scholarly journals Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Luis Javier Galindo ◽  
Purificación López-García ◽  
Guifré Torruella ◽  
Sergey Karpov ◽  
David Moreira
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Repertoire ◽  
Parasitic Fungi ◽  
Hyphal Morphogenesis ◽  
Specific Proteins ◽  
Phylogenomic Analyses ◽  
Protein Datasets

AbstractCompared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living flagellated stages (zoospores) remain poorly known and their phylogenetic position is often unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and Sanchytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchytrids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages.

scholarly journals Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

2020 ◽  
Author(s):  
Luis Javier Galindo ◽  
Purificación López-García ◽  
Guifré Torruella ◽  
Sergey Karpov ◽  
David Moreira
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Repertoire ◽  
Protein Markers ◽  
Parasitic Fungi ◽  
Molecular Phylogenetic ◽  
Phylogenomic Analyses

AbstractCompared to well-known multicellular fungi and unicellular yeast, unicellular fungi with zoosporic, free-living flagellated stages remain poorly known and their phylogenetic position is often unresolved. Recently, 18S+28S rRNA gene molecular phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and record-long simplified kinetosomes, Amoeboradix gromovi and Sanchytrium tribonematis, showed that they formed a monophyletic group without affinity with any known fungal clade. To assess their phylogenetic position and unique trait evolution, we sequenced single-cell genomes for both species. Phylogenomic analyses using 264 protein markers and a comprehensive taxon sampling retrieved and almost fully-resolved fungal tree with these species forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Chytridiomycota branched as sister to all other fungi, and the zoosporic fungus Olpidium bornovanus as sister to non-flagellated fungi. Comparative genomic analyses across Holomycota revealed an atypically reduced metabolic repertoire for sanchytrids given their placement in the tree. We infer four independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. The highly reduced sanchytrid flagellar machinery, notably their long kinetosome, might have been retained to support a putative light-sensing lipid organelle. Together with their phylogenetic position, these unique traits justify the erection of the novel phylum Sanchytriomycota. Our results also show that most of the hyphal morphogenesis gene repertoire of multicellular Fungi had already evolved in early holomycotan lineages.

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.

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 Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3203-3215 ◽  
Author(s):  
Chantal Campbell ◽  
Mobolaji Adeolu ◽  
Radhey S. Gupta
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Core Protein ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Conserved Signature Indels ◽  
The Family ◽  
Genomic Analyses

The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.

Morphological reports on two species of Dexiotricha (Ciliophora, Scuticociliatia), with a note on the phylogenetic position of the genus

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 680-688 ◽  
Author(s):  
Xinpeng Fan ◽  
Saleh A. Al-Farraj ◽  
Feng Gao ◽  
Fukang Gu
Keyword(s):  
Phylogenetic Analyses ◽  
Eastern China ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Contractile Vacuole ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
North West ◽  
Rdna Sequences

Two Dexiotricha species (Dexiotricha elliptica nov. comb. and Dexiotricha cf. granulosa), respectively isolated from soil north-west of Riyadh, Saudi Arabia, and freshwater in Shanghai, eastern China, were investigated using standard methods. The species Loxocephalus ellipticus Kahl, 1931 is reclassified here in the genus Dexiotricha and was characterized mainly by constantly showing 16 somatic kineties, three post-oral kineties with the middle one shortened, a contractile vacuole located subcaudally with an excretory pore near the posterior end of somatic kinety 2 and single caudal cilia. A Dexiotricha granulosa-like organism having a subcaudally located contractile vacuole and fewer somatic kineties was designated D. cf. granulosa. The small-subunit rRNA gene (SSU rDNA) sequences of these two species were characterized and their phylogenetic positions based on SSU rDNA sequences were revealed by means of Bayesian inference and maximum-likelihood analysis. Phylogenetic analyses confirmed Dexiotricha as a monophyletic genus and supported its assignment to the order Loxocephalida. However, its family assignment remains unsupported.

scholarly journals ‘Candidatus Midichloria mitochondrii’, an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle

2006 ◽  
Vol 56 (11) ◽  
pp. 2535-2540 ◽  
Author(s):  
Davide Sassera ◽  
Tiziana Beninati ◽  
Claudio Bandi ◽  
Edwin A. P. Bouman ◽  
Luciano Sacchi ◽  
...  
Keyword(s):  
Ixodes Ricinus ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Hard Tick ◽  
Intermembrane Space ◽  
16S Rrna Gene Sequences ◽  
Ovarian Cells ◽  
Midichloria Mitochondrii

An intracellular bacterium with the unique ability to enter mitochondria exists in the European vector of Lyme disease, the hard tick Ixodes ricinus. Previous phylogenetic analyses based on 16S rRNA gene sequences suggested that the bacterium formed a divergent lineage within the Rickettsiales (Alphaproteobacteria). Here, we present additional phylogenetic evidence, based on the gyrB gene sequence, that confirms the phylogenetic position of the bacterium. Based on these data, as well as electron microscopy (EM), in situ hybridization and other observations, we propose the name ‘Candidatus Midichloria mitochondrii’ for this bacterium. The symbiont appears to be ubiquitous in females of I. ricinus across the tick's distribution, while lower prevalence is observed in males (44 %). Based on EM and in situ hybridization studies, the presence of ‘Candidatus M. mitochondrii’ in females appears to be restricted to ovarian cells. The bacterium was found to be localized both in the cytoplasm and in the intermembrane space of the mitochondria of ovarian cells. ‘Candidatus M. mitochondrii’ is the first bacterium to be identified that resides within animal mitochondria.

Multilocus sequence analysis and 16S rRNA gene sequencing reveal that Yersinia frederiksenii genospecies 2 is Yersinia massiliensis

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3124-3129 ◽  
Author(s):  
Roberto A. Souza ◽  
Priscilla F. M. Imori ◽  
Juliana P. Falcão
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequencing ◽  
The Other ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Since Yersinia frederiksenii was first described in 1980, it has been recognized genotypically as a heterogeneous species, comprising three phenotypically indistinguishable genospecies. In this study, the sequence of the 16S rRNA gene and the concatenated sequences of six housekeeping genes (glnA, gyrB, hsp60, recA, rpoB and sodA) of all the currently known species of the genus Yersinia were used to determine the phylogenetic position of Y. frederiksenii genospecies 2 in the genus Yersinia . The phylogenetic analyses grouped the Y. frederiksenii genospecies 2 strains in a monophyletic group together with representative strains of Yersinia massiliensis . Moreover, the Y. frederiksenii genospecies 2 strains were also grouped apart from the other species of the genus Yersinia and far from the other two genospecies of Y. frederiksenii . All of the observations made in this study support the conclusion that Y. frederiksenii genospecies 2 should be reclassified as Y. massiliensis .

scholarly journals Phylogenomic revision of the family Streptosporangiaceae, reclassification of Desertactinospora gelatinilytica as Spongiactinospora gelatinilytica comb. nov. and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae

2020 ◽  
Vol 70 (4) ◽  
pp. 2569-2579 ◽  
Author(s):  
Hilal Ay ◽  
Hayrettin Saygin ◽  
Nevzat Sahin
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Genome Data ◽  
The Family ◽  
Taxonomic Affiliation ◽  
Phylogenomic Analyses ◽  
Genome Comparisons

In recent years, the results of genome-based phylogenetic analyses have contributed to microbial systematics by increasing the availability of sequenced microbial genomes. Therefore, phylogenomic analysis within large taxa in the phylum Actinobacteria has appeared as a useful tool to clarify the taxonomic positions of ambiguous groups. In this study, we provide a revision of the actinobacterial family Streptosporangiaceae using a large collection of genome data and phylogenomics approaches. The phylogenomic analyses included the publicly available genome data of the members of the family Streptosporangiaceae and the state-of-the-art tools are used to infer the taxonomic affiliation of these species within the family. By comparing genome-based and 16S rRNA gene-based trees, as well as pairwise genome comparisons, the recently described genera Spongiactinospora and Desertactinospora are combined in the genus Spongiactinospora . In conclusion, a comprehensive phylogenomic revision of the family Streptosporangiaceae is proposed.

Nodularia (Cyanobacteria, Nostocaceae): a phylogenetically uniform genus with variable phenotypes

Phytotaxa ◽  
2014 ◽  
Vol 172 (3) ◽  
pp. 235 ◽  
Author(s):  
Klára Řeháková ◽  
Jan Mareš ◽  
Alena Lukešová ◽  
Eliška Zapomělová ◽  
Kateřina Bernardová ◽  
...  
Keyword(s):  
Phenotypic Variability ◽  
Phylogenetic Analyses ◽  
Morphological Variability ◽  
Taxonomic Resolution ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Traditional System ◽  
Ecological Features ◽  
Close Relationship ◽  
Relationship Of

The taxonomy of cyanobacteria currently faces the challenge of overhauling the traditional system to better reflect the results of phylogenetic analyses. In the present study, we assessed the phylogenetic position, morphological variability, ability to produce the toxin nodularin, and source habitat of 17 benthic and soil isolates of Nodularia. A combined analysis of two loci (partial 16S rRNA gene and rbcLX region) confirmed the genus as a monophyletic unit and the close relationship of its members. However, the taxonomic resolution at the subgeneric level was extremely problematic. The phylogenetic clustering did not show any reasonable congruence with either morphological or ecological features commonly used to separate taxa in heterocytous cyanobacteria. Despite the near phylogenetic similarity of planktonic, benthic and soil Nodularia strains, we did not find any new nodularin-producing strains among the non-planktonic isolates. The relatively low variability in conserved molecular markers within the genus Nodularia exemplifies the limitations of the currently accepted taxonomic workflow and polyphasic approach. Elucidation of mechanisms that drive the phenotypic variability in such groups presents a major challenge in cyanobacterial research.

An opisthorchiid concept of the genus Liliatrema (Trematoda: Plagiorchiida: Opisthorchioidea): an unexpected systematic position

2020 ◽  
Author(s):  
Sergey Sokolov ◽  
Evgeniy Frolov ◽  
Semen Novokreshchennykh ◽  
Dmitry Atopkin
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Systematic Position ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
28S Rrna ◽  
The Family ◽  
Using Data ◽  
Terminal Genitalia ◽  
Rdna Analysis

Abstract Liliatrema is a small genus of trematodes consisting of two species. Its systematic position has long been debated, partly because of the confusing reports about the structure of male terminal genitalia. Here we test the phylogenetic position of the genus Liliatrema using data on complete 18S rRNA and partial 28S rRNA gene sequences obtained for Liliatrema skrjabini. We also provide a detailed description of terminal genitalia in adult specimens of L. sobolevi and metacercariae of both Liliatrema species. The results of the 28S rDNA-based phylogenetic analysis indicate that Liliatrema falls within a well-supported clade, which also includes Apophallus and traditional opisthorchiids. This clade, in turn, is nested within a well-supported clade, containing Euryhelmis, Cryptocotyle and Scaphanocephalus. In the 18S+8S rDNA analysis, Liliatrema appears as a sister-taxon to the Cryptocotyle + Euryhelmis group. The Liliatrema + (Cryptocotyle + Euryhelmis) clade is a well-supported sister-group to the traditional opisthorchiids. The morphology of the terminal genitalia of the liliatrematids also corresponds to that of the opisthorchioids. Thus, the results of our morphological and phylogenetic analyses favour an unexpected conclusion that the genus Liliatrema belongs to the Opisthorchioidea. We propose that the genera Liliatrema, Apophallus, Euryhelmis, Cryptocotyle and Scaphanocephalus belong, respectively, within the subfamilies Liliatrematinae, Apophallinae, Euryhelminthinae and Cryptocotylinae of the family Opisthorchiidae.

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