scholarly journals Dinoflagellates with relic endosymbiont nuclei as novel models for elucidating organellogenesis

2019 ◽  
Author(s):  
Chihiro Sarai ◽  
Goro Tanifuji ◽  
Takuro Nakayama ◽  
Ryoma Kamikawa ◽  
Kazuya Takahashi ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Process ◽  
Dna Transfer ◽  
Free Living ◽  
Genus Level ◽  
Green Algal ◽  
New Models ◽  
Endosymbiotic Alga ◽  
Algal Groups ◽  
Genetic Level

AbstractNucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process integrating an endosymbiont alga into be a host-governed plastid (organellogenesis). Nevertheless, past studies suggested that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet to pinpoint the closest free-living relative of the endosymbiotic alga engulfed by the ancestral chlorarachniophyte or cryptophyte, making difficult to infer how organellogenesis altered the endosymbiont genome. To counter the above issues, we need novel nucleomorph-bearing algae, in which from-endosymbiont-to-host DNA transfer is on-going and of which endosymbiont/plastid origins can be inferred at a fine taxonomic scale. Here, we report two previously undescribed dinoflagellates, strains MGD and TGD, with green algal endosymbionts enclosing plastids as well as relic nuclei (nucleomorphs). We provide the evidence for the presence of DNA in the two nucleomorphs and transfer of endosymbiont genes to the host (dinoflagellate) genomes. Furthermore, DNA transfer between the host and endosymbiont nuclei was found to be in progress in both MGD and TGD systems. Phylogenetic analyses successfully resolved the origins of the endosymbionts at the genus level. Combined, we conclude that the host-endosymbiont integration in MGD/TGD is less advanced than that in cryptophytes/chrorarachniophytes, and propose the two dinoflagellates as new models for elucidating organellogenesis.

scholarly journals Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis

2020 ◽  
Vol 117 (10) ◽  
pp. 5364-5375 ◽  
Author(s):  
Chihiro Sarai ◽  
Goro Tanifuji ◽  
Takuro Nakayama ◽  
Ryoma Kamikawa ◽  
Kazuya Takahashi ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Process ◽  
Dna Transfer ◽  
Free Living ◽  
Genus Level ◽  
Green Algal ◽  
Endosymbiotic Alga ◽  
Two Systems ◽  
Algal Groups ◽  
Genetic Level

Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggest that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet to pinpoint the closest free-living relative of the endosymbiotic alga engulfed by the ancestral chlorarachniophyte or cryptophyte, making it difficult to infer how organellogenesis altered the endosymbiont genome. To counter the above issues, we need novel nucleomorph-bearing algae, in which endosymbiont-to-host DNA transfer is on-going and for which endosymbiont/plastid origins can be inferred at a fine taxonomic scale. Here, we report two previously undescribed dinoflagellates, strains MGD and TGD, with green algal endosymbionts enclosing plastids as well as relic nuclei (nucleomorphs). We provide evidence for the presence of DNA in the two nucleomorphs and the transfer of endosymbiont genes to the host (dinoflagellate) genomes. Furthermore, DNA transfer between the host and endosymbiont nuclei was found to be in progress in both the MGD and TGD systems. Phylogenetic analyses successfully resolved the origins of the endosymbionts at the genus level. With the combined evidence, we conclude that the host–endosymbiont integration in MGD/TGD is less advanced than that in cryptophytes/chrorarachniophytes, and propose the two dinoflagellates as models for elucidating organellogenesis.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

scholarly journals The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes

2016 ◽  
Vol 283 (1835) ◽  
pp. 20160942 ◽  
Author(s):  
Jinshui Zheng ◽  
Donghai Peng ◽  
Ling Chen ◽  
Hualin Liu ◽  
Feng Chen ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Evolutionary Process ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Free Living ◽  
C Elegans ◽  
Free Living Nematode ◽  
Plant Nematode ◽  
Ditylenchus Destructor ◽  
Plant Parasitic

Plant-parasitic nematodes were found in 4 of the 12 clades of phylum Nematoda. These nematodes in different clades may have originated independently from their free-living fungivorous ancestors. However, the exact evolutionary process of these parasites is unclear. Here, we sequenced the genome sequence of a migratory plant nematode, Ditylenchus destructor . We performed comparative genomics among the free-living nematode, Caenorhabditis elegans and all the plant nematodes with genome sequences available. We found that, compared with C. elegans , the core developmental control processes underwent heavy reduction, though most signal transduction pathways were conserved. We also found D. destructor contained more homologies of the key genes in the above processes than the other plant nematodes. We suggest that Ditylenchus spp. may be an intermediate evolutionary history stage from free-living nematodes that feed on fungi to obligate plant-parasitic nematodes. Based on the facts that D. destructor can feed on fungi and has a relatively short life cycle, and that it has similar features to both C. elegans and sedentary plant-parasitic nematodes from clade 12, we propose it as a new model to study the biology, biocontrol of plant nematodes and the interaction between nematodes and plants.

scholarly journals Testing Host-Plant Driven Speciation in Phytophagous Insects: A Phylogenetic Perspective

2019 ◽  
Author(s):  
Emmanuelle Jousselin ◽  
Marianne Elias
Keyword(s):  
Host Plant ◽  
Evolutionary Biology ◽  
Phylogenetic Analyses ◽  
Evolutionary Process ◽  
Niche Differentiation ◽  
Ecological Speciation ◽  
Model Systems ◽  
Phytophagous Insects ◽  
Ecological Specialization ◽  
Recent Developments

During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation. Phytophagous insects represent model systems for the study of this evolutionary process. The host-plants on which these insects feed and often spend parts of their life cycle constitute ideal agents of divergent selection for these organisms. Adaptation to feeding on different host-plant species can potentially lead to ecological specialization of populations and subsequent speciation. This process is thought to have given birth to the astonishing diversity of phytophagous insects and is often put forward in macroevolutionary scenarios of insect diversification. Consequently, numerous phylogenetic studies on phytophagous insects have aimed at testing whether speciation driven by host-plant adaptation is the main pathway for the diversification of the groups under investigation. The increasing availability of comprehensive and well-resolved phylogenies and the recent developments in phylogenetic comparative methods are offering an unprecedented opportunity to test hypotheses on insect diversification at a macroevolutionary scale, in a robust phylogenetic framework. Our purpose here is to review the contribution of phylogenetic analyses to investigate the importance of plant-mediated speciation in the diversification of phytophagous insects and to present suggestions for future developments in this field.

Phylogenetic analyses of potentially free-living Symbiodinium spp. isolated from coral reef sand in Okinawa, Japan

2008 ◽  
Vol 155 (1) ◽  
pp. 105-112 ◽  
Author(s):  
Mamiko Hirose ◽  
James D. Reimer ◽  
Michio Hidaka ◽  
Shoichiro Suda
Keyword(s):  
Coral Reef ◽  
Phylogenetic Analyses ◽  
Free Living

Phylogeny of Subtribe Aeridinae (Orchidaceae) Inferred from DNA Sequences Data : Advanced Analyses Including Australasian Genera

2012 ◽  
Vol 59 (1) ◽  
Author(s):  
Topik Hidayat ◽  
Peter H. Weston ◽  
Tomohisa Yukawa ◽  
Motomi Ito ◽  
Rod Rice
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Its Region ◽  
Classification Systems ◽  
Genus Level ◽  
Preliminary Work ◽  
Secondary Center ◽  
Generic Position ◽  
Australasian Region

Advanced phylogenetic analyses of the orchid subtribe Aeridinae has been conducted using DNA sequences of ITS region of nrDNA andmatK of cpDNA. In the preliminary work, we only involved the most representative Asian genera of the subtribe. Further, to establish more robust relationships in the Aeridinae, in this study we have extended the sampling to include Australasian specimens. Our analyses revealed that: (1) the subtribe is reorganised by four major groups with 11 subgroups (This is inconsistent with previous classification systems of the subtribe); (2) the Australasian region is a secondary center of diversification of the subtribe; (3) vegetative features have shown to have greater value than reproductive one in determining major groups in the subtribe; and (4) at genus level, some genera, i.e. Phalaenopsis,Cleisostoma, Sarcochilus, and Aerides are shown to be non-monophyletic. This study also resolved the taxonomic status ofAerides flabellata Rolve ex Downie, a species with a debatable generic position.

scholarly journals Morphology and phylogenetic position of Spongiochrysis hawaiiensis gen. et sp. nov., the first known terrestrial member of the order Cladophorales (Ulvophyceae, Chlorophyta)

2006 ◽  
Vol 56 (4) ◽  
pp. 913-922 ◽  
Author(s):  
Fabio Rindi ◽  
Juan M. López-Bautista ◽  
Alison R. Sherwood ◽  
Michael D. Guiry
Keyword(s):  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Holotype Specimen ◽  
Green Algal ◽  
Golden Yellow ◽  
Terrestrial Habitats ◽  
Well Differentiated ◽  
Globular Cells

Spongiochrysis hawaiiensis gen. et sp. nov. is described from material collected at two sites on O'ahu, Hawaiian Islands. This alga produced golden-yellow crusts on the bark of Casuarina trees and consisted of globular cells with an axial stellate chloroplast. The only form of reproduction was a specialized type of autosporulation in which a budding-like division of the mother cell produced daughter cells of different sizes. Phylogenetic analyses of the 18S rRNA gene showed that Spongiochrysis hawaiiensis is a member of the freshwater clade of the Cladophorales/Siphonocladales lineage in the green algal class Ulvophyceae. On the basis of its unicellular habit and terrestrial habitat, this species is well differentiated from all other members of the same lineage and can be considered as the first known successful step of a member of the order Cladophorales into terrestrial habitats. The implications of the description of this species with regard to both green algal evolution and conservation of little-known tropical habitats are discussed. The holotype specimen of Spongiochrysis hawaiiensis is GALW015489 and isotype specimens have also been deposited in the BISH and BM herbaria.

Genetics of plant-microbe nitrogen-fixing symbiosis

1985 ◽  
Vol 85 (3-4) ◽  
pp. 239-252
Author(s):  
G. C. Machray ◽  
W. D. P. Stewart
Keyword(s):  
Nitrogen Fixation ◽  
Genetic Analysis ◽  
Symbiotic Nitrogen Fixation ◽  
Model System ◽  
Present Knowledge ◽  
Nitrogen Fixing ◽  
Free Living ◽  
Genetic Level ◽  
And Control ◽  
Control Of Expression

SynopsisA wide variety of plant-microbe nitrogen-fixing symbioses which include cyanobacteria as the nitrogenfixing partner exist. While some information has been gathered on the biochemical changes in the cyanobacterium upon entering into symbiosis, very little is known about the accompanying changes at the genetic level. Much of our present knowledge of the organisation and control of expression of nitrogenfixation (nif) genes is derived from studies of the free-living diazotroph Klebsiella pneumoniae. This organism thus provides a model system and source of experimental material for the genetic analysis of symbiotic nitrogen fixation. We describe the use of cloned K. pneumoniae genes for nitrogen fixation and its regulation in the genetic analysis' of nitrogen fixation in cyanobacteria which can enter into symbiosis with plants. These studies reveal some dissimilarities in the organisation of nif genes and raise questions as to the genetic control of nitrogen fixation in symbiosis.

scholarly journals The aphelid-like phagotrophic origins of fungi

2017 ◽  
Author(s):  
Guifre Torruella ◽  
Xavier Grau-Bove ◽  
David Moreira ◽  
Sergey A Karpov ◽  
John Burns ◽  
...  
Keyword(s):  
Cell Wall ◽  
Metabolic Pathways ◽  
Phylogenetic Analyses ◽  
Algal Cell ◽  
Rrna Genes ◽  
Transcriptome Data ◽  
Free Living ◽  
Statistical Support ◽  
Phylogenomic Analyses ◽  
Protein Datasets

Aphelids are poorly known phagotrophic parasites of algae whose life cycle and morphology resemble those of the widely diverse parasitic rozellids (Cryptomycota, Rozellomycota). In previous phylogenetic analyses of RNA polymerase and rRNA genes, aphelids and rozellids formed a monophyletic group together with the extremely reduced parasitic Microsporidia, named Opisthosporidia, which was sister to Fungi. However, the statistical support for that group was always moderate. We generated the first transcriptome data for one aphelid species, Paraphelidium tribonemae. In-depth multi-gene phylogenomic analyses using various protein datasets place aphelids as the closest relatives of Fungi to the exclusion of rozellids and Microsporidia. In contrast with the comparatively reduced Rozella allomycis genome, we infer a rich, free-living-like aphelid proteome, including cellulases likely involved in algal cell-wall penetration, enzymes involved in chitin biosynthesis and several metabolic pathways. Our results suggest that Fungi evolved from a complex aphelid-like ancestor that lost phagotrophy and became osmotrophic.

scholarly journals CHARACTER ASSESSMENT, GENUS LEVEL BOUNDARIES, AND PHYLOGENETIC ANALYSES OF THE FAMILY RHACOPHORIDAE:

2000 ◽  
pp. 1-31 ◽  
Author(s):  
Jeffery A. Wilkinson ◽  
Robert C. Drewes
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Current Status ◽  
Phylogenetic Hypothesis ◽  
Genus Level ◽  
The Family ◽  
Character Assessment

The first comprehensive phylogenetic analysis of the family Rhacophoridae was conducted by Liem (1970) scoring 81 species for 36 morphological characters. Channing (1989), in a reanalysis of Liem’s study, produced a phylogenetic hypothesis different from that of Liem. We compared the two studies and produced a third phylogenetic hypothesis based on the same characters. We also present the synapomorphic characters from Liem that define the major clades and each genus within the family. Finally, we summarize intergeneric relationships within the family as hypothesized by other studies, and the family’s current status as it relates to other ranoid families.

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