The Melianthaceous seed and its Rhamnaceous affinity

. La semilla de Melianthaceae y su afinidad con Rhamnaceae. En el presente trabajo, se ha estudiado la anatomia y morfología de la semilla de Bersama (Bersamataceae) y Melianthus (Melianthaceae) con el objeto de clarificar su posición sistemática. La exotesta de Bersama y Melianthus, con una empalizada de células de Malpighi bien diferenciada, abundante endosperma y embrión recto y escasamente diferenciado, muestra ciertas afinidades con la exotesta albuminosa de las semillas de Rhamnaceae y Elaeagnaceae. Utilizando también datos carpológicos, florales y morfológico-vegetativos adicionales, se sugiere que Bersamataceae, junto con Melianthaceae y Rhamnaceae/Elaeagnaceae constituyen una ramificación lateral relíctica de un ancestro roside exo-mesotestado. La morfología y anatomía de las semillas evidencian la anómala y tradicional inclusión de Bersama y Melianthus en el orden Sapindales, cuyas semillas presentan diferente pautas en la estructura de la espermodermis y en la vascularización de la misma. La anatomía de la semilla, no confirma ninguna de las relaciones que se han sugerido, alternativamente, con Lardizabalaceae exo-mesotestales ni con Malvales exotegmicos. Por otra parte, consideramos insostenibles las afinidades con Celastrales exotégmicos, que han sido consideradas como una posible conexión entre Rosales arcaicos exo-mesotestados y Rhamnales/Elaeagnales exotestados. Se sugiere que ambas familias, Bersamataceae y Melianthaceae, constituyen el orden Melianthales que, junto con Rhamnaceae (Rhamnales, s. e.) y Elaeagnaceae (Elaeagnales) representan remanentes avanzados de un phyllum profusamente ramificado, cuyas relaciones se remontan directamente hacia Fabales, pasando por Rosales, Sapindales, Icacinales y Celastrales

Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens.

BACKGROUND: Plants deploy immune receptors to detect pathogen-derived molecules and initiate defense responses. Intracellular plant immune receptors called nucleotide-binding leucine-rich repeat (NLR) proteins contain a central nucleotide-binding (NB) domain followed by a series of leucine-rich repeats (LRRs), and are key initiators of plant defense responses. However, recent studies demonstrated that NLRs with non-canonical domain architectures play an important role in plant immunity. These composite immune receptors are thought to arise from fusions between NLRs and additional domains that serve as "baits" for the pathogen-derived effector proteins, thus enabling pathogen recognition. Several names have been proposed to describe these proteins, including "integrated decoys" and "integrated sensors". We adopt and argue for "integrated domains" or NLR-IDs, which describes the product of the fusion without assigning a universal mode of action. RESULTS: We have scanned available plant genome sequences for the full spectrum of NLR-IDs to evaluate the diversity of integrations of potential sensor/decoy domains across flowering plants, including 19 crop species. We manually curated wheat and brassicas and experimentally validated a subset of NLR-IDs in wild and cultivated wheat varieties. We have examined NLR fusions that occur in multiple plant families and identified that some domains show re-occurring integration across lineages. Domains fused to NLRs overlap with previously identified pathogen targets confirming that they act as baits for the pathogen. While some of the integrated domains have been previously implicated in disease resistance, others provide new targets for engineering durable resistance to plant pathogens. CONCLUSIONS: We have built a robust reproducible pipeline for detecting variable domain architectures in plant immune receptors across species. We hypothesize that NLR-IDs that we revealed provide clues to the host proteins targeted by pathogens, and that this information can be deployed to discover new sources of disease resistance

Terzyme: a tool for identification and analysis of the plant terpenome.

BACKGROUND: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data. RESULTS: We have developed Terzyme, a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes, known to generate the enormous structural and functional diversity of terpenoid compounds across the plant kingdom. Terzyme uses sequence information, plant taxonomy and machine learning methods for predicting TPSs and PTs in genome and proteome datasets. We demonstrate a significant enrichment of the currently identified terpenome by running Terzyme on more than 40 plants. CONCLUSIONS: Terzyme is the result of a rigorous analysis of evolutionary relationships between hundreds of characterized sequences of TPSs and PTs with known specificities, followed by analysis of genome-wide gene distribution patterns, ontology based clustering and optimization of various parameters for building accurate profile Hidden Markov Models. The predictive webserver and database is freely available at http://nipgr.res.in/terzyme.html and would serve as a useful tool for deciphering the species-specific phytochemical potential of plant genomes

Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)

Evolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep-level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep-level relationships of Vitaceae were retrieved by comprehensive comparisons of results from optimal partitioning analyses, multispecies coalescent approaches and the Bayesian concordance method. We found that partitioning schemes selected by PartitionFinder were preferred over those by gene or by codon position, and the unpartitioned model usually performed the worst. For a data set with conflicting signals, however, the unpartitioned model outperformed models that included more partitions, demonstrating some limitations to the effectiveness of concatenation for these data. For a transcriptome data set, fast coalescent methods (STAR and MP-EST) and a Bayesian concordance approach yielded congruent topologies with trees from the concatenated analyses and previous studies. Our results highlight that well-resolved gene trees are critical for the effectiveness of coalescent-based methods. Future efforts to improve the accuracy of phylogenomic analyses should emphasize the development of newmethods that can accommodate multiple biological processes and tolerate missing data while remaining computationally tractable. (C) The Willi Hennig Society 2017.National Natural Science Foundation of China [NNSF 31500179, 31590822, 31270268]; National Basic Research Program of China [2014CB954101]; National Science Foundation [DEB0743474]; Smithsonian Scholarly Studies Grant Program and the Endowment Grant Program; CAS/SAFEA International Partnership Program for Creative Research Teams; Laboratory of Analytical Biology of the National Museum of Natural History, Smithsonian Institution; Science and Technology Basic Work [2013FY112100]info:eu-repo/semantics/publishedVersio

Great Diversity of Insect Floral Associates May Partially Explain Ecological Success of Poison Ivy (\u3ci\u3eToxicodendron Radicans\u3c/i\u3e Subsp. \u3ci\u3eNegundo\u3c/i\u3e [Greene] Gillis, Anacardiaceae)

Little is known about insect floral associates of poison ivy (Toxicodendron radicans, Anacardiaceae), despite the species’ ubiquity and importance in nature and society. Poison ivy’s pollination syndrome and results from prior studies suggest that the plant is not specialized for any particular pollinator type; however, a systematic survey exploring this hypothesis has been lacking. For this study, insect floral associates of Toxicodendron radicans subsp. negundo from a central Iowa site were observed during the flowering season of 2005. Thirty- seven distinct insect floral associates were observed: 8 coleopterans (beetles), 7 dipterans (flies), 2 hemipterans (true bugs), 19 hymenopterans (ants, bees, wasps), and 1 lepidopteran (butterfly). Hymenopterans appeared to be the most important contributors to poison ivy pollination on a per species basis; however, coleopterans and dipterans were also frequent associates. Poison ivy’s ability to utilize a diverse assemblage of insect pollinators may partially explain its ecological success in varied habitats

Endogenous caulimovirid sequences are widespread in plant genomes

Endogenous sequences from members of the Caulimoviridae and Geminiviridae families have been identified in the genome of several plant species. They are thought to result from illegitimate recombination events and are generally replication-defective. However, some caulimovirid sequences of tobacco, petunia and banana are capable of causing infection. We performed in silico analyses on nucleotide sequences from plant genome databases and reconstituted 11 full length and potentially infectious viral genomes from endogenous viral sequences embedded in the genomes of monocotyledonous and dicotyledonous Brassicaceae, Euphorbiacae, Fabacae, Myrtaceae, Poaceae, Rutaceae, Saliaceae and Vitaceae plant species. Sequence comparisons show that the corresponding viruses belong to a new genus in the family Caulimoviridae, tentatively named Dionyvirus. Mapping of endogenous Dionyvirus sequences was achieved in two fully sequenced grape genomes, allowing for the first time the study of the distribution pattern of endogenous viral sequences at the host plant genome scale. Dionyvirus-specific primers were designed and used for a PCR-based large scale screening of plant germplasm. It showed that endogenous Dionyvirus sequences are widespread among plants of temperate, tropical and arctic origins, and belong to distinct viral species. Endogenous Dionyvirus sequences belonging to distinct viral species were also identified in single host plants, showing that endogenization of viral sequences is a common phenomenon in plants. Our work shed new lights on plant/virus molecular interactions. The potential contributions of endogenous viral sequences to normal plant functions and to plant and virus evolution will be discussed. (Texte intégral

X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early-diverging members of the genus

PREMISE OF THE STUDY: Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and biogeography of Cissus and for African early Miocene paleoenvironments.METHODS: Micro-computed tomography (µCT) and synchrotron-based X-ray tomographic microscopy (SRXTM) were used to study seed morphology and anatomy. Virtual taphonomy, using SRXTM data sets, produced digital fossils to elucidate seed taphonomy. Phylogenetic relationships within Cissus were reconstructed using existing and newly produced DNA sequences for African species. Paleobiology and paleoecology were inferred from African nearest living relatives.KEY RESULTS: The fossils were assigned to four new Cissus species, related to four modern clades. The fossil plants were interpreted as climbers inhabiting a mosaic of riverine woodland and forest to more open habitats. Virtual taphonomy explained how complex mineral infill processes concealed key seed features, causing the previous taxonomic misidentification. Newly sampled African species, with seeds most similar to the fossils, belong to four clades within core Cissus, two of which are early diverging.CONCLUSIONS: Virtual taphonomy, combined with X-ray imaging, has enabled recognition of the first fossil Cissus and Vitaceae from Africa. Early-divergent members of the core Cissus clade were present in Africa by at least the early Miocene, with an African origin suggested for the Cissus sciaphila clade. The fossils provide supporting evidence for mosaic paleoenvironments inhabited by early Miocene hominoids