Browsing by Subject "Asteraceae"

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  • Sennikov, Alexander Nikolaevich; Kazakova, Marina (2015)
    The records of H. murorum s.l. or H. gentile from the Ryazan Region were found to belong to H. lepistoides (native), H. sylvularum (established alien, new to the Ryazan Region) and an unidentified species of Hieracium (alien). The records of H. vulgatum or H. jaccardii from the Ryazan Region belong to another unidentified alien species. Hieracium lepistoides is reported as new to the Vladimir Region, restricted to the Meshchera Lowlands. Hieracium robustum (new to the Ryazan Region) was found sympatric with H. virosum.
  • Abdullah,; Mehmood, Furrukh; Heidari, Parviz; Ahmed, Ibrar; Poczai, Péter (2021)
    The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 25 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content and genome organization comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The contraction and expansion of inverted repeats also show high similarities among the species. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16-trnQ, ycf1, ndhF-rpl32, rps15, petN-psbM, and rpl32-trnL, and they may be suitable for the development of robust, authentic, and cost-effective markers for bar coding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. Our study supports a sister relationship between “Astereae and Anthemideae,” while Gnaphalieae roots these two tribes, whereas in a previous study a sister relationship was reported between “Senecioneae and Anthemideae” and “Astereae and Gnaphalieae” using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between chloroplast and nuclear genome data require further investigation.
  • Sharma, Himanshu; Hyvönen, Jaakko; Poczai, Péter (2020)
    Premise Plant invasions are increasing globally, and extensive study of the genetic background of the source and invading populations is needed to understand such biological processes. For this reason, chloroplast microsatellite markers were identified to explore the genetic diversity of the noxious weed Ambrosia trifida (Asteraceae). Methods and Results The complete chloroplast genome of A. trifida was mined for microsatellite loci, and 15 novel chloroplast primers were identified to assess the genetic diversity of 49 Ambrosia samples. The number of alleles amplified ranged from two to six, with an average of 3.2 alleles per locus. Shannon's information index varied from 0.305 and 1.467, expected heterozygosity ranged from 0.178 to 0.645, and the polymorphism information content value ranged from 0.211 to 0.675 (average 0.428). The cross-species transferability of the 15 microsatellite loci was also evaluated in four related Ambrosia species (A. artemisiifolia, A. maritima, A. psilostachya, and A. tenuifolia). Conclusions The novel chloroplast microsatellite markers developed in the current study demonstrate substantial cross-species transferability and will be helpful in future genetic diversity studies of A. trifida and related species.
  • Zhao, Yafei; Zhang, Teng; Broholm, Suvi K.; Tähtiharju, Sari; Mouhu, Katriina; Albert, Victor A; Teeri, Teemu H.; Elomaa, Paula (2016)
    The evolutionary success of Asteraceae, the largest family of flowering plants, has been attributed to the unique inflorescence architecture of the family, which superficially resembles an individual flower. Here, we show that Asteraceae inflorescences (flower heads, or capitula) resemble solitary flowers not only morphologically but also at the molecular level. By conducting functional analyses for orthologs of the flower meristem identity genes LEAFY (LFY) and UNUSUAL FLORAL ORGANS (UFO) in Gerbera hybrida, we show that GhUFO is the master regulator of flower meristem identity, while GhLFY has evolved a novel, homeotic function during the evolution of head-like inflorescences. Resembling LFY expression in a single flower meristem, uniform expression of GhLFY in the inflorescence meristem defines the capitulum as a determinate structure that can assume floral fate upon ectopic GhUFO expression. We also show that GhLFY uniquely regulates the ontogeny of outer, expanded ray flowers but not inner, compact disc flowers, indicating that the distinction of different flower types in Asteraceae is connected with their independent evolutionary origins from separate branching systems.
  • Cardueae Radiations Grp (2018)
    Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: Arctium, Cousinia, Saussurea, and Jurinea. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, Arctium-Cousinia and Saussurea-Jurinea, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of Arctium, Cousinia, and Saussurea are also well defined. Conversely, conflicting species relationships remain for Jurinea. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.
  • Das, Bishwajit (Helsingin yliopisto, 2020)
    Asteraceae comprises of approximately 10% of all angiosperm plant species. These species are well known for their highly compressed inflorescences known as capitula which consists of morphologically different types of flowers: ray, trans and disc flowers. This immense morphological difference excels Gerbera as an ideal plant to study flower type differentiations. Even though this complex process is governed by several genes, the ray flower identity is believed to be greatly influenced by GhCYC3 promoter mediated gene regulations. In previous studies two TCP transcription factors (TF): GhCIN1and GhCIN2, and two MADS TFs: GAGA1 and RCD5 were identified as the potential upstream regulators of GhCYC3. So, the aim of this study is to test whether these potential upstream regulators physically bind to GhCYC3 promoter in in vitro conditions. In order to achieve the goal, these transcription factor proteins from Gerbera hybrida were successfully expressed in E. coli and purified as fusion proteins to maltose-binding protein (MBP). Physical binding of the purified fusion proteins to the putative target DNA sites in the promoter region of GhCYC3 gene was tested by electrophoretic mobility shift assay (EMSA). The results showed that none of the gerbera transcription factors (GhCIN1, GhCIN2, GAGA1 and RCD5) bind to their putative target sites under the condition tested in this study. However, it might not be justifiable to deduce that these TFs do not interact with GhCYC3 promoter. The absence of in vitro interaction between the tested TFs and GhCYC3 promoter might be caused by either lack of proper folding and activity of the TFs or absence of co-factors which are available in vivo.
  • Shiradhonkar, Rohan (Helsingin yliopisto, 2019)
    The complex inflorescence architecture in Asteraceae is characterized by the presence of morphologically distinct flowers having specialized functions. In gerbera, the presence of three different flower types (ray, trans and disc), intricate inflorescence organization and an underlying complex molecular control makes it an excellent target for research on functional genomics, flower development and evolution. The genes governing flower development have been shown to have undergone sub- and neo-functionalization in gerbera leading to morphological features that are not present in the conventional model plant species. The genes encoding the CYC2 subclade of CYC/TB1-like TCP domain transcription factors are known to regulate the flower type identity in gerbera inflorescence. Although most genes of the CYC2 subclade have demonstrated functional redundancy, one such gene, GhCYC5, was found to have diverged function in regulating rate of initiation of flowers. This study aimed at investigating and affirming the function of GhCYC5 by studying two RNAi lines. Phenotypic analysis of the RNAi inflorescences showed that the length of ray ligules was significantly decreased along with the number of disc flowers and the number of involucral bracts. However, gene expression analysis could not confirm the downregulation of GhCYC5 in the RNAi lines mainly due to low endogenous expression of the gene. However, GhCYC3, another CYC2 clade gene was found to be downregulated due to the off-target silencing effect of the RNAi product and the observed phenotype was associated with suppression of GhCYC3. Further, the role of GhCYC5 in regulating the rate of involucral bract and flower initiation was unclear based on the SEM imaging and expression analysis of the inflorescence meristem, and still requires further studies.
  • Kontturi, Juha; Osama, Raisa; Deng, Xianbao; Bashandy, Hany; Albert, Victor A.; Teeri, Teemu H. (2017)
    The chalcone synthase superfamily consists of type III polyketidesynthases (PKSs), enzymes responsible for producing plant secondary metabolites with various biological and pharmacological activities. Anther-specific chalcone synthase-like enzymes (ASCLs) represent an ancient group of type III PKSs involved in the biosynthesis of sporopollenin, the main component of the exine layer of moss spores and mature pollen grains of seed plants. In the latter, ASCL proteins are localized in the tapetal cells of the anther where they participate in sporopollenin biosynthesis and exine formation within the locule. It is thought that the enzymes responsible for sporopollenin biosynthesis are highly conserved, and thus far, each angiosperm species with a genome sequenced has possessed two ASCL genes, which in Arabidopsis thaliana are PKSA and PKSB. The Gerbera hybrida (gerbera) PKS protein family consists of three chalcone synthases (GCHS1, GCHS3 and GCHS4) and three 2-pyrone synthases (G2PS1, G2PS2 and G2PS3). In previous studies we have demonstrated the functions of chalcone synthases in flavonoid biosynthesis, and the involvement of 2-pyrone synthases in the biosynthesis of antimicrobial compounds found in gerbera. In this study we expanded the gerbera PKS-family by functionally characterizing two gerbera ASCL proteins. In vitro enzymatic studies using purified recombinant proteins showed that both GASCL1 and GASCL2 were able to use medium and long-chain acyl-CoA starters and perform two to three condensation reactions of malonyl-CoA to produce tri- and tetraketide 2-pyrones, usually referred to as alpha-pyrones in sporopollenin literature. Both GASCL1 and GASCL2 genes were expressed only floral organs, with most expression observed in anthers. In the anthers, transcripts of both genes showed strict tapetum-specific localization. (C) 2016 Elsevier Ltd. All rights reserved.
  • Juntheikki-Palovaara, Inka; Tahtiharju, Sari; Lan, Tianying; Broholm, Suvi K.; Rijpkema, Anneke S.; Ruonala, Raili; Kale, Liga; Albert, Victor A.; Teeri, Teemu H.; Elomaa, Paula (2014)
  • Cardueae Radiations Grp (2019)
    Classification of tribe Cardueae in natural subtribes has always been a challenge due to the lack of support of some critical branches in previous phylogenies based on traditional Sanger markers. With the aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae species representing all subtribes and informal groups defined in the tribe, targeting 1061 nuclear conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as by-product of off-target reads. For the extraction of the target nuclear data, we used two strategies, PHYLUCE and HybPiper, and 776 and 1055 COS loci were recovered with each of them, respectively. Additionally, 87 chloroplast genes were assembled and annotated. With three datasets, phylogenetic relationships were reconstructed using both concatenation and coalescent approaches. Phylogenetic analyses of the nuclear datasets fully resolved virtually all nodes with very high support. Nuclear and plastid tree topologies are mostly congruent with a very limited number of incongruent nodes. Based on the well-solved phylogenies obtained, we propose a new taxonomic scheme of 12 monophyletic and morphologically consistent subtribes: Carlininae, Cardopatiinae, Echinopsinae, Dipterocominae (new), Xerantheminae (new), Berardiinae (new), Staehelininae (new), Onopordinae (new), Carduinae (redelimited), Arctiinae (new), Saussureinae (new), and Centaureinae. In addition, we further updated the temporal framework for origin and diversification of these subtribes. Our results highlight the power of Hyb-Seq over Sanger sequencing of a few DNA markers in solving phylogenetic relationships of traditionally difficult groups.
  • Cai, Xiaobo (Helsingin yliopisto, 2020)
    Inflorescence meristems (IMs) either keep producing new flowers, thereby being indeterminate, or terminate after initiation of a finite number of flowers, thereby being determinate. Gerbera hybrida (Asteraceae) has determinate inflorescences. It has been found that the LEAFY (LFY) homolog GhLFY and SEPALLATA (SEP)-like GRCD2/7 promote IM termination in Gerbera as LFY and SEP genes do in Arabidopsis. Downregulation of their expression in Gerbera leads to indeterminate inflorescences. Considering the roles of WUSCHEL (WUS), CLAVATA3 (CLV3) and SHOOT MERISTEMLESS (STM) in meristem maintenance and of TERMINAL FLOWER 1 (TFL1) in IM determinacy in Arabidopsis, it is possible that GhLFY and GRCD2/7 contribute to IM termination by regulating the expression of the homologs of these genes, namely GhWUSb, GhWOX2a, GhCLV3, GhSTM and GhTFL1. It is also possible that GhLFY upregulates the expression of GRCD2/7 in Gerbera, since LFY upregulates SEP gene expression in Arabidopsis. To test these hypotheses, the expression of these candidate genes in Gerbera IMs was compared between IM-expanding and terminating stages, as well as between transgenic plants with downregulated GhLFY or GRCD2/7 expression and wild-type plants. In addition, the pOpOn2 inducible expression vector was used in Gerbera for the first time, in order to induce GhWUSb overexpression in transgenic plants and to study the function of GhWUSb in IM determinacy. Expression analysis showed that during IM termination, GRCD7 expression was upregulated, while the expression of GhWUSb, GhCLV3 and GhWOX2a was downregulated. GhLFY upregulated the expression of GRCD7, and both of them downregulated the expression of GhWUSb, GhCLV3 and GhWOX2a. The expression of GhSTM and GRCD2 was neither affected by IM termination nor regulated by GhLFY or GRCD7. GhTFL1 expression was not detected in any IM samples. Induced GhWUSb overexpression delayed IM termination, confirming the role of GhWUSb in meristem maintenance. These results suggest that GRCD7 may contribute to IM termination by suppressing the expression of the meristem maintenance gene GhWUSb, and the upregulation of GRCD7 by GhLFY may be required for IM termination. GRCD2 and GhSTM may not play a significant role in inflorescence determinacy.
  • Zhang, Teng; Wang, Feng; Elomaa, Paula (2021)
    The Asteraceae plant family is characterized by inflorescences, called flower heads or capitula that may combine hundreds of individual florets into a single flower-like structure. The florets are arranged in a regular phyllotactic pattern with Fibonacci numbers of left- and right-winding spirals. Such a pattern may be disrupted due to physical constraints or by wounding occur-ring during the early meristem development. Recovery from wounding re-establishes patterning although the mechanisms have remained elusive. In this study, we applied Gerbera hybrida as a model system and established methods to conduct wounding experiments either with syringe needles or using laser ablation combined with live imaging of head meristems. By revisiting the historical experiments in sunflower, we conducted wounding to transgenic auxin reporter lines of gerbera and followed the recovery of cellular growth and meristem patterning. We show that wounding disrupted the expression of the gerbera CLAVATA3 (GhCLV3) gene that marks the undifferentiated meristematic region and led to de novo re-initiation of patterning at the wound margin. During the recovery growth, three to five layers of elongated cells showing periclinal cell division planes and lacking auxin signal were formed at the wound rim. DR5 auxin signal was shown to localize and form regularly spaced maxima in a distance from the wound rim. Consequently, spiral pattern of contact parastichies was re-established by stacking of new auxin maxima on top of the previous ones. The developed methods facilitate future studies on understanding the molecular mechanisms of de novo patterning of meristems.
  • Deng, Xianbao; Elomaa, Paula; Nguyen, Cuong X.; Hytonen, Timo; Valkonen, Jari P. T.; Teeri, Teemu H. (2012)