The rhizodynamics robot: Automated imaging system for studying long-term dynamic root growth.

The study of plant root growth in real time has been difficult to achieve in an automated, high-throughput, and systematic fashion. Dynamic imaging of plant roots is important in order to discover novel root growth behaviors and to deepen our understanding of how roots interact with their environments. We designed and implemented the Generating Rhizodynamic Observations Over Time (GROOT) robot, an automated, high-throughput imaging system that enables time-lapse imaging of 90 containers of plants and their roots growing in a clear gel medium over the duration of weeks to months. The system uses low-cost, widely available materials. As a proof of concept, we employed GROOT to collect images of root growth of Oryza sativa, Hudsonia montana, and multiple species of orchids including Platanthera integrilabia over six months. Beyond imaging plant roots, our system is highly customizable and can be used to collect time- lapse image data of different container sizes and configurations regardless of what is being imaged, making it applicable to many fields that require longitudinal time-lapse recording.

A Bird's Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data.

Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species of high economic importance, such as the crop sweet potato (Ipomoea batatas L.), the ornamental morning glories (Ipomoea L.), bindweeds (Convolvulus L.), and dodders, the parasitic vines (Cuscuta L.). Earlier phylogenetic studies, based predominantly on chloroplast markers or a single nuclear region, have provided a framework for systematic studies of the family, but uncertainty remains at the level of the relationships among subfamilies, tribes, and genera, hindering evolutionary inferences and taxonomic advances. One of the enduring enigmas has been the relationship of Cuscuta to the rest of Convolvulaceae. Other examples of unresolved issues include the monophyly and relationships within Merremieae, the "bifid-style" clade (Dicranostyloideae), as well as the relative positions of Erycibe Roxb. and Cardiochlamyeae. In this study, we explore a large dataset of nuclear genes generated using Angiosperms353 kit, as a contribution to resolving some of these remaining phylogenetic uncertainties within Convolvulaceae. For the first time, a strongly supported backbone of the family is provided. Cuscuta is confirmed to belong within family Convolvulaceae. "Merremieae," in their former tribal circumscription, are recovered as non-monophyletic, with the unexpected placement of Distimake Raf. as sister to the clade that contains Ipomoeeae and Decalobanthus Ooststr., and Convolvuleae nested within the remaining "Merremieae." The monophyly of Dicranostyloideae, including Jacquemontia Choisy, is strongly supported, albeit novel relationships between genera are hypothesized, challenging the current tribal delimitation. The exact placements of Erycibe and Cuscuta remain uncertain, requiring further investigation. Our study explores the benefits and limitations of increasing sequence data in resolving higher-level relationships within Convolvulaceae, and highlights the need for expanded taxonomic sampling, to facilitate a much-needed revised classification of the family.

Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci.

PREMISE: Understanding relationships among orchid species and populations is of critical importance for orchid conservation. Target sequence capture has become a standard method for extracting hundreds of orthologous loci for phylogenomics. Up-front cost and time associated with design of bait sets makes this method prohibitively expensive for many researchers. Therefore, we designed a target capture kit to reliably sequence hundreds of orthologous loci across orchid lineages. METHODS: We designed an Orchidaceae target capture bait set for 963 single-copy genes identified in published orchid genome sequences. The bait set was tested on 28 orchid species, with representatives of the subfamilies Cypripedioideae, Orchidoideae, and Epidendroideae. RESULTS: Between 1,518,041 and 87,946,590 paired-end 150-base reads were generated for target-enriched genomic libraries. We assembled an average of 812 genes per library for Epidendroideae species and a mean of 501 genes for species in the subfamilies Orchidoideae and Cypripedioideae. Furthermore, libraries had on average 107 of the 254 genes that are included in the Angiosperms353 bait set, allowing for direct comparison of studies using either bait set. DISCUSSION: The Orchidaceae963 kit will enable greater accessibility and utility of next-generation sequencing for orchid systematics, population genetics, and identification in the illegal orchid trade.

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement.

Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. Agronomic improvement of sweetpotato has lagged behind other major food crops due to a lack of genomic and genetic resources and inherent challenges in breeding a heterozygous, clonally propagated polyploid. Here, we report the genome sequences of its two diploid relatives, I. trifida and I. triloba, and show that these high-quality genome assemblies are robust references for hexaploid sweetpotato. Comparative and phylogenetic analyses reveal insights into the ancient whole-genome triplication history of Ipomoea and evolutionary relationships within the Batatas complex. Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content. These resources will facilitate genome-enabled breeding in this important food security crop.

Parallel evolution of storage roots in morning glories (Convolvulaceae).

BACKGROUND: Storage roots are an ecologically and agriculturally important plant trait that have evolved numerous times in angiosperms. Storage roots primarily function to store carbohydrates underground as reserves for perennial species. In morning glories, storage roots are well characterized in the crop species sweetpotato, where starch accumulates in storage roots. This starch-storage tissue proliferates, and roots thicken to accommodate the additional tissue. In morning glories, storage roots have evolved numerous times. The primary goal of this study is to understand whether this was through parallel evolution, where species use a common genetic mechanism to achieve storage root formation, or through convergent evolution, where storage roots in distantly related species are formed using a different set of genes. Pairs of species where one forms storage roots and the other does not were sampled from two tribes in the morning glory family, the Ipomoeeae and Merremieae. Root anatomy in storage roots and fine roots was examined. Furthermore, we sequenced total mRNA from storage roots and fine roots in these species and analyzed differential gene expression. RESULTS: Anatomical results reveal that storage roots of species in the Ipomoeeae tribe, such as sweetpotato, accumulate starch similar to species in the Merremieae tribe but differ in vascular tissue organization. In both storage root forming species, more genes were found to be upregulated in storage roots compared to fine roots. Further, we find that fifty-seven orthologous genes were differentially expressed between storage roots and fine roots in both storage root forming species. These genes are primarily involved in starch biosynthesis, regulation of starch biosynthesis, and transcription factor activity. CONCLUSIONS: Taken together, these results demonstrate that storage roots of species from both morning glory tribes are anatomically different but utilize a common core set of genes in storage root formation. This is consistent with a pattern of parallel evolution, thus highlighting the importance of examining anatomy together with gene expression to understand the evolutionary origins of ecologically and economically important plant traits.

Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas].

Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.

Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences.

PREMISE OF THE STUDY: Morning glories are an emerging model system, and resolving phylogenetic relationships is critical for understanding their evolution. Phylogenetic studies demonstrated that the largest morning glory genus, Ipomoea, is not monophyletic, and nine other genera are derived from within Ipomoea. Therefore, systematic research is focused on the monophyletic tribe Ipomoeeae (ca. 650-900 species). We used whole plastomes to infer relationships across Ipomoeeae. METHODS: Whole plastomes were sequenced for 29 morning glory species, representing major lineages. Phylogenies were estimated using alignments of 82 plastid genes and whole plastomes. Divergence times were estimated using three fossil calibration points. Finally, evolution of root architecture, flower color, and ergot alkaloid presence was examined. KEY RESULTS: Phylogenies estimated from both data sets had nearly identical topologies. Phylogenetic results are generally consistent with prior phylogenetic hypotheses. Higher-level relationships with weak support in previous studies were recovered here with strong support. Molecular dating analysis suggests a late Eocene divergence time for the Ipomoeeae. The two clades within the tribe, Argyreiinae and Astripomoeinae, diversified at similar times. Reconstructed most recent common ancestor of the Ipomoeeae had blue flowers, an association with ergot-producing fungi, and either tuberous or fibrous roots. CONCLUSIONS: Phylogenetic results provide confidence in relationships among Ipomoeeae lineages. Divergence time estimation results provide a temporal context for diversification of morning glories. Ancestral character reconstructions support previous findings that morning glory morphology is evolutionarily labile. Taken together, our study provides strong resolution of the morning glory phylogeny, which is broadly applicable to the evolution and ecology of these fascinating species.