shrinking populations. Methods and Results We used a microsatellite-enriched library combined

Premise Pteroceltis tatarinowii (Ulmaceae), the only species of the genus Pteroceltis, is an endangered tree in China. Here, novel expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed to illuminate its genetic diversity for conservation and assisted breeding. Methods and Results Based on Illumina transcriptome data from P. tatarinowii, a total of 70 EST-SSR markers were initially

Premise Microsatellite markers were developed for the western Mediterranean tree Tamarix gallica (Tamaricaceae) as part of a study of its genetic diversity and structure. Methods and Results Seventeen microsatellite markers were developed for T. gallica, 14 of which were polymorphic. These microsatellites have di-, tri-, and tetranucleotide repeats with 1-13 alleles per locus and population. Levels

Premise Microsatellite markers were developed for the perennial herb Salvia pratensis (Lamiaceae), a species representative of European dry grasslands. The development of microsatellite markers is needed for genetic and phylogeographical studies of species from the genus Salvia. Methods and Results We used low-coverage Illumina sequencing to identify microsatellite loci. Based on these data, we have

Premise Plant invasions are increasing globally, and extensive study of the genetic background of the source and invading populations is needed to understand such biological processes. For this reason, chloroplast microsatellite markers were identified to explore the genetic diversity of the noxious weed Ambrosia trifida (Asteraceae). Methods and Results The complete chloroplast genome of A. trifida

Premise The field of biodiversity informatics has developed rapidly in recent years, with broad availability of large-scale information resources. However, online biodiversity information is biased spatially as a result of slow and uneven capture and digitization of existing data resources. The West African Plants Initiative approach to data capture is a prototype of a novel solution to the problems

The past six years have seen the rapid growth of studies of CRISPR/Cas9 in plant genome editing, a method that enormously facilitates both basic research and practical applications. Most studies have focused on genetic model species, but plant species that are not genetic models may also be economically important or biologically significant, or both. However, developing the CRISPR/Cas9 system in a

Premise Citizen science platforms for sharing photographed digital vouchers, such as iNaturalist, are a promising source of phenology data, but methods and best practices for use have not been developed. Here we introduce methods using Yucca flowering phenology as a case study, because drivers of Yucca phenology are not well understood despite the need to synchronize flowering with obligate pollinators

Premise We developed single-copy nuclear DNA markers for a perennial herb, Oreocharis auricula (Gesneriaceae), to help infer the evolutionary history of the genus Oreocharis in subtropical China. Methods and Results We screened 834 putative single-copy nuclear genes from transcriptomes of 11 species of Primulina using the Illumina HiSeq 2000 platform. Based on the screening results, we developed 16

Premise Microsatellite markers were developed to measure genetic diversity and relatedness of ex situ collections of Brighamia insignis (Campanulaceae). Methods and Results Potential microsatellite markers were identified from two sources; 28 were developed for B. insignis and an additional 12 markers from a previously published study of Lobelia villosa. Primer pairs were tested on 30 individuals of

Premise When plants are exposed to stress conditions, irreversible damage can occur, negatively impacting yields. It is therefore important to detect stress symptoms in plants, such as the accumulation of anthocyanin, as early as possible. Methods and Results Twenty-two regression models in five color spaces were trained to develop a prediction model for plant anthocyanin levels from digital color

Premise Microsatellite markers were developed in Echinomastus johnsonii (Cactaceae) for use in several morphologically similar, closely related taxa within the genus to study genetic structure and diversity within and among individuals and populations. Methods and Results Using reads from shallow, whole genome Illumina HiSeq high-throughput sequencing, we developed and characterized 15 microsatellite

Premise Cañahua is a semi-domesticated crop grown in high-altitude regions of the Andes. It is an A-genome diploid (2n = 2x = 18) relative of the allotetraploid (AABB) Chenopodium quinoa and shares many of its nutritional benefits. Cañahua seed contains a complete protein, a low glycemic index, and offers a wide variety of nutritionally important vitamins and minerals. Methods The reference assembly

Premise Simple sequence repeat (SSR) markers (microsatellites) are a mainstay of many labs, especially when working on a limited budget, carrying out preliminary analyses, and in teaching. Whether SSRs mined from plant genomes or transcriptomes are preferred for certain applications, and the depth of sequencing needed to allow efficient SSR discovery, has not been tested. Methods I used genome and

Premise Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. Methods Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group

Premise Astragalus lehmannianus (Fabaceae) is a vulnerable species found in the cold deserts of northwestern China. We aimed to characterize polymorphic microsatellite loci for A. lehmannianus to support future studies of population genetic dynamics and conservation management of the species. Methods and Results We used next-generation sequencing to detect polymorphic microsatellites. Twenty-five potential

Premise Alkanna tinctoria (Boraginaceae) is an important medicinal herb with its main distribution across the Mediterranean region. To reveal its genetic variation and population structure, microsatellite markers were developed and validated in four Greek populations. Methods and Results RNA-Seq data of the related species Arnebia euchroma and Echium plantagineum were assembled and mined to identify

Premise Chloroplast primers were developed for phylogenetic and comparative studies in Thalictrum (Ranunculaceae). Methods and Results We assembled and annotated the complete plastome sequence of T. thalictroides by combining multiple whole genome sequencing libraries. Using transcriptome-sequencing libraries, we also assembled a partial plastome of the related species T. hernandezii. From the newly

Premise Cycas is an important gymnosperm genus, and the most diverse of all cycad genera. The C. taiwaniana complex of species are morphologically similar and difficult to distinguish due to a lack of genomic resources. Methods We characterized the transcriptomes of two closely related and endangered Cycas species endemic to Hainan, China: C. hainanensis and C. changjiangensis. Three single-copy nuclear