The Phylogeny Predicts Potential New Sources of Antibiotics from Plants

The evolution and spread of antibiotic resistance has been the greatest threat to successful antibiotic treatment, and hence the driving force behind the search for new therapies. None of our modern pharmaceutical antibiotics have been developed from plants, albeit plants have been used since antiquity in traditional medicine to fight bacterial infections. We phylogenetically analyzed 138 plant species with antibacterial activity and found 5 plant families that are disproportionately important, with confamilials exerting similar antibacterial mechanisms, as expected due to common ancestry. Myrtaceae (guava family) was shown to inhibit quorum sensing, disrupting bacterial communication implicated in pathogenicity, due to its flavonoids. The unrelated families Fabaceae (bean family), Lamiaceae (mints), Lauraceae (laurel), and Zingiberaceae (ginger family) possessed phytochemicals, mostly essential oils, that affected bacterial cell membrane integrity. Species in these plant families may offer unique natural products that could be developed into new antibiotics. Our study reinforces the utility of the plant phylogeny in drug discovery

Ex Situ Propagation of Philippine Rafflesia in the United States: Challenges and Prospects

The large-flowered parasitic genus Rafflesia R.Br. (Rafflesiaceae) has long fascinated naturalists and scientists and is an iconic symbol for plant conservation. Techniques to effectively propagate members of the genus outside of their natural habitat are sparse, and grafting infected Tetrastigma K.Schum.(Vitaceae) host plants has previously been reported as a successful strategy for ex situ conservation of Rafflesia. Here we report our attempts in the United States to propagate host cuttings infected with Rafflesia speciosa Barcelona & Fernando and R. lagascae Blanco collectedfrom the Philippines, as well as uninfected host material. We also describe efforts to germinate R. speciosa seeds in vitro using various plant growth regulators (PGRs). After rooting, infected host cuttings survived for a maximum of 11 months, but did not produce shoots. However, an uninfected cutting of T. cf. magnum grafted onto an established Malaysian species of Tetrastigma in June 2017 has succeeded in the commencement of new growth. Three propagules of a second potential host, T. harmandii Planch., have also been vigorously growing at the United States Botanic Garden since June 2017. However, Rafflesia seeds did not germinate with the application of PGRs, even though the seeds were viable according to tetrazolium (TZ) testing.These ex situ propagation attempts have revealed challenges in propagating these species outside of their native ranges, but our incremental success in rooting infected Tetrastigma, as well as grafting interspecific Tetrastigma species, bodes well for further advances. With Philippine host species, T. harmandii and T. cf. magnum in cultivation, we can begin using these specimens for future experimentation involving grafting of infected material and Rafflesia seed inoculation trials.Furthermore, we describe new avenues of propagation techniques for Rafflesia as practised by Marius Gabin, one of the owners of the Vivian Rafflesia garden, which contains a natural Rafflesia forest habitat at Poring Springs, Sabah, Malaysia. Gabin openly shared his successes in artificially inoculating Rafflesia seeds into a mature Tetrastigma vine. Gabin’s willingness to share his experience highlights the importance of collaborating with practitioners who have developed local knowledge of Rafflesia horticulture and conservation

Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae)

Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth

Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection

Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa—indica and tropical japonica—as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups

Evolution, pollination biology, and biogeography of the grape relative Leea (Leeaceae, vitales):

Leea D. Royen ex L. is the sole member of the tropical family Leeaceae, which is closely related to the economically important grape family, Vitaceae. Both comprise the order Vitales. In spite of its affinity with the grape family, Leea's molecular systematics has remained unexplored. This study presents the first phylogeny (chapter 1) of Leeaceae using molecular markers to provide an evolutionary framework to understand its taxonomy, morphological evolution (chapter 2), ecology (chapter 3), and biogeography (chapter 4). Ridsdale (1974, 1976) estimated that there are 34 Leea species inhabiting the tropics of Africa and Asia. DNA sequences for the internal transcribed spacer (ITS) and the 5S non-transcribed spacer (NTS) were extracted and amplified from leaf material of 22 species, representing the morphological and geographical diversity of Leea. The ITS secondary structure for the type species, L. aequata L., facilitated homology assessments in ITS sequence alignments, while 5S-NTS data helped resolve terminal relationships. The concatenated matrix was used to estimate the phylogeny and divergence times and generate the topology for ancestral area reconstructions. Area optimization was also performed on the Vitales topology estimated from previously published sequences to locate the geographic origin of Leeaceae, but either an out-of-Asia (i.e. Indochina) or out-of-India origin was inferred possible. The molecular phylogeny recovered four major clades, with the Indian/Indochinese L. asiatica (L.) Ridsdale (clade I) diverging 65.5 mya from the rest of the family. Its primitive trait of free stamens supports its position as the earliest-diverging clade. Clades II, III, and IV form a monophyletic group that had evolved in the Eocene (50.8 mya) in Indochina and/or West Malesia and exhibit the derived feature of fused stamens. Clade II, the spine-bearing species, is sister to Clade III, whose species have large flowers. Clade IV, which is unique in having multi-pinnate leaves and small stipules, evolved by the end of the Oligocene (25.6 mya) and comprise the polyphyletic 'species' (sensu Ridsdale) L. guineensis G. Don and L. indica (Burm. f.) Merr. nested among other morphologically discernible species. The radiation of Leea species mostly occurred in the Neogene (1.8-23.0 mya) during a time of dynamic geological and environmental changes in Southeast Asia. Africa and Australia were also colonized by Neogene dispersals of Asian Leea. Current species circumscriptions of L. guineensis and L. indica underestimate the genetic diversity of the genus and need to be revised. An updated checklist of 47 species reflecting clades recovered by the molecular phylogeny is presented including resurrected and putative new species. Field studies of three sympatric Philippine Leea morphospecies have revealed that habit and ecology must be considered in species circumscriptions.Ph.D.Includes bibliographical references (p. 95-107)by Jeanmaire E. Molin

The predictive utility of the plant phylogeny in identifying sources of cardiovascular drugs

Context: Cardiovascular disease (CVD) is the number one cause of death globally, responsible for over 17 million (31%) deaths in the world. Novel pharmacological interventions may be needed given the high prevalence of CVD. Objective: In this study, we aimed to find potential new sources of cardiovascular (CV) drugs from phylogenetic and pharmacological analyses of plant species that have experimental and traditional CV applications in the literature. Materials and methods: We reconstructed the molecular phylogeny of these plant species and mapped their pharmacological mechanisms of action on the phylogeny. Results: Out of 139 plant species in 71 plant families, seven plant families with 45 species emerged as phylogenetically important exhibiting common CV mechanisms of action within the family, as would be expected given their common ancestry: Apiaceae, Brassicaceae, Fabaceae, Lamiaceae, Malvaceae, Rosaceae and Zingiberaceae. Apiaceae and Brassicaceae promoted diuresis and hypotension; Fabaceae and Lamiaceae had anticoagulant/thrombolytic effects; Apiaceae and Zingiberaceae were calcium channel blockers. Moreover, Apiaceae, Lamiaceae, Malvaceae, Rosaceae and Zingiberaceae species were found to possess anti-atherosclerotic properties. Discussion and conclusions: The phylogeny identified certain plant families with disproportionately more species, highlighting their importance as sources of natural products for CV drug discovery. Though there were some species that did not show the same mechanism within the family, the phylogeny predicts that these species may contain undiscovered phytochemistry, and potentially, the same bioactivity. Evolutionary pharmacology, as applied here, may guide and expedite our efforts in discovering sources of new CV drugs

DNA barcoding of online herbal supplements: crowd-sourcing pharmacovigilance in high school

Herbal medicinal products (HMPs) have grown increasingly popular in the United States, many of them with imported raw materials and sold online. Yet due to the lack of regulation from the US Food and Drug Administration (FDA), manufacturers of the products can substitute or add in other herbs that are not advertised on the label. In this study, as part of the Urban Barcode Research Program (UBRP), an education initiative to engage New York City high school students in science, we aimed to taxonomically authenticate single-ingredient online-sold HMPs containing non-native plants through DNA barcoding of the internal transcribed spacer 2 region (ITS2) and matK. We were able to successfully barcode 20 HMPs, but four of these did not match the expected species. It was concluded that the four HMPs advertising astragalus, epazote, ginseng, and chanca piedra were contaminated/ substituted because their ITS2 and matK DNA sequences did not match the expected taxonomy in GenBank, a government database. Our study highlights the importance of herbal pharmacovigilance in the absence of strict government regulation of herbal supplements and motivates crowd-sourced DNA barcoding to enable American consumers make informed choices and be more empowered to safeguard their health

Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection

Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa—indica and tropical japonica—as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.</p

STS sequence alignments for O.rufipogon

There are 42 STS sequence alignments in FASTA format in the zip file. Each alignment include an outgroup sequence and 96 ingroup sequences (missing ones are not included). Name of each sequence start with a flow number and followed by sts number, organism/group annotation by IRRI, country of origin, IRGC number and chromosome number. Additional sample and loci information can be found in Table S1 and S2 of the supplementary information on Molecular Ecology website