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Premise of research. Extensins (EXTs) are members of the cell wall hydroxyproline-rich glycoprotein superfamily and play important roles in plant growth, development, and defense. Bioinformatic analysis has identified EXTs for a n...
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Premise of research. Extensins (EXTs) are members of the cell wall hydroxyproline-rich glycoprotein superfamily and play important roles in plant growth, development, and defense. Bioinformatic analysis has identified EXTs for a number of plant species, including the model plant Arabidopsis thaliana, but none of these studies examined plants from the same genus. Methodology. Here we report on the bioinformatic identification and analysis of EXTs in Arabidopsis lyrata and Arabidopsis halleri, two of the closest relatives of A. thaliana, based on amino acid motif searches using the BIO OHIO 2.0 program. Phylogenetic trees for the various EXT subclasses were constructed using both maximum likelihood and maximum parsimony methods. Homologous proteins were revealed using the OrthoMCL program. Pivotal results. The total numbers and subclasses of EXTs were similar in all three species. In A. lyrata, 61 EXTs were identified, including 15 classical EXTs, 10 short EXTs, eight leucine-rich repeat EXTs (LRXs), 14 proline-rich EXT-like receptor kinases (PERKs), five formin homology EXTs (FHXs), four hybrid hydroxyproline-rich glycoproteins (HRGPs), and five other chimeric EXTs. In A. halleri, 65 EXTs were identified, including 13 classical EXTs, 14 short EXTs, eight LRXs, 14 PERKs, six FHXs, four hybrid HRGPs, and six other chimeric EXTs. For comparison, 69 EXTs were identified in A. thaliana, including 19 classical EXTs, 13 short EXTs, 11 LRXs, 12 PERKs, six FHXs, four hybrid HRGPs, and four other chimeric EXTs. Phylogenetic trees and cluster analysis revealed a number of potential orthologous and paralogous proteins among the three species. Conclusions. The identified EXTs and their homologous proteins among A. lyrata, A. halleri, and A. thaliana provide insight into the evolution and functions of EXTs in related species within the same genus. This project offers an excellent example of studying a model system consisting of three closely related species, in which diverse genetic resources and biological data make it possible to address fundamental evolutionary questions that cannot be addressed in a single species.
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The MYB family of proteins is large, functionally diverse and represented in all eukaryotes. Most MYB proteins function as transcription factors with varying numbers of MYB domain repeats conferring their ability to bind DNA. In p...
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The MYB family of proteins is large, functionally diverse and represented in all eukaryotes. Most MYB proteins function as transcription factors with varying numbers of MYB domain repeats conferring their ability to bind DNA. In plants, the MYB family has selectively expanded, particularly through the large family of R2R3-MYB. Members of this family function in a variety of plant-specific processes, as evidenced by their extensive functional characterization in Arabidopsis (Arabidopsis thaliana). MYB proteins are key factors in regulatory networks controlling development, metabolism and responses to biotic and abiotic stresses. The elucidation of MYB protein function and regulation that is possible in Arabidopsis will provide the foundation for predicting the contributions of MYB proteins to the biology of plants in general
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How are the regular patterns of organs established along a plant stem and how[NON-BREAKING SPACE]are the transitions between different patterns regulated? Now genes of the[NON-BREAKING SPACE]PLETHORA family have been shown to modu...
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How are the regular patterns of organs established along a plant stem and how[NON-BREAKING SPACE]are the transitions between different patterns regulated? Now genes of the[NON-BREAKING SPACE]PLETHORA family have been shown to modulate these transitions by fine-tuning the mechanisms of polar transport of auxin, a key effector of organogenesis
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Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new ...
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Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.
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Белки семейства ERF - это факторы, участвующие в транскрипционной регуляции различных процессов метаболизма и развития, а такж...
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Белки семейства ERF - это факторы, участвующие в транскрипционной регуляции различных процессов метаболизма и развития, а также в реакциина биотический и абиотический стресс. Эти белки принадлежат к суперсемейству факторов транскрипции AP2/ERF и содержат консервативный ДНК-связывающий домен AP2/ERF. Основанная на филогении подробная классификация генов ERF дает возможность глубже понять функции различных подгрупп и членов этого семейства. Мы проверили классификацию белков семейства ERF Arabidopsis thaliana, построенную группой Nakano Т. на основе дерева, полученного методом ближайших соседей из матрицы межбелковых расстояний. Мы использовали байесовский вывод в модели нуклеотидных замен, оптимизированной для нуклеотидных последовательностей, кодирующих консервативный ДНК-связывающий домен AP2/ERF. Мы расширили набор данных, использованных Nakano T. et al при построении филогении, за счет включения так называемых VI- и Х-подобных групп. Наши результаты не подтверждают близости этих групп и групп VI и X, как это исходно предполагалось, поэтому мы предлагаем рассматривать VI- и Х-подобные группы как новые группы XI и XII. Группы VI и IX, предложенные Nakano T. et al, также не получили подтверждения, поскольку выглядели в нашем построении как парафилетические совокупности. Все остальные группы, предложенные Nakano Т. et al, были мо-нофилетическими и в полученном нами байесовском дереве. Представленные результаты могут способствовать функциональному описанию генов семейства ERF.
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Polyploid species possess more than two sets of chromosomes and may show high gene redundancy, hybrid vigor, and masking of deleterious alleles compared to their parent species. Following this, it is hypothesized that this makes t...
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Polyploid species possess more than two sets of chromosomes and may show high gene redundancy, hybrid vigor, and masking of deleterious alleles compared to their parent species. Following this, it is hypothesized that this makes them better at adapting to novel environments than their parent species, possibly due to phenotypic plasticity. The allopolyploid Arabidopsis suecica and its parent species A . arenosa and A . thaliana were chosen as a model system to investigate relationships between phenotypic plasticity, fitness, and genetic variation. Particularly, we test if A . suecica is more plastic, show higher genetic diversity, and/or have higher fitness than its parent species. Wild Norwegian populations of each species were analyzed for phenotypic responses to differences in availability of nutrient, water, and light, while genetic diversity was assessed through analysis of AFLP markers. Arabidopsis arenosa showed a higher level of phenotypic plasticity and higher levels of genetic diversity than the two other species, probably related to its outbreeding reproduction strategy. Furthermore, a general positive relationship between genetic diversity and phenotypic plasticity was found. Low genetic diversity was found in the inbreeding A . thaliana . Geographic spacing of populations might explain the clear genetic structure in A . arenosa , while the lack of structure in A . suecica could be due to coherent populations. Fitness measured as allocation of resources to reproduction, pointed toward A . arenosa having lower fitness under poor environmental conditions. Arabidopsis suecica , on the other hand, showed tendencies toward keeping up fitness under different environmental conditions.
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The final shape of shoot lateral organs, namely, leaves and flowers, is determined by coordinated growth after the initiation of primordia from shoot meristems in seed plants. This coordination is achieved by the complex action of...
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The final shape of shoot lateral organs, namely, leaves and flowers, is determined by coordinated growth after the initiation of primordia from shoot meristems in seed plants. This coordination is achieved by the complex action of many transcription factors, which include the TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) family. We have recently reported that CINCINNATA-like (CIN-like) TCP genes act dose-dependently to regulate the flat and smooth morphology of leaves in Arabidopsis thaliana. In contrast, the roles of CIN-like TCP genes in flower development are poorly understood. In this report, using multiple tcp mutants and transgenic plants in which the activity of CIN-like TCP transcription factors is dominantly inhibited, we found that these TCPs regulate the smooth and flat morphology of petals. Based on these findings, we discuss a possible strategy to generate a fringed morphology in floricultural plants.
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In Arabidopsis, expression of FLC and FLC-related genes (collectively called FLC clade) contributes to flowering time in response to environmental changes, such as day length and temperature, by acting as floral repressors. VIN3 i...
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In Arabidopsis, expression of FLC and FLC-related genes (collectively called FLC clade) contributes to flowering time in response to environmental changes, such as day length and temperature, by acting as floral repressors. VIN3 is required for vernalization-mediated FLC repression and a VIN3 related protein, VIN3-LIKE 1/VERNALIZATION 5 (VIL1/VRN5), acts to regulate FLC and FLM in response to vernalization. VIN3 also exists as a small family of PHD finger proteins in Arabidopsis, including VIL1/VRN5, VIL2/VEL1, VIL3/VEL2, and VIL4/VEL3. We showed that the PHD finger protein, VIL2, is required for proper repression of MAF5, an FLC clade member, to accelerate flowering under non-inductive photoperiods. VIL2 acts together with POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) to repress MAF5 in a photoperiod dependent manner.
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Leaves develop as planar organs, with a morphology that is specialized for photosynthesis. Development of a planar leaf requires genetic networks that set up opposing adaxial and abaxial sides of the leaf, which leads to establish...
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Leaves develop as planar organs, with a morphology that is specialized for photosynthesis. Development of a planar leaf requires genetic networks that set up opposing adaxial and abaxial sides of the leaf, which leads to establishment of dorsoventral polarity. While many genes have been identified that regulate adaxial and abaxial fate there is little information on how this is integrated with cellular function. EMBRYO DEFECTIVE DEVELOPMENT1 (EDD1) is a nuclear gene that encodes a plastid and mitochondrial localized glycyl-tRNA synthetase. Plants with partial loss of EDD1 function have changes in patterning of margin and distal regions of the leaf. In combination with mutations in the MYB domain transcription factor gene ASYMMETRIC LEAVES1 (AS1), partial loss of EDD1 function results in leaves with reduced adaxial fate. EDD1 may influence leaf dorsoventral polarity through regulating the abaxial fate genes KANADI1 (KAN1) and ETTIN (ETT)/AUXIN RESPONSE FACTOR3 (ARF3) since these genes are upregulated in the edd1 as1 double mutant. SCABRA3 (SCA3), a nuclear gene that encodes the plastid RNA polymerase is also required for leaf adaxial fate in the absence of AS1. These results add a novel component to networks of genetic regulation of leaf development and suggest that organelles, particularly plastids, are required in leaf patterning. Potentially, signalling from organelles is essential for coordination of different cell fates within the developing leaf.
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We have established a detailed framework for the process of shoot regeneration from Arabidopsis root and hypocotyl explants grown in vitro. Using transgenic plant lines in which the GUS or GFP genes were fused to promoters of deve...
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We have established a detailed framework for the process of shoot regeneration from Arabidopsis root and hypocotyl explants grown in vitro. Using transgenic plant lines in which the GUS or GFP genes were fused to promoters of developmental genes (WUS, CLV1, CLV3, STM, CUC1, PLT1, RCH1, QC25), or to promoters of genes encoding indicators of the auxin response (DR5) or transport (PIN1), cytokinin (CK) response (ARR5) or synthesis (IPT5), or mitotic activity (CYCB1), we showed that regenerated shootsoriginated directly or indirectly from the pericycle cells adjacent to xylem poles. In addition, shoot regeneration appeared to be partly similar to the formation of lateral root meristems (LRMs). During pre-culture on a 2, 4-dichlorophenoxyacetic acid (2, 4-D)-rich callus-inducing medium (CIM), xylem pericycle reactivation established outgrowths that were not true calli but had many characteristics of LRMs. Transfer to a CK-rich shoot-inducing medium (SIM) resulted in early LRM-like primordia changingto shoot meristems. Direct origin of shoots from the xylem pericycle occurred upon direct culture on CK-containing media without prior growth on CIM. Thus, it appeared that the xylem pericycle is more pluripotent than previously thought. This pluripotency was accompanied by the ability of pericycle derivatives to retain diploidy, even after several rounds of cell division. In contrast, the phloem pericycle did not display such developmental plasticity, and responded to CKs with only periclinal divisions. Such observations reinforce the view that the pericycle is an 'extended meristem' that comprises two types of cell populations. They also suggest that the founder cells for LRM initiation are not initially fully specified for this developmental pathway
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