scholarly journals Investigation of orthologous pathogen recognition gene-rich regions in solanaceous species

Genome ◽  
2017 ◽  
Vol 60 (10) ◽  
pp. 850-859 ◽  
Author(s):  
A. Di Donato ◽  
G. Andolfo ◽  
A. Ferrarini ◽  
M. Delledonne ◽  
M.R. Ercolano
Keyword(s):  
Evolutionary Dynamics ◽  
Plant Immunity ◽  
Parallel Evolution ◽  
Protein Domain ◽  
Plant Genome ◽  
Pathogen Recognition ◽  
Leading Role ◽  
The Family ◽  
Powerful Approach ◽  
Plant Families

Pathogen receptor proteins such as receptor-like protein (RLP), receptor-like kinase (RLK), and nucleotide-binding leucine-rich repeat (NLR) play a leading role in plant immunity activation. The genome architecture of such genes has been extensively investigated in several plant species. However, we still know little about their elaborate reorganization that arose during the plant speciation process. Using recently released pepper and eggplant genome sequences, we were able to identify 1097 pathogen recognition genes (PRGs) in the cultivated pepper Zunla-1 and 775 in the eggplant line Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping. Orthologous relationships among clustering loci were found, and interesting reshuffling within given loci was observed for each analysed species. The information obtained was integrated into a comparative map to highlight the evolutionary dynamics in which the PRG loci were involved. Diversification of 14 selected PRG-rich regions was also explored using a DNA target-enrichment approach. A large number of gene variants were found as well as rearrangements of sequences encoding single protein domain and changes in chromosome gene order among species. Gene duplication and transposition activity have clearly influenced plant genome R-gene architecture and diversification. Our findings contribute to addressing several biological questions concerning the parallel evolution that occurred between genomes of the family Solanaceae. Moreover, the integration of different methods proved a powerful approach to reconstruct the evolutionary history in plant families and to transfer important biology findings among plant genomes.

scholarly journals Landscape and evolutionary dynamics of terminal-repeat retrotransposons in miniature (TRIMs) in 48 whole plant genomes

2014 ◽  
Author(s):  
Dongying Gao ◽  
Yupeng Li ◽  
Brian Abernathy ◽  
Scott Jackson
Keyword(s):  
Evolutionary Dynamics ◽  
De Novo ◽  
Gene Evolution ◽  
Terminal Repeat ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Functional Roles ◽  
Whole Plant ◽  
Plant Families ◽  
Transposition Mechanism

Terminal-repeat retrotransposons in miniature (TRIMs) are structurally similar to long terminal repeat (LTR) retrotransposons except that they are extremely small and difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes and the evolutionary and biological impacts and transposition mechanism of TRIMs are poorly understood. In this study, we combined de novo and homology-based methods to annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. We found 156 TRIM families, 146 previously undescribed. Notably, we identified the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families were highly conserved and shared within and between plant families. Even though TRIMs contribute only a small fraction of any plant genome, they are enriched in or near genes and may play important roles in gene evolution. TRIMs were frequently organized into tandem arrays we called TA-TRIMs, another unique feature distinguishing them from LTR retrotransposons. Importantly, we identified putative autonomous retrotransposons that may mobilize specific TRIM elements and detected very recent transpositions of a TRIM in O. sativa. Overall, this comprehensive analysis of TRIMs across the entire plant kingdom provides insight into the evolution and conservation of TRIMs and the functional roles they may play in gene evolution.

RETROSPECTIVE ANALYSIS OF THE MEDICAL DOCUMENTATION OF PATIENTS WHO APPLIED TO THE AMBULATORY OF GENERAL PRACTICE - FAMILY MEDICINE

2019 ◽  
Vol 72 (5) ◽  
pp. 938-941
Author(s):  
Оlexander Ye. Kononov ◽  
Liliana V. Klymenko ◽  
Ganna V. Batsiura ◽  
Larysa F. Matiukha ◽  
Olha V. Protsiuk ◽  
...  
Keyword(s):  
Family Medicine ◽  
Middle Ages ◽  
Risk Groups ◽  
Medical Documentation ◽  
Aged Patients ◽  
Family Doctors ◽  
Functional Changes ◽  
Medicine Clinic ◽  
Leading Role ◽  
The Family

Introduction: In today’s realities of health care reform in Ukraine family doctors play a leading role. The aim of our work was to analyze the medical cards of patients who applied for medical care to the family medicine clinic. Materials and methods: It was analyzed outpatient medical cards of 87 patients who applied to the family medicine clinic in the Khotov village, Kyiv region. The study included people aged 18 to 60 years, which corresponded to the groups of young and middle ages according to the WHO classification. Review: Our findings indicate the prevalence of functional changes among young people: somatoform dysfunction of the autonomic nervous system - 9 (37,5%) and the development of organic manifestations at middle-aged patients: arterial hypertension - 32 (62,7%) and coronary artery disease - 17 (33,3%). Conclusions: This study is important for determining the risk groups, early diagnosis and prevention of diseases.

scholarly journals JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Cong Li ◽  
Qiuyi Shen ◽  
Xiang Cai ◽  
Danni Lai ◽  
Lingshang Wu ◽  
...  
Keyword(s):  
Large Scale ◽  
Plant Immunity ◽  
Expression Patterns ◽  
Protein Domain ◽  
Functional Identification ◽  
Necrotrophic Pathogen ◽  
Southern Blight ◽  
Meja Treatment ◽  
Sclerotium Delphinii ◽  
Large Scale Cultivation

Abstract Background Dendrobium catenatum belongs to the Orchidaceae, and is a precious Chinese herbal medicine. In the past 20 years, D. catenatum industry has developed from an endangered medicinal plant to multi-billion dollar grade industry. The necrotrophic pathogen Sclerotium delphinii has a devastating effection on over 500 plant species, especially resulting in widespread infection and severe yield loss in the process of large-scale cultivation of D. catenatum. It has been widely reported that Jasmonate (JA) is involved in plant immunity to pathogens, but the mechanisms of JA-induced plant resistance to S. delphinii are unclear. Results In the present study, the role of JA in enhancing D. catenatum resistance to S. delphinii was investigated. We identified 2 COI1, 13 JAZ, and 12 MYC proteins in D. catenatum genome. Subsequently, systematic analyses containing phylogenetic relationship, gene structure, protein domain, and motif architecture of core JA pathway proteins were conducted in D. catenatum and the newly characterized homologs from its closely related orchid species Phalaenopsis equestris and Apostasia shenzhenica, along with the well-investigated homologs from Arabidopsis thaliana and Oryza sativa. Public RNA-seq data were investigated to analyze the expression patterns of D. catenatum core JA pathway genes in various tissues and organs. Transcriptome analysis of MeJA and S. delphinii treatment showed exogenous MeJA changed most of the expression of the above genes, and several key members, including DcJAZ1/2/5 and DcMYC2b, are involved in enhancing defense ability to S. delphinii in D. catenatum. Conclusions The findings indicate exogenous MeJA treatment affects the expression level of DcJAZ1/2/5 and DcMYC2b, thereby enhancing D. catenatum resistance to S. delphinii. This research would be helpful for future functional identification of core JA pathway genes involved in breeding for disease resistance in D. catenatum.

Structure of the secondary xylem and development of a cambial variant in Serjania mexicana (Sapindaceae)

IAWA Journal ◽  
2021 ◽  
pp. 1-11
Author(s):  
Kishore S. Rajput ◽  
Amit D. Gondaliya ◽  
Roger Moya
Keyword(s):  
Secondary Xylem ◽  
Secondary Growth ◽  
Stem Anatomy ◽  
The Family ◽  
Ray Cells ◽  
Cambial Variant ◽  
Proportional Increase ◽  
Plant Families ◽  
Ray Parenchyma Cells ◽  
Cambial Variants

Abstract The lianas in the family Sapindaceae are known for their unique secondary growth which differs from climbing species in other plant families in terms of their cambial variants. The present study deals with the stem anatomy of self-supporting and lianescent habit, development of phloem wedges, the ontogeny of cambial variants and structure of the secondary xylem in the stems of Serjania mexicana (L.) Willd. Thick stems (15–20 mm) were characterized by the presence of distinct phloem wedges and tangentially wide neo-formed cambial cylinders. As the stem diameter increases, there is a proportional increase in the number of phloem wedges and neo-formed vascular cylinders. The parenchymatous (pericyclic) cells external to phloem wedges that are located on the inner margin of the pericyclic fibres undergo dedifferentiation, become meristematic and form small segments of cambial cylinders. These cambia extend tangentially into wide and large segments of neoformations. Structurally, the secondary xylem and phloem of the neo-formed vascular cylinders remain similar to the derivatives produced by the regular vascular cambium. The secondary xylem is composed of vessels (wide and narrow), fibres, axial and ray parenchyma cells. The occurrence of perforated ray cells is a common feature in both regular and variant xylem.

scholarly journals Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

2014 ◽  
Vol 80 (17) ◽  
pp. 5503-5514 ◽  
Author(s):  
Christophe Habib ◽  
Armel Houel ◽  
Aurélie Lunazzi ◽  
Jean-François Bernardet ◽  
Anne Berit Olsen ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Multilocus Sequence Analysis ◽  
Fish Pathogens ◽  
Long Distance ◽  
Marine Aquaculture ◽  
Content Type ◽  
The Family ◽  
Cohesive Group

ABSTRACTThe genusTenacibaculum, a member of the familyFlavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogenTenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the speciesT. maritimumconstitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoringTenacibaculuminfections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related toT. dicentrarchi, a recently described species.

scholarly journals Perspectives from animal demography on incorporating evolutionary mechanism into plant population dynamics

2018 ◽  
Author(s):  
Maria Paniw
Keyword(s):  
Environmental Change ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Population Level ◽  
Plant Population ◽  
Future Research ◽  
Phenotypic Traits ◽  
Plant Population Dynamics ◽  
Future Research Agenda ◽  
Powerful Approach

AbstractWith a growing number of long-term, individual-based data on natural populations available, it has become increasingly evident that environmental change affects populations through complex, simultaneously occurring demographic and evolutionary processes. Analyses of population-level responses to environmental change must therefore integrate demography and evolution into one coherent framework. Integral projection models (IPMs), which can relate genetic and phenotypic traits to demographic and population-level processes, offer a powerful approach for such integration. However, a rather artificial divide exists in how plant and animal population ecologists use IPMs. Here, I argue for the integration of the two sub-disciplines, particularly focusing on how plant ecologists can diversify their toolset to investigate selection pressures and eco-evolutionary dynamics in plant population models. I provide an overview of approaches that have applied IPMs for eco-evolutionary studies and discuss a potential future research agenda for plant population ecologists. Given an impending extinction crisis, a holistic look at the interacting processes mediating population persistence under environmental change is urgently needed.

scholarly journals Revisiting Orthotospovirus Phylogeny Using Whole Genomic Data and a Hypothesis for their Geographic Origin and Diversification

2020 ◽  
Author(s):  
Anamarija Butković ◽  
Rubén González ◽  
Santiago F. Elena
Keyword(s):  
Phylogenetic Relationships ◽  
Geographic Origin ◽  
Genome Shuffling ◽  
Genomic Data ◽  
Genomic Sequences ◽  
Genome Database ◽  
Evolutionary Forces ◽  
The Family ◽  
Plant Families ◽  
Negative Sense

ABSTRACTThe family Tospoviridae, a member of the Bunyavirales order, is constituted of tri-segmented negative-sense single-stranded RNA viruses that infect plants and are also able of replicating in their insect vectors in a persistent manner. The family is composed of a single genus, the Orthotospovirus, whose type species is Tomato spotted wilt virus (TSWV). Previous studies assessing the phylogenetic relationships within this genus were based upon partial genomic sequences, thus resulting in unresolved clades and a poor assessment of the roles of recombination and genome shuffling during mixed infections. Complete genomic data for most Orthotospovirus species are now available at NCBI genome database. In this study we have used 62 complete genomes from 20 species. Our study confirms the existence of four phylogroups (A to D), grouped in two major clades (A-B and C-D), within the genus. We have estimated the split between the two major clades ∼3,100 years ago shortly followed by the split between the A and B phylogroups ∼2,860 years ago. The split between the C and D phylogroups happened more recently, ∼1,465 years ago. Segment reassortment has been shown to be important in the generation of novel viruses. Likewise, within-segment recombination events have been involved in the origin of new viral species. Finally, phylogeographic analyses of representative viruses suggests the Australasian ecozone as the possible origin of the genus, followed by complex patterns of migration, with rapid global spread and numerous reintroduction events.IMPORTANCEMembers of the Orthotospovirus genus infect a large number of plant families, including food crops and ornamentals, resulting in multimillionaire economical losses. Despite this importance, phylogenetic relationships within the genus were established years ago based in partial genomic sequences. A peculiarity of orthotospoviruses is their tri-segmented negative sense genomes, which makes segment reassortment and within-segment recombination, two forms of viral sex, potential evolutionary forces. Using full genomes from all described orthotospovirus species, we revisited their phylogeny and confirmed the existence of four major phylogroups with uneven geographic distribution. We have also shown a pervasive role of sex in the origin of new viral species. Finally, using Bayesian phylogeographic methods, we assessed the possible geographic origin and historical dispersal of representative viruses from the different phylogroups.

Liaison entre la religion et les fonctions culturelles de la famille

1969 ◽  
Vol 16 (3) ◽  
pp. 355-368 ◽  
Author(s):  
L. Voyé
Keyword(s):  
Family Environment ◽  
Parallel Evolution ◽  
Family Education ◽  
The Public ◽  
The Family ◽  
The One ◽  
Sociological Explanation ◽  
Hereditary Character ◽  
Socializing Agents ◽  
The Impact

The relatively hereditary character of diverse cultural phenomena has already drawn attention to the role that the family can play in this trans mission. It appears in particular that political orientations and the chances of access to different types and levels of education can frequently be explained by a specific family membership. Two types of argument are put forward here in order to explain how the family can appear as a privileged place of cultural apprenticeship: on the one hand psychological arguments linked with the primary and universal character of family education and the type of relations that this develops; on the other hand a more sociological explanation based on the repercussion that the more or less great complexity of learned language entails with regard to diverse exterior participations, and on the comparison between the impact of the family and those of other socializing agents on the successive choices which they will impose. To these explanatory elements of the existing link between cultural memberships and the family environment is added, for religion as much as for the family, the transition from the public to the private sphere. This parallel evolution will tend to increase the autonomy of religion on the plane of secondary elaborations for which it will borrow its mode of re-interpretation from the exigencies of daily life, particularly from the family.

scholarly journals Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae

2020 ◽  
Vol 10 (12) ◽  
pp. 4387-4398
Author(s):  
Dhanushya Ramachandran ◽  
Michael R. McKain ◽  
Elizabeth A. Kellogg ◽  
Jennifer S. Hawkins
Keyword(s):  
Insertional Mutagenesis ◽  
Evolutionary Dynamics ◽  
Diploid Species ◽  
Duplicate Gene ◽  
Plant Genome ◽  
Abiotic Stress Response ◽  
Repeat Content ◽  
Gene Copies ◽  
Polyploidization Event ◽  
Plant Genome Evolution

Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.

A new approach to the phylogeny of Euascomycetes with a cladistic outline of Arthoniales focussing on Roccellaceae

1990 ◽  
Vol 68 (11) ◽  
pp. 2458-2492 ◽  
Author(s):  
Anders Tehler
Keyword(s):  
Key Words ◽  
Type Species ◽  
Parallel Evolution ◽  
Special Focus ◽  
New Approach ◽  
Lichenicolous Fungi ◽  
Working Hypothesis ◽  
The Family ◽  
Traditional Sense ◽  
Bitunicate Ascus

A phylogenetic working hypothesis of euascomycete relationships is presented. Paraphysoidal ascolocular fungi are monophyletic and ascohymenial fungi are paraphyletic as paraphyses are considered plesiomorphic and paraphysoids apomorphic within euascomycete fungi. As a result it is not necessary to postulate parallel evolution of the bitunicate ascus, and furthermore presence of paraphyses in the prototunicate caliciaceous fungi is no longer in conflict with paraphyses in ascohymenial fungi. A cladistic outline of the order Arthoniales with special focus on the Roccellaceae including 20 taxa and 92 characters is presented. The type species of all genera considered are used as terminal taxa. It is suggested that the type species of Arthothelium should be excluded from the order Arthoniales. The Arthoniaceae are paraphyletic as Arthonia radiata and Arthothelium spectabile form a grade pair. The family Roccellaceae is monophyletic and corroborated in its traditional sense, but some rearrangements within the family are made. Opegrapha vulgata and Lecanactis abietina form a pair, but the family Opegraphaceae is paraphyletic if the pair Chiodecton sphaerale and Schismatomma pericleum are included. The originally described ascoma of the species Darbishirella gracillima, Ingaderia pulcherrima, and Reinkella fragillima are found to be lichenicolous fungi. The mycobiont ascomata of Darbishirella gracillima produce 3- not 2-septate spores. No ascomata of the mycobionts of the two latter species have as yet been found. Key words: Euascomycetes, Arthoniales, Roccellaceae, phylogeny, cladistics, lichenicolous.

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