Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

2014 ◽  
Vol 78 ◽  
pp. 36-42 ◽  
Author(s):  
E. Gentekaki ◽  
M. Kolisko ◽  
V. Boscaro ◽  
K.J. Bright ◽  
F. Dini ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Position ◽  
Phylogenomic Analysis ◽  
Phylogenetic Affinities

scholarly journals The phytopathogenic nature ofDickeya aquatica174/2 and the dynamic early evolution ofDickeyapathogenicity

2019 ◽  
Author(s):  
Alexandre Duprey ◽  
Najwa Taib ◽  
Simon Leonard ◽  
Tiffany Garin ◽  
Jean-Pierre Flandrois ◽  
...  
Keyword(s):  
Complete Genome ◽  
Type Strain ◽  
Large Scale ◽  
Plant Cell Wall ◽  
Soft Rot ◽  
Phylogenetic Position ◽  
Ecological Niches ◽  
Phylogenomic Analysis ◽  
Cell Wall Degrading Enzymes ◽  
Patterns And Processes

AbstractOriginality-Significance statementAlthough the reach of large-scale comparative studies has spread exponentially over the years, the phytopathogenicDickeyagroup remains overlooked. In this work, we sequence the complete genome ofDickeya aquaticatype strain, a species isolated from water that was first assumed to be non-phytopathogenic. We show that the proteome ofD. aquaticacontains a wide number of proteins involved inDickeyavirulence, including plant cell wall degrading enzymes, suggesting that this species could be in fact pathogenic. Using experimental approaches, we confirm this prediction and uncover the particular affinity ofD. aquaticafor acidic fruits. In-depth phylogenomic analyses reveal thatDickeyaspecies display a great degree of genetic plasticity in the pathogenicity determinants, explaining how this bacterial group was able to colonize a wide variety of plants growing in different climates. These observations greatly advance our understanding of how bacteria adapt to new ecological niches.SummaryDickeyais a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus,Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, whileD. aquaticawas proposed to represent a deep-branching species amongDickeyagenus, its precise phylogenetic position remained elusive.Here, we report the complete genome sequence of theD. aquaticatype strain 174/2. We demonstrate the affinity ofD. aquaticaTfor acidic fruits such as tomato and cucumber, and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all availableDickeyaproteomes pinpointsD. aquaticaas the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.):Dickeyags. poaceaephila (Dickeyasp NCPPB 569) andDickeyags. undicola (Dickeyasp 2B12), together with a new putative genus, tentatively namedProdigiosinella. Finally, from comparative analyses ofDickeyaproteomes we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes ofDickeyato different environmental niches and hosts. In particular, we hypothetize that the lack of xylanases and xylose degradation pathways inD. aquaticacould reflects adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

scholarly journals Genome and Metagenome of The Phytophagous Gall-Inducing Mite Fragariocoptes Setiger (Eriophyoidea): Are Symbiotic Bacteria Responsible For Gall-Formation?

2021 ◽  
Author(s):  
Pavel B. Klimov ◽  
Philipp E. Chetverikov ◽  
Irina E. Dodueva ◽  
Andrey E. Vishnyakov ◽  
Samuel J. Bolton ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Phylogenetic Position ◽  
Phylogenomic Analysis ◽  
Agricultural Pests ◽  
Gall Formation ◽  
Deep Soil ◽  
Comparative Metagenomics ◽  
Pathogenic Virus ◽  
Eriophyoid Mites ◽  
Phylogenetic Affinities

Abstract Eriophyoid mites represent a hyperdiverse, phytophagous lineage with an unclear phylogenetic position. These mites have succeeded in colonizing nearly every seed plant species, and this evolutionary success was in part due to the mites' ability to induce galls in plants. A gall is a unique niche that provides the inducer of this modification with vital resources. The exact mechanism of gall formation is still not understood, even as to whether it is endogenic (mites directly cause galls) or exogenic (symbiotic microorganisms are involved). Here we (i) investigate the phylogenetic affinities of eriophyoids and (ii) use comparative metagenomics to test the hypothesis that the endosymbionts of eriophyoid mites are involved in gall-formation. Our phylogenomic analysis robustly inferred eriophyoids as closely related to Nematalycidae, a group of deep-soil mites belonging to Endeostigmata. Our comparative metagenomics, fluorescence in situ hybridization, and electron microscopy experiments identified two candidate endosymbiotic bacteria shared across samples, however, it is unlikely that they are gall-inducers (morphotype1: novel Wolbachia, morphotype2: possibly Agrobacterium tumefaciens). We also detected an array of plant pathogens associated with galls that may be vectored by the mites; a mite pathogenic virus (Betabaculovirus) has the potential to be used in the biocontrol of agricultural pests.

scholarly journals OnProphocaandLeptophoca(Pinnipedia, Phocidae) from the Miocene of the North Atlantic realm: redescription, phylogenetic affinities and paleobiogeographic implications

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3024 ◽  
Author(s):  
Leonard Dewaele ◽  
Olivier Lambert ◽  
Stephen Louwye
Keyword(s):  
North America ◽  
Middle Miocene ◽  
New Combination ◽  
Phylogenetic Position ◽  
Appendicular Skeleton ◽  
Original Diagnosis ◽  
Sediment Samples ◽  
The North ◽  
The North Sea ◽  
Phylogenetic Affinities

BackgroundProphocaandLeptophocarepresent the oldest known genera of phocine seals, dating from the latest early to middle Miocene. Originally,Prophoca rousseauiandProphoca proximawere described based on fragmentary remains from the Miocene of Belgium. However, several researchers contested the union ofProphoca rousseauiandProphoca proximainto one genus, without providing evidence. The stratigraphic context ofProphocaremained poorly constrained due to the lack of precise data associated with the original specimens collected in the area of Antwerp (north of Belgium).MethodsProphocaandLeptophocaare redescribed and their phylogenetic position among Phocidae is reassessed using PAUP. Dinoflagellate biostratigraphy has been carried out on sediment samples associated with specimens fromProphocaandLeptophocato elucidate their approximate ages.ResultsWhereas the speciesProphoca rousseauiis redescribed,Prophoca proximais considered synonymous toLeptophoca lenis, with the proposal of a new combinationLeptophoca proxima(Van Beneden, 1877). Sediment samples from specimens of both taxa have been dated to the late Langhian–early Serravallian (middle Miocene). Following a reinvestigation ofLeptophoca amphiatlantica, characters from the original diagnosis are questioned and the specimens ofLeptophoca amphiatlanticaare consideredLeptophocacf.L. proxima. In a phylogenetic analysis,Prophoca rousseauiandLeptophoca proximaconstitute early branching stem-phocines.DiscussionLeptophoca proximafrom the North Sea Basin is younger than the oldest known find ofLeptophoca proximafrom North America, which does not contradict the hypothesis that Phocinae originated along the east coast of North America during the late early Miocene, followed by dispersal to Europe shortly after. Morphological features of the appendicular skeleton indicate thatProphoca rousseauiandLeptophoca proximahave archaic locomotory modes, retaining a more prominent use of the fore flipper for aquatic propulsion than extant Phocidae.

scholarly journals Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position

2019 ◽  
Vol 7 (11) ◽  
pp. 487
Author(s):  
Samrat Ghosh ◽  
Aditya Narayan Sarangi ◽  
Mayuri Mukherjee ◽  
Swati Bhowmick ◽  
Sucheta Tripathy
Keyword(s):  
Lactobacillus Casei ◽  
Large Scale ◽  
In Silico Analysis ◽  
Gene Families ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Lactobacillus Paracasei ◽  
Phylogenomic Analysis ◽  
Pan Genome ◽  
Important Pathway

Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism.

scholarly journals New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

2019 ◽  
Vol 36 (4) ◽  
pp. 757-765 ◽  
Author(s):  
Jürgen F H Strassert ◽  
Mahwash Jamy ◽  
Alexander P Mylnikov ◽  
Denis V Tikhonenkov ◽  
Fabien Burki
Keyword(s):  
Phylogenetic Signal ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Aquatic Environments ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Transcriptome Data ◽  
Phylogenetic Reconstructions ◽  
Phylogenomic Analyses ◽  
Alignment Length

AbstractThe resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these “orphan” groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

scholarly journals Solution to the phylogenetic enigma of Tetraplatia , a worm-shaped cnidarian

2005 ◽  
Vol 2 (1) ◽  
pp. 120-124 ◽  
Author(s):  
Allen G Collins ◽  
Bastian Bentlage ◽  
George I Matsumoto ◽  
Steven H.D Haddock ◽  
Karen J Osborn ◽  
...  
Keyword(s):  
Body Plan ◽  
Phylogenetic Position ◽  
Recent Origin ◽  
Phylogenetic Affinities

Tetraplatia is a genus containing two species of pelagic cnidarians of curious morphology. Their vermiform shape and four swimming flaps are difficult to relate to the features of other cnidarians, thus obscuring their phylogenetic affinities. Since their discovery in the mid-1800s, a number of prominent cnidarian workers have weighed in on this conundrum, some arguing that they are aberrant hydrozoans and others concluding that they are unusual scyphozoans. Current taxonomic practice conforms to the latter view. However, data presented here from the large and small subunits of the nuclear ribosome leave little doubt that Tetraplatia is in fact a hydrozoan genus. Indeed, its precise phylogenetic position is within Narcomedusae, as some authors had previously deduced based on structural characters. The distinctive body plan of Tetraplatia is remarkable because it appears to have a recent origin, in contrast to the prevailing pattern of metazoan history.

scholarly journals Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

2017 ◽  
Author(s):  
Matthew Parks ◽  
Teofil Nakov ◽  
Elizabeth Ruck ◽  
Norman J. Wickett ◽  
Andrew J. Alverson
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Genome Duplication ◽  
Gene Tree ◽  
Genomic Diversity ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Gene Trees ◽  
Angiosperm Evolution ◽  
Polyploid Formation

ABSTRACTPremise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.MethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.Key resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.ConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.

scholarly journals Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples

2020 ◽  
Author(s):  
Caoimhe E. O’Brien ◽  
João Oliveira-Pacheco ◽  
Eoin Ó Cinnéide ◽  
Max A. B. Hasse ◽  
Chris Todd Hittinger ◽  
...  
Keyword(s):  
Candida Tropicalis ◽  
Large Scale ◽  
Population Genomics ◽  
Phenotypic Diversity ◽  
Nitrogen Sources ◽  
Asia Pacific ◽  
Phylogenomic Analysis ◽  
Pathogenic Yeast ◽  
A Genome ◽  
Genome Level

AbstractCandida tropicalis is a human pathogen that primarily infects the immunocompromised. Whereas the genome of one isolate, C. tropicalis MYA-3404, was originally sequenced in 2009, there have been no large-scale, multi-isolate studies of the genetic and phenotypic diversity of this species. Here, we used whole genome sequencing and phenotyping to characterize 77 isolates C. tropicalis isolates from clinical and environmental sources from a variety of locations. We show that most C. tropicalis isolates are diploids with approximately 2 - 6 heterozygous variants per kilobase. The genomes are relatively stable, with few aneuploidies. However, we identified one highly homozygous isolate and six isolates of C. tropicalis with much higher heterozygosity levels ranging from 36 - 49 heterozygous variants per kilobase. Our analyses show that the heterozygous isolates represent two different hybrid lineages, where the hybrids share one parent (A) with most other C. tropicalis isolates, but the second parent (B or C) differs by at least 4% at the genome level. Four of the sequenced isolates descend from an AB hybridization, and two from an AC hybridization. The hybrids are MTLa/α heterozygotes. Hybridization, or mating, between different parents is therefore common in the evolutionary history of C. tropicalis. The new hybrids were predominantly found in environmental niches, including from soil. Hybridization is therefore unlikely to be associated with virulence. In addition, we used genotype-phenotype correlation and CRISPR-Cas9 editing to identify a genome variant that results in the inability of one isolate to utilize certain branched-chain amino acids as a sole nitrogen source.Author summaryCandida tropicalis is an important fungal pathogen, which is particularly common in the Asia-Pacific and Latin America. There is currently very little known about the diversity of genotype and phenotype of C. tropicalis isolates. By carrying out a phylogenomic analysis of 77 isolates, we find that C. tropicalis genomes range from very homozygous to highly heterozygous. We show that the heterozygous isolates are hybrids, most likely formed by mating between different parents. Unlike other Candida species, the hybrids are more common in environmental than in clinical niches, suggesting that for this species, hybridization is not associated with virulence. We also explore the range of phenotypes, and we identify a genomic variant that is required for growth on valine and isoleucine as sole nitrogen sources.

scholarly journals Total-Evidence Framework Reveals Complex Morphological Evolution in Nightbirds (Strisores)

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 143 ◽  
Author(s):  
Albert Chen ◽  
Noor D. White ◽  
Roger B.J. Benson ◽  
Michael J. Braun ◽  
Daniel J. Field
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Anatomical Data ◽  
Evidence Framework

Strisores is a clade of neoavian birds that include diurnal aerial specialists such as swifts and hummingbirds, as well as several predominantly nocturnal lineages such as nightjars and potoos. Despite the use of genome-scale molecular datasets, the phylogenetic interrelationships among major strisorean groups remain controversial. Given the availability of next-generation sequence data for Strisores and the clade’s rich fossil record, we reassessed the phylogeny of Strisores by incorporating a large-scale sequence dataset with anatomical data from living and fossil strisoreans within a Bayesian total-evidence framework. Combined analyses of molecular and morphological data resulted in a phylogenetic topology for Strisores that is congruent with the findings of two recent molecular phylogenomic studies, supporting nightjars (Caprimulgidae) as the extant sister group of the remainder of Strisores. This total-evidence framework allowed us to identify morphological synapomorphies for strisorean clades previously recovered using molecular-only datasets. However, a combined analysis of molecular and morphological data highlighted strong signal conflict between sequence and anatomical data in Strisores. Furthermore, simultaneous analysis of molecular and morphological data recovered differing placements for some fossil taxa compared with analyses of morphological data under a molecular scaffold, highlighting the importance of analytical decisions when conducting morphological phylogenetic analyses of taxa with molecular phylogenetic data. We suggest that multiple strisorean lineages have experienced convergent evolution across the skeleton, obfuscating the phylogenetic position of certain fossils, and that many distinctive specializations of strisorean subclades were acquired early in their evolutionary history. Despite this apparent complexity in the evolutionary history of Strisores, our results provide fossil support for aerial foraging as the ancestral ecological strategy of Strisores, as implied by recent phylogenetic topologies derived from molecular data.

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