A Foundational Population Genetics Investigation of the Sexual Systems of Solanum (Solanaceae) in the Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit from Increased Genetic Admixture via Obligate Outcrossing.

Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor-including sexual system-that influences genetic patterns. Importantly, results indicate that dioecious S. asymmetriphyllum maintains less genetic structure and greater admixture among populations than cosexual S. raphiotes at the same three locations where they co-occur. This suggests that when certain conditions are met, the evolution of dioecy may have proceeded as a means to avoid genetic consequences of self-compatibility and may support hypotheses of benefits gained through differential resource allocation partitioned across sexes. Arguably, the most significant finding of this study is that all taxa are strongly inbred, possibly reflective of a shared response to recent climate shifts, such as the increased frequency and intensity of the region's fire regime.

Phenotypic trait variation in the North American Tragopogon allopolyploid complex.

PREMISE: Recently formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. The allopolyploid species have also been resynthesized, allowing comparisons between the youngest possible allopolyploid lineages and their natural, established counterparts. For the first time, we compared phenotypic traits on a large scale in Tragopogon diploids, natural allopolyploids, and three generations of synthetic allopolyploids. METHODS: Our large common-garden experiment measured traits in growth, development, physiology, and reproductive fitness. We analyzed trait differences between allopolyploids and their parental species, and between synthetic and natural allopolyploids. RESULTS: As in many polyploids, the allopolyploid species had some larger physical traits and a higher capacity for photosynthesis than diploid species. Reproductive fitness traits were variable and inconsistent. Allopolyploids had intermediate phenotypes compared to their diploid parents in several traits, but patterns of variation often varied between allopolyploid complexes. Resynthesized and natural allopolyploid lines generally showed minor to nonexistent trait differences. CONCLUSIONS: In Tragopogon, allopolyploidy results in some typical phenotypic changes, including gigas effects and increased photosynthetic capacity. Being polyploid did not produce a significant reproductive advantage. Comparisons between natural and synthetic T. mirus and T. miscellus are consistent with very limited, idiosyncratic phenotypic evolution following allopolyploidization.

Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future.

Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020-2030 frames our ability to perform vital and far-reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1-4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant-based medicines, and "green infrastructure." Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a "parts store" that supports tinkering and supports query, prediction, and rapid-response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non-invasive imaging, sensors, and plug-and-play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence-assisted data integration, pattern identification, and decision making. Implementation of this vision will transform plant systems science and ripple outwards through society and across the globe. Beyond deepening our biological understanding, we envision entirely new applications. We further anticipate a wave of diversification of plant systems practitioners while stimulating community engagement, underpinning increasing entrepreneurship. This surge of engagement and knowledge will help satisfy and stoke people's natural curiosity about the future, and their desire to prepare for it, as they seek fuller information about food, health, climate and ecological systems.

A basic ddRADseq two-enzyme protocol performs well with herbarium and silica-dried tissues across four genera.

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.

Integrated pest management in the academic small greenhouse setting: A case study using Solanum spp. (Solanaceae).

PREMISE: Botanical faculty and staff at academic institutions are often tasked with establishing and/or caring for plant collections held in small greenhouse facilities. Once plants are in place, an especially acute challenge is managing plant pest/pathogen populations. Integrated pest management (IPM) approaches are an excellent option, but few examples exist in the literature of successful programs that have been developed in academic small greenhouse settings. METHODS AND RESULTS: Over several years, we developed an IPM program for two small research greenhouses on the campus of a primarily undergraduate institution where hundreds of plants have been grown for studies in the genus Solanum. We here present a synopsis of the cultural, mechanical, physical, and biological controls used as part of our successful IPM strategy-including details on the efficacy of multiple predatory insects-with the hope of providing a model for sustainable pest management in the higher education environment. CONCLUSIONS: IPM can be an effective strategy for maintaining healthy plant populations in small research greenhouses, but it requires a consistent investment of time and funding. A well-cared-for plant collection might help support numerous positive outcomes, including advances in faculty scholarship and opportunities for student learning and/or training.

Phylogeny of the Australian Solanum dioicum group using seven nuclear genes, with consideration of Symon's fruit and seed dispersal hypotheses.

The dioecious and andromonoecious Solanum taxa (the "S. dioicum group") of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed dispersal (strongly linked to calyx accrescence) is far more common among Australian Solanum than previously thought and support the hypothesis that the combination of large fleshy fruits and endozoochorous dispersal represents a reversal in this study group. The general lack of direct evidence related to biotic dispersal (epizoochorous or endozoochorous) may be a function of declines and/or extinctions of vertebrate dispersers. Because of this, some taxa might now rely on secondary dispersal mechanisms (e.g. shakers, tumbleweeds, rafting) as a means to maintain current populations and establish new ones.

New functionally dioecious bush tomato from northwestern Australia, Solanum ossicruentum, may utilize "trample burr" dispersal.

A new Australian species of functionally dioecious bush tomato of Solanum subgenus Leptostemonum is described. Solanum ossicruentum Martine & J.Cantley, sp. nov., is thought to be allied with members of the problematic "Dioicum Complex" lineage, but differs in its short silvery indumentum, long calyx lobes, larger stature, and an unusual fruit morphology that may represent "trample burr" seed dispersal. The species occurs in a range extending from the eastern Kimberley in Western Australia to far northwestern Northern Territory and has been recognized for decades as a variant of Solanum dioicum W.Fitzg. Specimens of this species were previously referred to by D.E. Symon and others as Solanum dioicum 'Tanami.' Ex situ crossing studies and SEM images of inaperturate pollen grains produced in morphologically hermaphrodite flowers indicate that this taxon is functionally dioecious. The scientific name was chosen with the help of 150 seventh grade life science students from Pennsylvania, USA.

Solanum watneyi, a new bush tomato species from the Northern Territory, Australia named for Mark Watney of the book and film "The Martian".

A new species of andromonoecious Solanum from the Australian "bush tomato clade" of Solanum subgenus Leptostemonum is described. Solanum watneyi Martine & Frawley, sp. nov. is closely allied with Solanum eburneum, and is sympatric with it in parts of its range in the Northern Territory. The new species has been recognized as a variant of Solanum eburneum for decades, at times being referred to by local botanists as Solanum sp. "Bullita" because of its relative abundance in the vicinity of the Bullita Station area of Judbarra/Gregory National Park. Morphometric analyses show that Solanum watneyi differs statistically from Solanum eburneum in several key reproductive and vegetative characters and field observations suggest that the two sister species may represent a case of edaphic speciation. We provide morphometric evidence for the novelty of Solanum watneyi, a complete description, and cite specimens for both species.

Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta.

PREMISE OF THE STUDY: Here we present a series of protocols for RNA extraction across a diverse array of plants; we focus on woody, aromatic, aquatic, and other chemically complex taxa. METHODS AND RESULTS: Ninety-one taxa were subjected to RNA extraction with three methods presented here: (1) TRIzol/TURBO DNA-free kits using the manufacturer's protocol with the addition of sarkosyl; (2) a combination method using cetyltrimethylammonium bromide (CTAB) and TRIzol/sarkosyl/TURBO DNA-free; and (3) a combination of CTAB and QIAGEN RNeasy Plant Mini Kit. Bench-ready protocols are given. CONCLUSIONS: After an iterative process of working with chemically complex taxa, we conclude that the use of TRIzol supplemented with sarkosyl and the TURBO DNA-free kit is an effective, efficient, and robust method for obtaining RNA from 100 mg of leaf tissue of land plant species (Embryophyta) examined. Our protocols can be used to provide RNA of suitable stability, quantity, and quality for transcriptome sequencing.

MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.

PREMISE OF THE STUDY: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. METHODS AND RESULTS: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. CONCLUSIONS: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.

Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥ 1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.

Next-generation sequencing and genome evolution in allopolyploids.

PREMISE OF THE STUDY: Hybridization and polyploidization (allopolyploidy) are ubiquitous in the evolution of plants, but tracing the origins and subsequent evolution of the constituent genomes of allopolyploids has been challenging. Genome doubling greatly complicates genetic analyses, and this has long hindered investigation in that most allopolyploid species are "nonmodel" organisms. However, recent advances in sequencing and genomics technologies now provide unprecedented opportunities to analyze numerous genetic markers in multiple individuals in any organism. METHODS: Here we review the application of next-generation sequencing technologies to the study of three aspects of allopolyploid genome evolution: duplicated gene loss and expression in two recently formed Tragopogon allopolyploids, intergenomic interactions and chromosomal evolution in Tragopogon miscellus, and repetitive DNA evolution in Nicotiana allopolyploids. KEY RESULTS: For the first time, we can explore on a genomic scale the evolutionary processes that are ongoing in natural allopolyploids and not be restricted to well-studied crops and genetic models. CONCLUSIONS: These approaches can be easily and inexpensively applied to many other plant species-making any evolutionarily provocative system a new "model" system.

Molecular phylogeny and systematics of the genus Draba (Brassicaceae) and identification of its most closely related genera.

Phylogenetic analyses of sequence data from the internal transcribed spacer regions of the nuclear ribosomal DNA (ITS) and the plastid trnL-F region were conducted to reconstruct the phylogenetic history of Draba and related genera. Out of the approximately 370 Draba species, 169 geographically and morphologically representative species are sampled here, including such "controversial" segregates as Abdra, Arabis, Athysanus, Drabopsis, Erophila, Graellsia, Heterodraba, Schivereckia and Tomostima. Phylogenetic analyses of the combined ITS and trnL-F markers indicate that Draba represents a monophyletic evolutionary lineage within the tribe Arabideae, but previously proposed infrageneric classification systems are mostly artificial (i.e. do not reflect true evolutionary history). Draba muralis formed an independent genus, possibly between Draba and Arabis, whereas D. hystrix fell outside Draba and was closely associated with Arabis. The New World annual, lowland Draba, D. platycarpa, D. reptans, D. cuneifolia, D. australis, D. arabidoides, (section Abdra) and D. brachycarpa and D. aspera (section Tomostima), appear to be independent genera that fall outside Draba and are monophyletic with the endemic North American Heterodraba unilateralis and Athysanus pusillus. Graellsia hederifolia and Erophila verna appear to be earlier diverging Draba species, with weak evidence of ancient hybridization in G. hederifolia. Core Draba species were organized into three major groups that encompass the segregate genera Drabopsis and Schivereckia. The three groups have geographic significance: Group I-Europe to Iran; Group II-North and South American Cordillera; Group III-Asian, Arctic, and Beringian. These three groups also have significant petal color and base chromosome level similarities. We also found that Arabis rimarum is a synonym for Draba aucheri, and is well within Group I of Core Draba. Therefore, we propose that many of the lowland and coastal temperate species often associated with Draba should be excluded from that genus. The compilation of these data indicate that true Draba are highly migrating arctic and higher alpine species that are most often perennial with white petals and n=8 as plesiomorphic characters.