Publications by authors named "Panagiota Malakasi"

9 Publications

  • Page 1 of 1

A higher-level nuclear phylogenomic study of the carrot family (Apiaceae).

Am J Bot 2021 07 21;108(7):1252-1269. Epub 2021 Jul 21.

Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK.

Premise: The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap.

Methods: Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches.

Results: We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (Platysace, Klotzchia, and Hermas); all three occupy isolated positions, with Platysace resolved as sister to all remaining Apiaceae. We placed nine genera (Apodicarpum, Bonannia, Grafia, Haplosciadium, Microsciadium, Physotrichia, Ptychotis, Tricholaser, Xatardia) that have never previously been included in any molecular phylogenetic study.

Conclusions: We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that Hermas, Klotzschia, and the Platysace clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus Phlyctidocarpa can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.
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http://dx.doi.org/10.1002/ajb2.1701DOI Listing
July 2021

Museomics Clarifies the Classification of (Asphodelaceae), the Iconic African Tree Aloes.

Front Plant Sci 2019 15;10:1227. Epub 2019 Oct 15.

Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Surrey, United Kingdom.

Arborescent succulent plants are regarded as keystone and indicator species in desert ecosystems due to their large stature and long lifespans. Tree aloes, the genus , are icons of the southern African deserts yet have proved elusive subjects due to the difficulty of obtaining material of known provenance for comparative study. Consequently, evolutionary relationships among representatives of the unusual arborescent life form have remained unclear until now. We used a museomics approach to overcome this challenge. Chloroplast genomes of six species and 12 other members of Asphodelaceae were sequenced from modern living collections and herbarium specimens, including the type specimens of all but two species, the earliest of which was collected 130 years ago. Maximum-likelihood trees estimated from full chloroplast genomes and the nuclear internal transcribed spacer (ITS) region show that , from the Arabian Peninsula, is nested within while the Madagascar endemic is most closely related to the Somalian . We observed phylogenetic conflicts between the plastid and nuclear topologies, which may be indicative of recurrent hybridisation or incomplete lineage sorting events in and in . Comparing species ecology in the context provided by our phylogeny suggests that habitat preference to either xeric deserts or humid forests/thickets evolved repeatedly in . Our findings demonstrate the value of botanical collections for the study and classification of taxonomically challenging succulent plants.
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http://dx.doi.org/10.3389/fpls.2019.01227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803536PMC
October 2019

The Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences.

PhytoKeys 2019 26;125:1-112. Epub 2019 Jun 26.

Silpakorn University, Department of Biology, Faculty of Science, Sanam Chandra Palace campus, Nakhon Pathom 73000, Thailand Silpakorn University Nakhon Pathom Thailand.

The Tribe Wisterieae (Zhu 1994), founded on the single genus , is emended and recircumscribed based on morphology and data from nuclear ITS and , and chloroplast DNA sequences. This newly enlarged tribe comprises 36 species and 9 infraspecific taxa within 13 described genera. Six genera are new, two are reinstated and five were previously placed in Tribe Millettieae. The genus is also reinstated comprising two species including the new combination . Other reinstated genera include , with four species, and , with three species, including the reinstatement of and the new combination P.filipesvar.tomentosa. The existing genera , , (with the new combination E.racemosavar.pallida), and , with the new combinations W.frutescenssubsp.macrostachya are evaluated. The new genera comprise three Australasian species in : , and ; with five species from east Asia has six new combinations: , and W.reticulatavar.stenophylla. Two species comprise the new Thai genus : and . comprises the two species: and and the monotypic genera and are based respectively on the species and . Lectotypes are designated for the names , , , , M.reticulatavar.stenophylla, , , , , and . A neotype is designated for the name .
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http://dx.doi.org/10.3897/phytokeys.125.34877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6610001PMC
June 2019

Flower preferences and pollen transport networks for cavity-nesting solitary bees: Implications for the design of agri-environment schemes.

Ecol Evol 2018 Aug 7;8(15):7574-7587. Epub 2018 Jul 7.

Department of Zoology University of Oxford Oxford UK.

Floral foraging resources are valuable for pollinator conservation on farmland, and their provision is encouraged by agri-environment schemes in many countries. Across Europe, wildflower seed mixtures are widely sown on farmland to encourage pollinators, but the extent to which key pollinator groups such as solitary bees exploit and benefit from these resources is unclear. We used high-throughput sequencing of 164 pollen samples extracted from the brood cells of six common cavity-nesting solitary bee species (, , , , and ) which are widely distributed across the UK and Europe. We documented their pollen use across 19 farms in southern England, UK, revealing their forage plants and examining the structure of their pollen transport networks. Of the 32 plant species included currently in sown wildflower mixes, 15 were recorded as present within close foraging range of the bees on the study farms, but only L. was identified within the pollen samples. L. was the most commonly found of the 23 plant species identified in the pollen samples, suggesting that, in addition to providing a nesting resource for leafcutter bees, it may be an important forage plant for these species. Higher levels of connectance and nestedness were characteristic of pollen transport networks on farms with abundant floral resources, which may increase resilience to species loss. Our data suggest that plant species promoted currently by agri-environment schemes are not optimal for solitary bee foraging. If a diverse community of pollinators is to be supported on UK and European farmland, additional species such as should be encouraged to meet the foraging requirements of solitary bees.
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http://dx.doi.org/10.1002/ece3.4234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106195PMC
August 2018

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

Am J Bot 2016 09 19;103(9):1657-77. Epub 2016 Sep 19.

Imaging and Analysis Centre, Natural History Museum, London, SW7 5BD, UK.

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.
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http://dx.doi.org/10.3732/ajb.1600177DOI Listing
September 2016

Madagascar's grasses and grasslands: anthropogenic or natural?

Proc Biol Sci 2016 Jan;283(1823)

Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich 8008, Switzerland.

Grasses, by their high productivity even under very low pCO2, their ability to survive repeated burning and to tolerate long dry seasons, have transformed the terrestrial biomes in the Neogene and Quaternary. The expansion of grasslands at the cost of biodiverse forest biomes in Madagascar is often postulated as a consequence of the Holocene settlement of the island by humans. However, we show that the Malagasy grass flora has many indications of being ancient with a long local evolutionary history, much predating the Holocene arrival of humans. First, the level of endemism in the Madagascar grass flora is well above the global average for large islands. Second, a survey of many of the more diverse areas indicates that there is a very high spatial and ecological turnover in the grass flora, indicating a high degree of niche specialization. We also find some evidence that there are both recently disturbed and natural stable grasslands: phylogenetic community assembly indicates that recently severely disturbed grasslands are phylogenetically clustered, whereas more undisturbed grasslands tend to be phylogenetically more evenly distributed. From this evidence, it is likely that grass communities existed in Madagascar long before human arrival and so were determined by climate, natural grazing and other natural factors. Humans introduced zebu cattle farming and increased fire frequency, and may have triggered an expansion of the grasslands. Grasses probably played the same role in the modification of the Malagasy environments as elsewhere in the tropics.
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http://dx.doi.org/10.1098/rspb.2015.2262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795014PMC
January 2016

Two-component mediated peroxide sensing and signal transduction in fission yeast.

Antioxid Redox Signal 2011 Jul 31;15(1):153-65. Epub 2011 Mar 31.

Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.

Two-component related proteins play a major role in regulating the oxidative stress response in the fission yeast, Schizosaccharomyces pombe. For example, the peroxide-sensing Mak2 and Mak3 histidine kinases regulate H(2)O(2)-induced activation of the Sty1 stress-activated protein kinase pathway, and the Skn7-related response regulator transcription factor, Prr1, is essential for activation of the core oxidative stress response genes. Here, we investigate the mechanism by which the S. pombe two-component system senses H(2)O(2), and the potential role of two-component signaling in the regulation of Prr1. Significantly, we demonstrate that PAS and GAF domains present in the Mak2 histidine kinase are essential for redox-sensing and activation of Sty1. In addition, we find that Prr1 is required for the transcriptional response to a wide range of H(2)O(2) concentrations and, furthermore, that two-component regulation of Prr1 is specifically required for the response of cells to high levels of H(2)O(2). Significantly, this provides the first demonstration that the conserved two-component phosphorylation site on Skn7-related proteins influences resistance to oxidative stress and oxidative stress-induced gene expression. Collectively, these data provide new insights into the two-component mediated sensing and signaling mechanisms underlying the response of S. pombe to oxidative stress.
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http://dx.doi.org/10.1089/ars.2010.3345DOI Listing
July 2011

Ybp1 is required for the hydrogen peroxide-induced oxidation of the Yap1 transcription factor.

J Biol Chem 2003 Aug 12;278(33):30896-904. Epub 2003 May 12.

School of Cell and Molecular Biosciences, Faculty of Medical Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom.

We describe the characterization of Ybp1, a novel protein, in Saccharomyces cerevisiae, that is required for the oxidative stress response to peroxides. Ybp1 is required for H2O2-induced expression of the antioxidant encoding gene TRX2. Our data indicate that the effects of Ybp1 are mediated through the Yap1 transcription factor. Indeed, Ybp1 forms a stress-induced complex with Yap1 in vivo and stimulates the nuclear accumulation of Yap1 in response to H2O2 but not in response to the thiol-oxidizing agent diamide. The H2O2-induced nuclear accumulation of Yap1 is regulated by the oxidation of specific cysteine residues and is dependent on the thiol peroxidase Gpx3. Our data suggest that Ybp1 is required for the H2O2-induced oxidation of Yap1 and acts in the same pathway as Gpx3. Consequently, Ybp1 represents a novel class of stress regulator of Yap1. These data have important implications for the regulation of protein oxidation and stress responses in eukaryotes.
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http://dx.doi.org/10.1074/jbc.M303542200DOI Listing
August 2003

Role of fission yeast Tup1-like repressors and Prr1 transcription factor in response to salt stress.

Mol Biol Cell 2002 Sep;13(9):2977-89

School of Biochemistry and Genetics, University of Newcastle upon Tyne, United Kingdom.

In Schizosaccharomyces pombe, the Sty1 mitogen-activated protein kinase and the Atf1 transcription factor control transcriptional induction in response to elevated salt concentrations. Herein, we demonstrate that two repressors, Tup11 and Tup12, and the Prr1 transcription factor also function in the response to salt shock. We find that deletion of both tup genes together results in hypersensitivity to elevated cation concentrations (K(+) and Ca(2+)) and we identify cta3(+), which encodes an intracellular cation transporter, as a novel stress gene whose expression is positively controlled by the Sty1 pathway and negatively regulated by Tup repressors. The expression of cta3(+) is maintained at low levels by the Tup repressors, and relief from repression requires the Sty1, Atf1, and Prr1. Prr1 is also required for KCl-mediated induction of several other Sty1-dependent genes such as gpx1(+) and ctt1(+). Surprisingly, the KCl-mediated induction of cta3(+) expression occurs independently of Sty1 in a tup11Delta tup12Delta mutant and so the Tup repressors link induction to the Sty1 pathway. We also report that in contrast to a number of other Sty1- and Atf1-dependent genes, the expression of cta3(+) is induced only by high salt concentrations. However, in the absence of the Tup repressors this specificity is lost and a range of stresses induces cta3(+) expression.
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http://dx.doi.org/10.1091/mbc.01-12-0568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124137PMC
September 2002
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