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  • 1
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    Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor (2015)
    Oxford University Press
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    Publication Date: 2015-12-30
    Description: Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana . In A. lyrata , we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification (2012)
    Oxford University Press
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    Publication Date: 2012-11-10
    Description: Comparative genome biology has unveiled the polyploid origin of all angiosperms and the role of recurrent polyploidization in the amplification of gene families and the structuring of genomes. Which species share certain ancient polyploidy events, and which do not, is ill defined because of the limited number of sequenced genomes and transcriptomes and their uneven phylogenetic distribution. Previously, it has been suggested that most, but probably not all, of the eudicots have shared an ancient hexaploidy event, referred to as the gamma triplication. In this study, detailed phylogenies of subfamilies of MADS-box genes suggest that the gamma triplication has occurred before the divergence of Gunnerales but after the divergence of Buxales and Trochodendrales. Large-scale phylogenetic and K S - based approaches on the inflorescence transcriptomes of Gunnera manicata (Gunnerales) and Pachysandra terminalis (Buxales) provide further support for this placement, enabling us to position the gamma triplication in the stem lineage of the core eudicots. This triplication likely initiated the functional diversification of key regulators of reproductive development in the core eudicots, comprising 75% of flowering plants. Although it is possible that the gamma event triggered early core eudicot diversification, our dating estimates suggest that the event occurred early in the stem lineage, well before the rapid speciation of the earliest core eudicot lineages. The evolutionary significance of this paleopolyploidy event may thus rather lie in establishing a species lineage that was resilient to extinction, but with the genomic potential for later diversification. We consider that the traits generated from this potential characterize extant core eudicots both chemically and morphologically.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Phylogenetics of Impatiens and Hydrocera (Balsaminaceae) using chloroplast atpB-rbcL spacer sequences (2006)
    In:  Systematic Botany vol. 31 no. 1, pp. 171-180
    Details
    Publication Date: 2024-01-12
    Description: Balsaminaceae are a morphologically diverse family with ca. 1,000 representatives that are mainly distributed in the Old World tropics and subtropics. To understand the relationships of its members, we obtained chloroplast atpB-rbcL sequences from 86 species of Balsaminaceae and five outgroups. Phylogenetic reconstructions using parsimony and Bayesian approaches provide a well-resolved phylogeny in which the sister group relationship between Impatiens and Hydrocera is confirmed. The overall topology of Impatiens is strongly supported and is geographically structured. Impatiens likely originated in South China from which it colonized the adjacent regions and afterwards dispersed into North America, Africa, India, the Southeast Asian peninsula, and the Himalayan region.
    Keywords: Balsaminaceae ; phylogeny ; reconstruction ; sister group relationship ; Impatiens ; Hydrocera
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 4
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    Palynological Variation in Balsaminoid Ericales. II. Balsaminaceae, Tetrameristaceae, Pellicieraceae and General Conclusions (2005)
    In:  Annals of Botany vol. 96 no. 6, pp. 1061-1073
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    Publication Date: 2024-01-12
    Description: Background and Aims The objective of this study is to examine the palynological diversity of Balsaminaceae (two genera/61000 species), Tetrameristaceae (two genera/two species) and Pellicieraceae (one genus/one species). The diversity found will be used to infer the systematic value of pollen features within the balsaminoid clade. Methods Pollen morphology and ultrastructure of 29 species, representing all families of the balsaminoid clade except Marcgraviaceae, are investigated by means of light microscopy, scanning electron microscopy and transmission electron microscopy. Key Results Balsaminaceae pollen is small to medium sized with three to four apertures, which can be either colpate or porate, and a sexine sculpturing varying from coarsely reticulate to almost microreticulate. Tetrameristaceae pollen is small sized, 3-colporate, with a heterobrochate reticulate sculpturing and granules present in the lumina. Pellicieraceae pollen is large sized, 3-colporate with long ectocolpi and a perforate sexine sculpturing with large verrucae. Furthermore, Pelliciera is characterized by the occurrence of aggregated orbicules, while orbicules are completely absent in both Balsaminaceae and Tetrameristaceae. Balsaminaceae pollen differs from the other balsaminoid families due to the occurrence of colpate or porate grains with an oblate to peroblate shape, a very thin foot layer and a lamellated endexine. Conclusions From a pollen morphological point of view, Balsaminaceae are completely different from the other balsaminoid families. Therefore, no pollen morphological synapomorphies could be defined for the balsaminoid clade. However, various pollen features were observed that could indicate a possible relationship between Tetrameristaceae, Pellicieraceae and Marcgraviaceae. Despite the palynological similarities in the latter three families, it remains unclear to what extent they are related to each other.
    Keywords: Balsaminaceae ; Ericales ; orbicules ; Pellicieraceae ; pollen ; SEM ; TEM ; Tetrameristaceae
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
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    Petaloidy and petal identity MADS-box genes in the balsaminoid genera Impatiens and Marcgravia (2006)
    In:  The Plant Journal vol. 47, pp. 501-518
    Details
    Publication Date: 2024-01-12
    Description: Impatiens and Marcgravia have striking morphological innovations associated with the flowers. One of the sepals in Impatiens is spurred and petaloid, while in Marcgravia the petals are fused into a cap and nectary cups are associated with the inflorescence. Balsaminaceae (Impatiens) and Marcgraviaceae have surprisingly been shown to be closely related, since both belong to the balsaminoid clade of Ericales (basal asterids). However, several thorough morphological studies thus far have not revealed shared derived characters (synapomorphies) that support a close relationship between these families. In the balsaminoid clade, transitions from entirely green flowers to flowers with heterotopic petaloid organs can be observed. The primary role of class B genes in core eudicots is to specify the identity of petal and stamen floral organs. E-class genes, of which SEP3 is a representative, have been identified as redundant mediators that confer transcriptional activation potential on protein complexes that specify organ identity. Given the conserved function of organ-identity MADS-box genes in model plants, but the rapid molecular evolution in angiosperms, it remains controversial whether these genes have been involved in shaping floral diversity. We have identified a SEP3-like gene and a total of five class B genes from Impatiens hawkeri and Marcgravia umbellata and report their quantitative expression in the floral organs. In Impatiens, two AP3/DEF-like genes were identified with strongly divergent C-terminal domains, one truncated and one unusually long. Both genes show a gradual decrease in expression towards the outer perianth organs, but no GLO-like gene expression is observed in the petaloid sepal. Remarkably, SEP3-like gene expression in the Impatiens perianth is absent from the green sepals but present in the petaloid sepal and in the petals. Dimeric protein interactions of the cloned Impatiens genes were studied in yeast and by using gel retardation. In Marcgravia, strong overlapping class B gene expression is limited to the stamens, but a SEP3-like gene is strongly expressed in the Marcgravia nectary, indicating that both Impatiens and Marcgravia show heterotopic expression of a SEP3-like gene. We discuss several candidate mechanisms for heterotopic petaloidy involving modified gene expression and protein interaction of SEP3-like and class B genes.
    Keywords: SEPALLATA3 ; class B genes ; petal identity ; MADS-box genes ; Impatiens ; Marcgravia
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 6
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    Gomphocalyx and Phylohydrax (Rubiaceae): sister taxa excluded from Spermacoceae s.s., featuring a remarkable case of convergent evolution (2005)
    In:  TAXON vol. 54 no. 1, pp. 91-107
    Details
    Publication Date: 2024-01-12
    Description: The genera Gomphocalyx and Phylohydrax (Rubiaceae) have been invariably placed in the tribe Spermacoceae s.s. based on the uni-ovulate ovary locules and pluri-aperturate pollen grains. Sequence data from the rps16 intron and the rbcL gene here presented exclude Gomphocalyx and Phylohydrax from Spermacoceae s.s. The two genera are closely related and their nearest relatives are found among members of the former tribe Hedyotideae. This position may be surprising at first, because the growth form of Phylohydrax is similar to some observed in Spermacoceae s.s. A detailed survey of morphological and anatomical characters shows, however, that the character states of the two genera are largely consistent with the here-proposed position in Hedyotideae. The creeping growth form, the uni-ovulate ovaries and the pluri-colporate pollen grains of Gomphocalyx and Phylohydrax are the result of convergence between this pair of genera and Spermacoceae s.s. The taxonomic position of Lathraeocarpa, sometimes considered closely related to Gomphocalyx, is also discussed.
    Keywords: convergent evolution ; Gomphocalyx ; Hydrophylax ; Phylohydrax ; Rubiaceae ; Spermacoceae
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
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    The distribution and phylogeny of aluminium accumulating plants in the Ericales (2004)
    In:  Plant Biology vol. 6, pp. 498-505
    Details
    Publication Date: 2024-01-12
    Description: The distribution of aluminium (Al) accumulation in the Ericales is surveyed, based on semi-quantitative tests of 114 species and literature data. Al accumulation mainly characterises the families Diapensiaceae, Pentaphylacaceae, Symplocaceae, Ternstroemiaceae, and Theaceae. Al accumulation is consistently present or absent in most families examined, but the character appears to be more variable in a few taxa (e.g., Lecythidaceae, Myrsinaceae). Although the interfamilial relationships within the Ericales require further research, the ability to accumulate high levels of Al appears to show considerable taxonomic significance. While the majority of Al accumulating Ericales includes woody, tropical plants, the feature is remarkably present in several herbaceous Diapensiaceae, which have a distribution in cold to temperate areas. The association of different mycorrhizae types with plant roots is suggested to play a role in the exclusion of high Al levels from the shoot.
    Keywords: aluminium accumulation ; Ericales ; phyogeny ; Diapensiaceae ; Pentaphylacaceae ; Symplocaceae ; Ternstroemiaceae ; Theaceae
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 8
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    Phylogenetic utility of the AP3/DEF K-domain and its molecular evolution in Impatiens (Balsaminaceae) (2007)
    In:  Molecular Phylogenetics and Evolution vol. 43, pp. 225-239
    Details
    Publication Date: 2024-01-12
    Description: APETALA3 (AP3)/DEFICIENS (DEF) is a MADS-box transcription factor that is involved in establishing the identity of petal and stamen floral organs. The AP3/DEF gene lineage has been extensively examined throughout the angiosperms in order to better understand its role in floral diversity and evolution. As a result, a large number of cloned AP3/DEF orthologues are available, which can be used for the design of taxon specific primers for phylogeny reconstruction of close relatives of the group of interest. Following this reasoning, we investigated the phylogenetic utility of the two AP3/DEF paralogues (ImpDEF1 and ImpDEF2) that were recently identified in the genus Impatiens (Balsaminaceae). K-domain introns 4 and 5 of both AP3/DEF duplicates were amplified and sequenced for 59 Impatiens species. Phylogenetic analyses of the separated and combined ImpDEF1 and ImpDEF2 data sets result in highly congruent topologies with the previously obtained chloroplast atpB-rbcL data set. Combination of chloroplast and nuclear matrices results in a well-supported evolutionary hypothesis of Impatiens. Our results show that introns 4 and 5 in AP3/DEF-like genes are a valuable source of characters for phylogenetic studies at the infrageneric level.
    Keywords: APETALA3/DEFICIENS ; Gene duplication ; Impatiens ; ImpDEF1 ; ImpDEF2 ; K-domain ; Phylogenetic utility
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 9
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    Selection on length mutations after frameshift can explain the origin and retention of the AP3/DEF-like paralogues in Impatiens (2008)
    In:  Journal of Molecular Evolution vol. 66 no. 5, pp. 424-435
    Details
    Publication Date: 2024-01-12
    Description: Evolution of class B genes through gene duplication has been proposed as an evolutionary mechanism that contributed to the enormous floral diversity. Frameshift mutations are a likely mechanism to explain the divergent C-terminal sequences of MIKC gene subfamilies. So far, the inferences for frameshifts and selective pressures on the C-terminal domain are made for old duplications for which the exact selective pressures are obscured by evolutionary time. This motivated us to study an example of a recent duplication, which allows us to consider in more detail the selective pressures that are involved after duplication. We find that after duplication and frameshift of Impatiens class B genes, the individual codons show no evidence for adaptive selection. It is rather the length of the C-terminal domain that either is strictly conserved or varies strongly. This suggests a role for the length of the C-terminal domain in the retention of duplicated genes.
    Keywords: APETALA3 /DEFICIENS ; C-terminal domain ; frameshift ; gene duplication ; impatiens ; selection ; indels
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 10
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    Phylogenetic relationships in Nartheciaceae (Dioscoreales), with focus on pollen and orbicule morphology (2008)
    In:  Belgian Journal of Botany vol. 141 no. 1, pp. 64-77
    Details
    Publication Date: 2024-01-12
    Description: Amolecular phylogenetic analysis of Nartheciaceae is presented, with nine species of the family\xe2\x80\x99s five genera. The main phylogenetic findings are: (a) Nietneria and Narthecium are placed in a clade sister to Lophiola; (b) sister to the Lophiola-Narthecium- Nietneria clade is a clade formed by Aletris and the monospecific Metanarthecium; (c) the inclusion of Metanarthecium luteo-viride in Aletris, as proposed by several authors, is well supported. The pollen and orbicule morphology of representatives of five genera is described. The results underline a close relationship between Nietneria, Narthecium, and Lophiola and confirm the previously reported observations of Metanarthecium pollen and the types of sexine ornamentation in Aletris. Pollen grains of Nietneria are monosulcate with a microreticulate sexine, confirming a close relationship with Lophiola and Narthecium. Spherical smoothsurfaced orbicules were observed in all genera of Nartheciaceae and the presence of a circular perforation on the orbicule surface is potentially synapomorphic for the family.
    Keywords: Dioscoreales ; Nartheciaceae ; Nietneria ; molecular phylogeny ; orbicules ; pollen morphology
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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