scholarly journals Prokaryotic and Eukaryotic Horizontal Transfer of Sailor (DD82E), a New Superfamily of IS630-Tc1-Mariner DNA Transposons

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1005
Author(s):  
Shasha Shi ◽  
Mikhail Puzakov ◽  
Zhongxia Guan ◽  
Kuilin Xiang ◽  
Mohamed Diaby ◽  
...  

Here, a new superfamily of IS630-Tc1-mariner (ITm) DNA transposons, termed Sailor, is identified, that is characterized by a DD82E catalytic domain and is distinct from all previously known superfamilies of the ITm group. Phylogenetic analyses revealed that Sailor forms a monophyletic clade with a more intimate link to the clades of Tc1/mariner and DD34E/Gambol. Sailor was detected in both prokaryotes and eukaryotes and invaded a total of 256 species across six kingdoms. Sailor is present in nine species of bacteria, two species of plantae, four species of protozoa, 23 species of Chromista, 12 species of Fungi and 206 species of animals. Moreover, Sailor is extensively distributed in invertebrates (a total of 206 species from six phyla) but is absent in vertebrates. Sailor transposons are 1.38–6.98 kb in total length and encoded transposases of ~676 aa flanked by TIRs with lengths between 18, 1362 and 4 bp (TATA) target-site duplications. Furthermore, our analysis provided strong evidence of Sailor transmissions from prokaryotes to eukaryotes and internal transmissions in both. These data update the classification of the ITm group and will contribute to the understanding of the evolution of ITm transposons and that of their hosts.

Author(s):  
Timothy L Collins ◽  
Jeremy J Bruhl ◽  
Alexander N Schmidt-Lebuhn ◽  
Ian R H Telford ◽  
Rose L Andrew

Abstract Golden everlasting paper daisies (Xerochrysum, Gnaphalieae, Asteraceae) were some of the earliest Australian native plants to be cultivated in Europe. Reputedly a favourite of Napoléon Bonaparte and Empress Joséphine, X. bracteatum is thought to have been introduced to the island of St Helena in the South Atlantic during Napoléon’s exile there. Colourful cultivars were developed in the 1850s, and there is a widely held view that these were produced by crossing Xerochrysum with African or Asian Helichrysum spp. Recent molecular phylogenetic analyses and subtribal classification of Gnaphalieae cast doubt on this idea. Using single-nucleotide polymorphism (SNP) data, we looked for evidence of gene flow between modern cultivars, naturalized paper daisies from St Helena and four Xerochrysum spp. recorded in Europe in the 1800s. There was strong support for gene flow between cultivars and X. macranthum. Paper daisies from St Helena were genotypically congruent with X. bracteatum and showed no indications of ancestry from other species or from the cultivars, consistent with the continuous occurrence of naturalized paper daisies introduced by Joséphine and Napoléon. We also present new evidence for the origin of colourful Xerochrysum cultivars and hybridization of congeners in Europe from Australian collections.


Genome ◽  
2010 ◽  
Vol 53 (3) ◽  
pp. 180-202 ◽  
Author(s):  
Bernard R. Baum ◽  
Tara Edwards ◽  
Douglas A. Johnson

To complete our study of the genus Hordeum and to elaborate a phylogeny of species based upon 5S rDNA sequences, we have cloned and sequenced PCR amplicons from seven American polyploid species to generate 164 new 5S rRNA gene sequences. These sequences were analysed along with the more than 2000 5S rDNA sequences previously generated from the majority of species in Hordeum to provide a comprehensive picture of the distribution (presence or absence) of 5S rDNA unit classes (orthologous groups) in this genus as well as insights into the phylogeny of Hordeum. Testing of substitution models for each unit class based upon the consensus sequences of all the taxa as well as for each unit class within the genus found that the general best fit was TPM3uf+G, from which a maximum-likelihood tree was calculated. A novel application of cophylogenetic analysis, where relationships among unit classes were treated as host–parasite interactions, depicted some significant pair links under tests of randomness indicative of nonrandom codivergence among several unit classes within the same taxon. The previous classification of four genomic groups is reflected in combinations of unit classes, and it is proposed that current taxa developed from ancient diploidized paleopolyploids and that some were subjected to gene loss, i.e., unit class loss. Finally, separate phylogenetic analyses performed for the tetraploid and hexaploid species were used to derive a working model describing the phylogeny of the polyploid taxa from their putative diploid ancestry.


Author(s):  
M. Belaganahalli ◽  
S. Maan ◽  
P. P.C. Mertens

Viruses that are normally safely contained within their host spe­cies can emerge due to intense livestock farming, trade, travel, climate change and encroachment of human activities into new environments. The unexpected emergence of bluetongue virus (BTV), the prototype species of the genus Orbivirus, in economi­cally important livestock species (sheep and cattle) across the whole of Europe (since 1998), indicates that other orbiviruses represent a potential further threat to animal and human popula­tions in Europe and elsewhere. The genus Orbivirus is the largest within the family Reoviridae, containing 22 virus species, as well as 14 unclassified orbiviruses, some of which may repre­sent additional or novel species. The orbiviruses are transmitted primarily by arthropod vectors (e.g. Culicoides, mosquitoes or ticks).  Viral genome sequence data provide a basis for virus taxonomy and diagnostic test development, and make it possible to address fundamental questions concerning virus biology, pathogenesis, virulence and evolution, that can be further explored in mutation and reverse genetics studies. Genome sequences also provide criteria for the classification of novel isolates within individual Orbivirus species, as well as the identification of different sero­types, topotypes, reassortants and even closely related but dis­tinct virus lineages.  Full-length genome characterization of Tilligerry virus (TILV), a member of the Eubenangee virus species, and Mitchell River virus (MRV), a member of the Warrego virus species, have revealed highly conserved 5’ and 3’ terminal hexanucleotide sequences. Phylogenetic analyses of orbivirus T2 ‘sub-core-shell’ protein sequences reinforce the hypothesis that this protein is an important evolutionary marker for these viruses. The T2 protein shows high levels of amino acid (AA) sequence identity (> 91%) within a single Orbivirus species / serogroup, which can be used for species identification. The T2-protein gene has therefore been given priority in sequencing studies. The T2 protein of TILV is closely related to that of Eubenangee virus (~91% identity), con­firming that they are both members of the same Eubenangee virus species. Although TILV is reported to be related to BTV in serological assays, the TILV T2 protein shows only 68-70% AA identity to BTV. This supports its current classification within a different serogroup (Eubenangee).  Warrego virus and MRV are currently classified as two distinct members (different serotypes) within the Warrego virus species. However, they show only about 79% AA identity in their T2 pro­tein (based on partial sequences). It is therefore considered likely that they could be reclassified as members of distinct Orbivirus species. The taxonomic classification of MRV will be reviewed after generating full length sequences for the entire genomes of both viruses. The taxonomic status of each of these viruses will also be tested further by co-infections and attempts to create reassortants between them (only viruses belonging to the same species can reassort their genome segments). TILV and MRV are the first viruses from their respective serogroups / virus species to be genetically fully characterized, and will provide a basis for the further characterization / identification of additional viruses within each group / species. These data will assist in the devel­opment of specific diagnostic assays and potentially in control of emerging diseases. The sequences generated will also help to evaluate current diagnostic [reverse transcriptase - polymerase chain reaction (RT-PCR)] tests for BTV, African horse sickness virus, epizootic haemorrhagic disease virus, etc., in silico, by identifying any possibility of cross reactivity.


2021 ◽  
Vol 9 (08) ◽  
pp. 505-514
Author(s):  
Nguyen Chi Mai ◽  
◽  
NinhThi Ngoc ◽  
Nguyen Xuan Cuong ◽  
Nguyen Hoai Nam ◽  
...  

Vietnam contains diverse marine ecosystems with the high biodiversity of marine organisms, including gorgonian corals of Alcyonacea order. In order to support traditional classification of these corals, in this study mitochondrial barcoding markers msh1 and nuclear 28S rDNA were developed for analysis of 11 specimens collected in 2015 and 2016 from different islands and bays along the North Central coast of Vietnam. Phylogenetic analyses based on msh1 and 28S sequence polymorphism showed that all specimens belonged to Anthozoa class, Octocorallia sub-class and Alcyonacea order. At lower taxa levels, they were divided into 4 sub-orders, 7 families and 7 genera according to 7 distinct clades with bootstrap values from 99-100%.The identifications of 7 out of 11 specimens including Sinularia brassica (2 specimens)and Sinularialeptoclados, Dichotellagemmacea, Annella reticulata, S. conferta and S. nanolobata were in concordance between morphological and molecular methods. The other 4 specimens were only identified at genus levels of Astrogorgia sp., Melithaea sp. Scleronephthya sp. and Muricella sp. by either msh1-morphology or msh1-28S markers. These results highlight the importance of molecular markers to elucidate patterns of biodiversity and species identification of soft coral.


MycoKeys ◽  
2020 ◽  
Vol 74 ◽  
pp. 17-74
Author(s):  
Martina Réblová ◽  
Jana Nekvindová ◽  
Jacques Fournier ◽  
Andrew N. Miller

The Chaetosphaeriaceae are a diverse group of pigmented, predominantly phialidic hyphomycetes comprised of several holomorphic genera including Chaetosphaeria, the most prominent genus of the family. Although the morphology of the teleomorphs of the majority of Chaetosphaeria is rather uniform, their associated anamorphs primarily exhibit the variability and evolutionary change observed in the genus. An exception from the morphological monotony among Chaetosphaeria species is a group characterised by scolecosporous, hyaline to light pink, multiseptate, asymmetrical ascospores and a unique three-layered ascomatal wall. Paragaeumannomyces sphaerocellularis, the type species of the genus, exhibits these morphological traits and is compared with similar Chaetosphaeria with craspedodidymum- and chloridium-like synanamorphs. Morphological comparison and phylogenetic analyses of the combined ITS-28S sequences of 35 isolates and vouchers with these characteristics revealed a strongly-supported, morphologically well-delimited clade in the Chaetosphaeriaceae containing 16 species. The generic name Paragaeumannomyces is applied to this monophyletic clade; eight new combinations and five new species, i.e. P. abietinussp. nov., P. eleganssp. nov., P. granulatussp. nov., P. sabinianussp. nov. and P. smokiensissp. nov., are proposed. A key to Paragaeumannomyces is provided. Using morphology, cultivation studies and phylogenetic analyses of ITS and 28S rDNA, two additional new species from freshwater and terrestrial habitats, Codinaea paniculatasp. nov. and Striatosphaeria castaneasp. nov., are described in the family. A codinaea-like anamorph of S. castanea forms conidia with setulae at each end in axenic culture; this feature expands the known morphology of Striatosphaeria. A chaetosphaeria-like teleomorph is experimentally linked to Dendrophoma cytisporoides, a sporodochial hyphomycete and type species of Dendrophoma, for the first time.


Phytotaxa ◽  
2019 ◽  
Vol 427 (3) ◽  
pp. 186-199
Author(s):  
ARCHANA SINGH ◽  
NIKHIL KUMAR SINGH ◽  
PARAS NATH SINGH ◽  
RAGHVENDRA SINGH ◽  
NAWAL KISHORE DUBEY

Ochroconis helicteris, a novel species of the oligotrophic genus Ochroconis (Sympoventuriaceae, Venturiales), has been described and illustrated. Morphologically, this species has characters similar to allied species in the genus Ochroconis, but differs in conidial dimensions and shape. Phylogenetic analyses using nuclear ribosomal DNA gene ITS and protein coding gene BT2 revealed it clustering as monophyletic clade which was separated from known Ochroconis species. New species was isolated from leaf surface of medicinal plant Helicteris isora L.


Phytotaxa ◽  
2019 ◽  
Vol 416 (1) ◽  
pp. 79-87 ◽  
Author(s):  
YAO FENG ◽  
SHENG-NAN ZHANG ◽  
ZUO-YI LIU

An Ascomycetous species was found from decaying woody stems in Guizhou, China. Morphologically, the fungus can be assigned well in Tremateia in having immersed ascomata, cellular pseudoparaphyses and muriform ascospores, but it differs from other species in having the 3–7 transverse septa ascospores surrounded by a gelatinous sheath. Phylogenetic analyses based on a concatenated dataset of ITS, LSU, SSUand TEF1-α sequence data indicated that the fungus belongs to the genus Tremateia, Didymosphaeriaceae, four taxa formed a monophyletic clade and represent the genus Tremateia with well supported. The new collection formed a distinct lineage and can be recognized as a new species. Therefore, a new species Tremateia murispora is introduced with detailed description and illustration, the notes on its morphologically and phylogenetically related taxa is provided.


Phytotaxa ◽  
2017 ◽  
Vol 319 (1) ◽  
pp. 84 ◽  
Author(s):  
XUDONG LIU ◽  
HUAN ZHU ◽  
BENWEN LIU ◽  
GUOXIANG LIU ◽  
ZHENGYU HU

The genus Nephrocytium Nägeli is a common member of phytoplankton communities that has a distinctive morphology. Its taxonomic position is traditionally considered to be within the family Oocystaceae (Trebouxiophyceae). However, research on its ultrastructure is rare, and the phylogenetic position has not yet been determined. In this study, two strains of Nephrocytium, N. agardhianum Nägeli and N. limneticum (G.M.Smith) G.M.Smith, were identified and successfully cultured in the laboratory. Morphological inspection by light and electron microscopy and molecular phylogenetic analyses were performed to explore the taxonomic position. Ultrastructure implied a likely irregular network of dense and fine ribs on the surface of the daughter cell wall that resembled that of the genus Chromochloris Kol & Chodat (Chromochloridaceae). Phylogenetic analyses revealed that Nephrocytium formed an independent lineage in the order Sphaeropleales (Chlorophyceae) with high support values and a close phylogenetic relationship with Chromochloris. Based on combined morphological, ultrastructural and phylogenetic data, we propose a re-classification of Nephrocytium into Sphaeropleales, sharing a close relationship with Chromochloris.


Author(s):  
Benoit Morel ◽  
Pierre Barbera ◽  
Lucas Czech ◽  
Ben Bettisworth ◽  
Lukas Hübner ◽  
...  

Abstract Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.


2020 ◽  
Vol 94 (S78) ◽  
pp. 1-103 ◽  
Author(s):  
Adam D. Marsh ◽  
Timothy B. Rowe

AbstractDilophosaurus wetherilli was the largest animal known to have lived on land in North America during the Early Jurassic. Despite its charismatic presence in pop culture and dinosaurian phylogenetic analyses, major aspects of the skeletal anatomy, taxonomy, ontogeny, and evolutionary relationships of this dinosaur remain unknown. Skeletons of this species were collected from the middle and lower part of the Kayenta Formation in the Navajo Nation in northern Arizona. Redescription of the holotype, referred, and previously undescribed specimens of Dilophosaurus wetherilli supports the existence of a single species of crested, large-bodied theropod in the Kayenta Formation. The parasagittal nasolacrimal crests are uniquely constructed by a small ridge on the nasal process of the premaxilla, dorsoventrally expanded nasal, and tall lacrimal that includes a posterior process behind the eye. The cervical vertebrae exhibit serial variation within the posterior centrodiapophyseal lamina, which bifurcates and reunites down the neck. Iterative specimen-based phylogenetic analyses result in each of the additional specimens recovered as the sister taxon to the holotype. When all five specimens are included in an analysis, they form a monophyletic clade that supports the monotypy of the genus. Dilophosaurus wetherilli is not recovered as a ceratosaur or coelophysoid, but is instead a non-averostran neotheropod in a grade with other stem-averostrans such as Cryolophosaurus ellioti and Zupaysaurus rougieri. We did not recover a monophyletic ‘Dilophosauridae.’ Instead of being apomorphic for a small clade of early theropods, it is more likely that elaboration of the nasals and lacrimals of stem-averostrans is plesiomorphically present in early ceratosaurs and tetanurans that share those features. Many characters of the axial skeleton of Dilophosaurus wetherilli are derived compared to Late Triassic theropods and may be associated with macropredation and an increase in body size in Theropoda across the Triassic-Jurassic boundary.


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