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Evolution of the bHLH Genes Involved in Stomatal Development: Implications for the Expansion of Developmental Complexity of Stomata in land plants

Evolution of the bHLH Genes Involved in Stomatal Development...

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生态文明建设中的植物学：现在与未来——中国植物学会第十...

作者： Jin-Hua Ran Ting-Ting Shen Wen-Juan Liu Xiao-Quan Wang State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany the Chinese Academy of Sciences

Stomata play significant roles in plant evolution. A trio of closely related basic Helix-Loop-Helix (bHLH) subgroup Ia genes, SPCH, MUTE and FAMA, mediate sequential steps of stomatal development, and their functions may be conserved in land plants. However, the evolutionary history of the putative SPCH/MUTE/FAMA-like genes is still greatly controversial, especially the phylogenetic positions of the bHLH Ia members from basal land plants. To better understand the evolutionary pattern and functional diversity of the bHLH genes involved in stomatal development, we made a comprehensive evolutionary analysis of the homologous genes from 54 species representing the major lineages of green plants. The phylogenetic analysis indicated: (1) All bHLH Ia genes from the two basal land plants Physcomitrella and Selaginella were closely related to the FAMA-like genes of seed plants;and (2) the angiosperm SPCH-like and MUTE-like genes formed a clade with the gymnosperm ’SPCH’ genes at the basal position, while the FAMA-like genes of gymnosperms and angiosperms had a sister relationship. The revealed phylogenetic relationships are also supported by the distribution of

关键词： SPCH FAMA MUTE Stomatal development Evolution land plants

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Plant cytochrome P450 plasticity and evolution

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Molecular Plant 2021年第10期14卷 1244-1265页

作者： Cecilie Cetti Hansen David R.Nelson Birger Lindberg Moller Daniele Werck-Reichhart Plant Biochemistry Laboratory Department of Plant and Environ mental ScienceUniversity of CopenhagenCopenhage nDenmark VILLUM Research Center for Plant Plasticity University of CopenhagenCopenhagenDenmark Department of Microbiology Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTNUSA Institute of Plant Molecular Biology Centre National de la Recherche Scientifique(CNRS)University of StrasbourgStrasbourgFrance

The superfamily of cytochrome P450(CYP)enzymes plays key roles in plant evolution and metabolic diversification.This review provides a status on the CYP Iandscape within green algae and land plants.The 11 conserved CYP clans known from vascular plants are all present in green algae and several green algaespecific clans are recognized.Clan 71,72,and 85 remain the largest CYP clans and include many taxaspecific CYP(sub)families reflecting emergence of linage-specific pathways.Molecular features and dynamics of CYP plasticity and evolution are discussed and exemplified by selected biosynthetic pathways.High substrate promiscuity is commonly observed for CYPs from large families,favoring retention of gene duplicates and neofunctionalization,thus seeding acquisition of new functions.Elucidation of biosynthetic pathways producing metabolites with sporadic distribution across plant phylogeny reveals multiple exampies of convergent evolution where CYPs have been independently recruited from the same or different CYP families,to adapt to similar environmental challenges or ecological niches.Sometimes only a single or a few mutations are required for functional interconversion.A compilation of functionally characterized plant CYPs is provided online through the Plant P450 Database(erda.dk/public/vgrid/PlantP450/).

关键词： land plants green algae diversificati on promiscuity neofunctionalization convergent evolution functionalities plant metabolism

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Dissecting Abscisic Acid Signaling Pathways Involved in Cuticle Formation

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Molecular Plant 2016年第6期9卷 926-938页

作者： Fuqiang Cui Mikael Brosche Mikko T. Lehtonen Ali Amiryousefi Enjun Xu Matleena Punkkinen Jari P.T. Valkonen Hiroaki Fujii Kirk Overmyer Division of Plant Biology Viikki Plant Science Centre Department of Biosciences University of Helsinki 00014 Helsinki Finland Department of Agricultural Sciences University of Helsinki PO Box 27 00014 Helsinki Finland Department of Biochemistry Molecular Plant Biology University of Turku Turku 20014 Finland Institute of Technology University of Tartu Nooruse 1 Tartu 50411 Estonia Present address: Institute of Botany The Chinese Academy of Sciences Beijing China

The cuticle is the outer physical barrier of aerial plant surfaces and an important interaction point between plants and the environment. Many environmental stresses affect cuticle formation, yet the regulatory pathways involved remain undefined. We used a genetics and gene expression analysis in Arabidopsis thaliana to define an abscisic acid （ABA） signaling loop that positively regulates cuticle formation via the core ABA signaling pathway, including the PYR/PYL receptors, PP2C phosphatase, and SNF1-Related Protein Kinase （SnRK） 2.21SnRK2.3/SnRK2.6. Downstream of the SnRK2 kinases, cuticle formation was not regulated by the ABA-responsive element-binding transcription factors but rather by DEWAX, MYB16, MYB94, and MYB96. Additionally, low air humidity increased cuticle formation independent of the core ABA pathway and cell death/reactive oxygen species signaling attenuated expression of cuticle-biosynthesis genes. In Physcornitrella patens, exogenous ABA suppressed expression of cuticle- related genes, whose Arabidopsis orthologs were ABA-induced. Hence, the mechanisms regulating cuticle formation are conserved but sophisticated in land plants. Signaling specifically related to cuticle deficiency was identified to play a major role in the adaptation of ABA signaling pathway mutants to increased humidity and in modulating their immunity to Botrytis cinerea in Arabidopsis. These results define a cuticle-specific downstream branch in the ABA signaling pathway that regulates responses to the external environment.

关键词： cuticle abscisic acid Arabidopsis Physcomitrella Botrytis land plants

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Extreme plastid RNA editing may confound phylogenetic reconstruction:A case study of Selaginella(lycophytes)

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Plant Diversity 2020年第5期42卷 356-361页

作者： Xin-Yu Du Jin-Mei Lu De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of Sciences132 Lanhei RoadKunmingYunnan 650201China Kunming College of Life Science University of Chinese Academy of Sciences19 Qingsong RoadKunmingYunnan 650201China

Cytidine-to-uridine(C-to-U)RNA editing is common in coding regions of organellar genomes throughout land plants.In most cases RNA editing alters translated amino acids or creates new start codons,potentially confounds phylogenetic reconstructions.In this study,we used the spike moss genus Selaginella(lycophytes),which has the highest frequency of RNA editing,as a model to test the effects of extreme RNA editing on phylogenetic reconstruction.We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes,and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences,first and second codon positions,and translated amino acid sequences,respectively.We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes.The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions,but not correlated with the GC content of plastomes as a whole.Contrast phylogenetic analyses showed that there were substantial differences(e.g.,the placement of clade B in Selaginella)between the phylogenies generated by the plastome and RNA-edited data sets.This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction,and might even confound phylogenetic reconstruction.Therefore,RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies,particularly in those lineages with abundant organellar RNA editing sites,such as hornworts,quillworts,spike mosses,and some seed plants.

关键词： GC content land plants Organellar genome Phylogenomics RNA editing

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Phylogenetic Relationships of 3/3 and 2/2 Hemoglobins in Archaeplastida Genomes to Bacterial and Other Eukaryote Hemoglobins

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Molecular Plant 2011年第1期4卷 42-58页

作者： Serge N. Vinogradov Ivan Fernandez David Hoogewijs Rail Arredondo-Peter Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI 48201 USA Laboratorio de Biofisica y Biologia Molecular Facultad de Ciencias Universidad Autonoma del Estado de Morelos 62210 Cuernavaca Morelos Mexico Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP) University of Zurich Zurich Switzerland

land plants and algae form a supergroup, the Archaeplastida, believed to be monophyletic. We report the results of an analysis of the phylogeny of putative globins in the currently available genomes to bacterial and other eu- karyote hemoglobins （Hbs）. Archaeplastida genomes have 3/3 and 2/2 Hbs, with the land plant genomes having group 2 2/ 2 Hbs, except for the unexpected occurrence of two group 1 2/2 Hbs in Ricinus communis. Bayesian analysis shows that plant 3/3 Hbs are related to vertebrate neuroglobins and bacterial flavohemoglobins （FHbs）. We sought to define the bacterial groups, whose ancestors shared the precursors of Archaeplastida Hbs, via Bayesian and neighbor-joining anal- yses based on COBALTalignment of representative sets of bacterial 3/3 FHb-like globins and group I and 2 2/2 Hbs with the corresponding Archaeplastida Hbs. The results suggest that the Archaeplastida 3/3 and group 1 2/2 Hbs could have orig- inated from the horizontal gene transfers （HGTs） that accompanied the two generally accepted endosymbioses of a pro- teobacterium and a cyanobacterium with a eukaryote ancestor. In contrast, the origin of the group 2 212 Hbs unexpectedly appears to involve HGT from a bacterium ancestral to Chloroflexi, Deinococcales, Bacilli, and Actinomycetes. Furthermore, although intron positions and phases are mostly conserved among the land plant 3/3 and 2/2 globin genes, introns are absent in the algal 3/3 genes and intron positions and phases are highly variable in their 2/2 genes. Thus, introns are irrelevant to globin evolution in Archaeplastida.

关键词： Algae Archaeplastida evolution hemoglobin land plants truncated Hbs

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Correlation of Lopingian to Middle Triassic Palynozones

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Journal of Earth Science 2018年第4期29卷 755-777页

作者： Hendrik Nowak Elke Schneebeli-Hermann Evelyn Kustatscher Museum of Nature South Tyrol Bindergasse/Via Bottai 1 Bozen/Bolzano 39100 Italy Palaiontologisehes Institut und Museum Karl-Schmid-Strasse 4 Zurich 8006 Switzerland Department for Geo- und Umweltwissenschafien Pala'ontologie und Geobiologie Ludwig-Maximilians-Universitait and Bayerische Staatssammlung Jur P alaiontologie und Geob iologie Richard-Wagner-Strafle 10 Munchen 80333 Germany

Terrestrial floras underwent important changes during the Lopingian （Late Permian）, Early Triassic, and Middle Triassic, i.e., before, during, and after the end-Permian mass extinction. An accurate account of these developments requires reliable correlation. Macrofossils of land plants can only provide a low-resolution biostratigraphy, while detailed zonation schemes based on palynomorphs are available for many regions. Their applicability is still limited due to several factors, such as （micro-）floral provincialism, a lack of suitable marker taxa commonly occurring at important boundaries, and in many cases a lack of independent age control. Nevertheless, these palynostratigraphic schemes are regularly used for dating and correlation of successions between different regions. To support such efforts, the biozonation schemes based on palynomorphs from the Lopingian up to and including the Middle Triassic from across the world are summarized and revised. Thus, a consistent correlation of palynozones with the currently recognized international stages is established.

关键词： Permian Triassic land plants palynomorpbs biostratigraphy.

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End-Triassic nonmarine biotic events

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Journal of Palaeogeography 2015年第4期4卷 331-348页

作者： Spencer G.Lucas Lawrence H.Tanner New Mexico Museum of Natural History Department of Biological Sciences Le Moyne College

The Late Triassic was a prolonged interval of elevated extinction rates and low origination rates that manifested themselves in a series of extinctions during Carnian, Norian and Rhaetian time. Most of these extinctions took place in the marine realm, particularly affecting radiolarians, conodonts, bivalves, ammonoids and reef-building organisms. On land, the case for a Late Triassic mass extinction is much more tenuous and has largely focused on tetrapod vertebrates（amphibians and reptiles）, though some workers advocate a sudden endTriassic（TJB） extinction of land plants. Nevertheless, an extensive literature does not identify a major extinction of land plants at the TJB, and a comprehensive review of palynological records concluded that TJB vegetation changes were non-uniform（different changes in different places）, not synchronous and not indicative of a mass extinction of land plants. Claims of a substantial perturbation of plant ecology and diversity at the TJB in East Greenland are indicative of a local change in the paleoflora largely driven by lithofacies changes resulting in changing taphonomic filters. Plant extinctions at the TJB were palaeogeographically localized events, not global in extent. With new and more detailed stratigraphic data, the perceived TJB tetrapod extinction is mostly an artifact of coarse temporal resolution, the compiled correlation effect. The amphibian, archosaur and synapsid extinctions of the Late Triassic are not concentrated at the TJB, but instead occur stepwise, beginning in the Norian and extending into the Hettangian. There was a disruption of the terrestrial ecosystem across the TJB, but it was more modest than generally claimed. The ecological severity of the end-Triassic nonmarine biotic events are relatively low on the global scale. Biotic turnover at the end of the Triassic was likely driven by the CAMP（Central Atlantic Magmatic Province） eruptions, which caused significant environmental perturbations（cooling, warming, acidification） through outgassing, but the effec

关键词： Triassic-Jurassic boundary mass extinction land plants East Greenland tetrapods Newark Supergroup CAMP volcanism

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BarcodeFinder: An Integrated Tool for Discovering Novel DNA Barcode Efficiently

BarcodeFinder: An Integrated Tool for Discovering Novel DNA ...

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Ping Wu University of Chinese Academy of Sciences State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of Sciences

DNA barcode has been widely used for species identification and classification.Although standard barcodes for land plants were proposed,such as matK,rbcL and trnH-psbA,they generally presents inadequate resolution in lower taxonomic rank or specific taxa.Currently,the explosion of sequencing data offers abundant possibilities to uncover extra DNA barcodes,yet it was hindered by the complexity of traditional practice of screening candidate barcodes as well as the lack of automatic tools.Here we developed BarcodeFinder,an all-in-one pipeline which integrated data collecting and filtering,sequence variance evaluating and primer designing functions to accelerate the development of novel DNA barcodes.With the assistance,we successfully found thirteen hyper-variant regions on chloroplast genome for Asteraceae suitable to be DNA barcode.Plus,validated（in silico and in vitro） pairs of universal primers for amplification were also generated.

关键词： BarcodeFinder DNA barcode universal primer land plants

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