Members Of Clade Research Articles

The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.

The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.

Genome-Wide Analysis of the Common Fig (Ficus carica L.) R2R3-MYB Genes Reveals Their Structure, Evolution, and Roles in Fruit Color Variation.

The R2R3-MYB transcription factor (TF) family is crucial for regulating plant growth, stress response, and fruit ripening. Although this TF family has been examined in a multitude of plants, the R2R3-MYB TFs in Ficus carica, a Mediterranean fruit species, have yet to be characterized. This study identified and classified 63 R2R3-MYB genes (FcMYB1 to FcMYB63) in the F. carica genome. We analyzed these genes for physicochemical properties, conserved motifs, phylogenetic relationships, gene architecture, selection pressure, and gene expression profiles and networks. The genes were classified into 29 clades, with members of the same clade showing similar exon-intron structures and motif compositions. Of the 54 orthologous gene pairs shared with mulberry (Morus notabilis), 52 evolved under negative selection, while two pairs (FcMYB55/MnMYB20 and FcMYB59/MnMYB31) experienced diversifying selection. RNA-Seq analysis showed that FcMYB26, FcMYB33, and FcMYB34 were significantly overexpressed in fig fruit peel during maturation phase III. Weighted gene co-expression network analysis (WGCNA) indicated that these genes are part of an expression module associated with the anthocyanin pathway. RT-qPCR validation confirmed these findings and revealed that the Tunisian cultivars 'Zidi' and 'Soltani' have cultivar-specific R2R3-FcMYB genes highly overexpressed during the final stage of fruit maturation and color acquisition. These genes likely influence cultivar-specific pigment synthesis. This study provides a comprehensive overview of the R2R3-MYB TF family in fig, offering a framework for selecting genes related to fruit peel color in breeding programs.

Tuber cumberlandense and T. canirevelatum, two new edible Tuber species from eastern North America discovered by truffle-hunting dogs

ABSTRACT Ectomycorrhizal fungi in the genus Tuber form hypogeous fruiting bodies called truffles. Many Tuber species are highly prized due to their edible and aromatic ascomata. Historically, there has been attention on cultivating and selling European truffle species, but there is growing interest in cultivating, wild-harvesting, and selling species of truffles endemic to North America. North America has many endemic Tuber species that remain undescribed, including some that have favorable culinary qualities. Here, we describe two such Tuber species from eastern North America. Maximum likelihood and Bayesian phylogenetic analyses of ITS (internal transcribed spacer), tef1 (translation elongation factor 1-alpha), and rpb2 (second largest subunit of RNA polymerase II) sequences were used to place these species within a phylogenetic context. We coupled these data with morphological analyses and volatile analyses based on gas chromatography–mass spectrometry. Tuber cumberlandense, sp. nov. (previously referred to as Tuber sp. 66), is a member of the Rufum clade that has been opportunistically harvested for commercial sale from T. melanosporum orchards across eastern North America. Tuber canirevelatum, sp. nov. belongs in the Macrosporum clade and thus far is only known from eastern Tennessee, USA. Both new species were discovered with the assistance of trained truffle dogs. The volatile profiles of T. canirevelatum and T. cumberlandense were measured in order to characterize aromas based on the chemical compounds produced by these fungi. Ascomata from both species were enriched in acetone, dimethyl sulfide, 1-(methylthio)-1-propene, and 1-(methylthio)propane. In this work, we celebrate and encourage the use of trained truffle-hunting dogs for fungal biodiversity discovery and research.

An Analysis of Combined Molecular Weight and Hydrophobicity Similarity between the Amino Acid Sequences of Spike Protein Receptor Binding Domains of Betacoronaviruses and Functionally Similar Sequences from Other Virus Families

Recently, we proposed a new method, based on protein profiles derived from physicochemical dynamic time warping (PCDTW), to functionally/structurally classify coronavirus spike protein receptor binding domains (RBD). Our method, as used herein, uses waveforms derived from two physicochemical properties of amino acids (molecular weight and hydrophobicity (MWHP)) and is designed to reach into the twilight zone of homology, and therefore, has the potential to reveal structural/functional relationships and potentially homologous relationships over greater evolutionary time spans than standard primary sequence alignment-based techniques. One potential application of our method is inferring deep evolutionary relationships such as those between the RBD of the spike protein of betacoronaviruses and functionally similar proteins found in other families of viruses, a task that is extremely difficult, if not impossible, using standard multiple alignment-based techniques. Here, we applied PCDTW to compare members of four divergent families of viruses to betacoronaviruses in terms of MWHP physicochemical similarity of their RBDs. We hypothesized that some members of the families Arteriviridae, Astroviridae, Reoviridae (both from the genera rotavirus and orthoreovirus considered separately), and Toroviridae would show greater physicochemical similarity to betacoronaviruses in protein regions similar to the RBD of the betacoronavirus spike protein than they do to other members of their respective taxonomic groups. This was confirmed to varying degrees in each of our analyses. Three arteriviruses (the glycoprotein-2 sequences) clustered more closely with ACE2-binding betacoronaviruses than to other arteriviruses, and a clade of 33 toroviruses was found embedded within a clade of non-ACE2-binding betacoronaviruses, indicating potentially shared structure/function of RBDs between betacoronaviruses and members of other virus clades.

Complete mitochondrial genome sequence and phylogenetic analysis of the hybrid flat fish Platichthys stellatus (♀) × Platichthys bicoloratus (♂)

We report the complete mitochondrial genome of the hybrid flounder Platichthys stellatus (♀) × Platichthys bicoloratus (♂). The mitochondrial genome contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 control region (D-loop), for a total length of 16,874 bp. The nucleotide composition of the heavy strand was 29.15% C, 26.99% A, 26.14% T, and 17.71% G. A maximum-likelihood phylogenetic analysis showed that the hybrid flat fish was a member of the same clade as P. stellatus (maternal inheritance). Our findings add to the extant data on the subfamily Pleuronecidae and provide insight into their molecular phylogeny and taxonomy.

Evolutionary Relationships of Omani Macrotermes subhyalinus, Macrotermitinae.

A study was conducted to investigate the evolutionary relationships of Macrotermes subhyalinus from Oman, in the southeastern part of the Arabian Peninsula. Sequences of the mitochondrial COI and the nuclear large-subunit ribosomal RNA (LSU rRNA, 28S) genes were used to investigate the populations of M. subhyalinus across their distribution in Oman to determine their relationships with other Macrotermes species. Our findings indicate that M. subhyalinus in Oman is a member of an East African clade, distinct from those in West Africa. Analyses of the COI showed that there is base composition bias among the taxa (non-stationarity) that has not been considered in earlier studies. We provide the first report of pseudogene copies of 28S in M. subhyalinus that are differentially amplified.

FaNPR3 Members of the NPR1-like Gene Family Negatively Modulate Strawberry Fruit Resistance against Colletotrichum acutatum.

Strawberry fruit is highly appreciated worldwide for its organoleptic and healthy properties. However, this plant is attacked by many pathogenic fungi, which significantly affect fruit production and quality at pre- and post-harvest stages, making chemical applications the most effective but undesirable strategy to control diseases that has been found so far. Alternatively, genetic manipulation, employing plant key genes involved in defense, such as members of the NPR-like gene family, has been successful in many crops to improve resistance. The identification and use of the endogenous counterpart genes in the plant of interest (as it is the case of strawberry) is desirable as it would increase the favorable outcome and requires prior knowledge of their defense-related function. Using RNAi technology in strawberry, transient silencing of Fragaria ananassa NPR3 members in fruit significantly reduced tissue damage after Colletotrichum acutatum infection, whereas the ectopic expression of either FaNPR3.1 or FaNPR3.2 did not have an apparent effect. Furthermore, the ectopic expression of FaNPR3.2 in Arabidopsis thaliana double-mutant npr3npr4 reverted the disease resistance phenotype to Pseudomonas syringe to wild-type levels. Therefore, the results revealed that members of the strawberry FaNPR3 clade negatively regulate the defense response to pathogens, as do their Arabidopsis AtNPR3/AtNPR4 orthologs. Also, evidence was found showing that FaNPR3 members act in strawberry (F. ananassa) as positive regulators of WRKY genes, FaWRKY19 and FaWRKY24; additionally, in Arabidopsis, FaNPR3.2 negatively regulates its orthologous genes AtNPR3/AtNPR4. We report for the first time the functional characterization of FaNPR3 members in F. ananassa, which provides a relevant molecular basis for the improvement of resistance in this species through new breeding technologies.

Genome reduction in novel, obligately methyl-reducing Methanosarcinales isolated from arthropod guts (Methanolapillus gen. nov. and Methanimicrococcus).

Recent metagenomic studies have identified numerous lineages of hydrogen-dependent, obligately methyl-reducing methanogens. Yet, only a few representatives have been isolated in pure culture. Here, we describe six new species with this capability in the family Methanosarcinaceae (order Methanosarcinales), which makes up a substantial fraction of the methanogenic community in arthropod guts. Phylogenomic analysis placed the isolates from cockroach hindguts into the genus Methanimicrococcus (M. hacksteinii, M. hongohii, and M. stummii) and the isolates from millipede hindguts into a new genus, Methanolapillus (M. africanus, M. millepedarum, and M. ohkumae). Members of this intestinal clade, which includes also uncultured representatives from termites and vertebrates, have substantially smaller genomes (1.6-2.2 Mbp) than other Methanosarcinales. Genome reduction was accompanied by the loss of the upper part of the Wood-Ljungdahl pathway, several energy-converting membrane complexes (Fpo, Ech, and Rnf), and various biosynthetic pathways. However, genes involved in the protection against reactive oxygen species (catalase and superoxide reductase) were conserved in all genomes, including cytochrome bd (CydAB), a high-affinity terminal oxidase that may confer the capacity for microaerobic respiration. Since host-associated Methanosarcinales are nested within omnivorous lineages, we conclude that the specialization on methyl groups is an adaptation to the intestinal environment.

New data on the crown proteid Bishara backa from the Upper Cretaceous (Bostobe Formation) of Kazakhstan: implications for early evolution and palaeobiogeography of proteidae

ABSTRACT We provide a detailed redescription of all available material for the geologically oldest proteid salamander Bishara backa from the Upper Cretaceous (Santonian – lower Campanian) Bostobe Formation in Kazakhstan, consisting an atlantal centrum (neotype of Bishara backa) and a trunk vertebra. Bishara backa is characterised by the following combination of characters: large, dorsoventrally compressed and almost flat anterior cotyles of atlas enclosing an angle about 230°; anterior cotylar surfaces are continuous medially across lateral surfaces of small, dorsally placed intercotylar tubercle; ventrolateral ridges are alar-like; atlantal transverse processes are bicipitate; oblique anterior alar processes and lateral fossae on atlas present; transverse processes on trunk vertebra are bicipitate and divergent; alar processes on trunk vertebra are prominent; anterodorsal ridge on trunk vertebra is present; neural arch of trunk vertebra with high neural spine and grooves on its posterior face; two large subcentral foramina on ventral surface of the centrum. Our phylogenetic analyses finds Bishara backa as a crown proteid and a basal member of Eurasian clade of crown proteids (Bishara+Proteus+Mioproteus). We propose a model of proteid evolution that includes three main episodes of radiations with the last two taking place during the Late Cretaceous and the Palaeocene – Eocene thermal maximum.

Arcobacteraceae are ubiquitous mixotrophic bacteria playing important roles in carbon, nitrogen, and sulfur cycling in global oceans.

Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous Arcobacteraceae based on our deep-sea in situ incubations and the global data. The phylogenomic tree of Arcobacteraceae is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea in situ incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of Arcobacteraceae in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized Arcobacteraceae to carbon, nitrogen, and sulfur cycling in global oceans.IMPORTANCEMarine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the "hot time" of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.

Majority of the highly variable NLRs in maize share genomic location and contain additional target-binding domains.

Nucleotide-binding, Leucine Rich Repeat proteins (NLRs) are a major class of immune receptors in plants. NLRs include both conserved and rapidly evolving members, however their evolutionary trajectory in crops remains understudied. Availability of crop pan-genomes enables analysis of the recent events in the evolution of this highly complex gene family within domesticated species. Here, we investigated the NLR complement of 26 nested association mapping (NAM) founder lines of maize. We found that maize has just four main subfamilies containing rapidly evolving highly variable NLR (hvNLR) receptors. Curiously, three of these phylogenetically distinct hvNLR lineages are located in adjacent clusters on chromosome 10. Members of the same hvNLR clade show variable expression and methylation across lines and tissues, consistent with their rapid evolution. By combining sequence diversity analysis and AlphaFold2 computational structure prediction we predicted ligand binding sites in the hvNLRs. We also observed novel insertion domains in the LRR regions of two hvNLR subfamilies that likely contribute to target recogniton. To make this analysis accessible, we created NLRCladeFinder, a Google Colaboratory notebook, that accepts any newly identified NLR sequence, places it in the evolutionary context of the maize pan-NLRome, and provides an updated clade alignment, phylogenetic tree, and sequence diversity information for the gene of interest.

Description of Babesiacoryicola sp. nov. from Florida pumas (Puma concolor coryi) from southern Florida, USA

Previously, a high prevalence of piroplasms has been reported from Florida pumas (Puma concolor coryi) from southern Florida. In the current study, we describe the biological characteristics of a novel Babesia species in Florida pumas. Ring-stage trophozoites were morphologically similar to trophozoites of numerous small babesids of felids including B. leo, B. felis, and Cytauxzoon felis. Parasitemias in Florida pumas were very low (<1%) and hematologic values of 25 Babesia-infected Florida pumas were within normal ranges for P. concolor. Phylogenetic analysis of near full-length 18S rRNA gene, β-tubulin, cytochrome c oxidase subunit I, cytochrome c oxidase subunit III, and cytochrome b gene sequences indicated that this Babesia species is a member of the Babesia sensu stricto clade and is related to groups of Babesia spp. from carnivores or ungulates, although the closest group varied by gene target. Internal transcribed spacer (ITS)-1 region sequences from this Babesia sp. from 19 Florida pumas were 85.7–99.5% similar to each other and ∼88% similar to B. odocoilei. Similarly, an ITS-2 sequence from one puma was 96% similar to B. bigemina and 92% similar to a Babesia sp. from a red panda (Ailurus fulgens). Infected pumas were positive for antibodies that reacted with B. odocoilei, B. canis, and B. bovis antigens with titers of 1:256, 1:128, and 1:128, respectively. No serologic reactivity was noted for Theileria equi. No molecular evidence of congenital infection was detected in 24 kittens born to 11 Babesia-infected female pumas. Pumas from other populations in the United States [Louisiana (n = 1), North Dakota (n = 5) and Texas (n = 28)], British Columbia, Canada (n = 9), and Costa Rica (n = 2) were negative for this Babesia sp. Collectively, these data provide morphologic, serologic, genetic, and natural history data for this novel Babesia sp. which we propose the name Babesia coryicola sp. nov. sp. This is the first description of a felid-associated Babesia species in North America.

Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species.

Candida is a polyphyletic genus of asexually reproducing yeasts in the Saccharomycotina with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades, approximately half of the Candida species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. Candida auris is an important, globally emerging opportunistic pathogen that has caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the Candida auris-Candida haemuli (CAH) clade in the Metschnikowiaceae, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from natural environments. The clade is phylogenetically positioned remotely from the type species of the genus Candida that is Candida vulgaris (currently interpreted as a synonym of Candida tropicalis) and belongs to the family Debaryomycetaceae. Although previous phylogenetic and phylogenomic studies confirmed the position of C. auris in the Metschnikowiaceae, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera Clavispora and Metschnikowia. To resolve the position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of C. auris and related species in the Metschnikowiaceae using several metrics, such as the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). Based on those approaches, 13 new genera are proposed for various Candida and Hyphopichia species, including members of the CAH clade in the Metschnikowiaceae. As a result, C. auris and related species are reassigned to the genus Candidozyma. Fifty-five new combinations and nine new species are introduced and this will reduce the polyphyly of the genus Candida. Citation: Liu F, Hu Z-D, Zhao X-M, et al. 2024. Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species. Persoonia 52: 22-43. https://doi.org/10.3767/persoonia.2024.52.02 .

The isoprenyl chain length of coenzyme Q mediates the nutritional resistance of fungi to amoeba predation.

Ubiquinones (CoQ) are universal electron carriers in the respiratory chain of all aerobic bacteria and eukaryotes. Usually 8-10 isoprenyl units ensure their localization within the lipid bilayer. Members of the Saccharomyces clade among fungi are unique in using only 6. The reason for this is unclear. Here we provide evidence that the use of CoQ6 efficiently protects these fungi from predation by the ubiquitous fungivorous amoeba Protostelium aurantium which lacks its own biosynthetic pathway for this vitamin. The amoebae were starving on a diet of CoQ6 yeasts which could be complemented by either the addition of longer CoQs or the genetic engineering of a CoQ9 biosynthetic pathway.

First Sauropodomorpha (Dinosauria) for the Vila Botucaraí site (Hyperodapedon Assemblage Zone, Candelária Sequence), Rio Grande do Sul, Brazil

The Vila Botucaraí site is located west of the municipality of Candelária, Rio Grande do Sul State, southern Brazil, and is particularly important because it represents the type locality of the species Exaeretodon riograndensis (Cynodontia, Traversodontidae), Charruodon tetracuspidatus (Cynodontia, Probainognathia) and Proterochampsa nodosa (Archosauriformes, Proterochampsidae). The site is correlated to the Hyperodapedon Assemblage Zone whose fossiliferous content allows to correlate it to the lower half of the Ischigualasto Formation (Ischigualasto-Villa Unión Basin), of late Carnian age, in Argentina. The aim of this study is to record the first remains of dinosaurs from this locality, found in 2001 during the Pró-Guaiba Project and stored in the Scientific Collection of the Paleontology Section of the Museu de Ciências Naturais, Secretaria Estadual do Meio Ambiente e Infraestrutura, Porto Alegre, RS. In addition to the taxa mentioned at the Vila Botucaraí site, the archosauromorph Hyperodapedon sp. was also preliminarily recorded. The Dinosauria specimen includes four dorsal vertebrae (MCN-PV 10347a, b, c, d). The general characteristics observed are: (i) absence of a ventral keel in the vertebral centra, shared with Guaibasaurus, Bagualosaurus, Pampadromaeus; (ii) amphicoelic centra with concave ventral surface, shared with Bagualosaurus, Guaibasaurus, and most non-sauropod sauropodomorphs (exceptions are, for example, Riojasaurus; also, this character does not appear in herrerasaurids); (iii) vertebral laminae connected to the diapophysis, and their arrangement results in different fossae, as in Bagualosaurus, Buriolestes, Guaibasaurus, and herrerasaurids; (iv) neural spine anteroposteriorly elongated and transversely narrow, as in Bagualosaurus, Pampadromaeus, Buriolestes, Macrocollum, differing from herrerasaurids and theropods. This set of characters is similar to that observed in basal sauropodomorphs, quite different from the neural spine with a spine table, such as the observed in herrerasaurids. Specimen MCN-PV 10347 is here considered a member of the Sauropodomorpha clade and tentatively identified as cf. Bagualosauria. The features of this specimen are shared among Carnian (e.g., Buriolestes schultzi, Bagualosaurus agudoensis) and Norian (e.g., Unaysaurus tolentinoi, Guaibasaurus candelariensis) sauropodomorphs. In addition to this, the new material expands the knowledge regarding the number of outcrops with the occurrence of sauropodomorphs for the Triassic in Brazil, as well as about the paleofauna of the Vila Botucaraí site, allowing us to infer its biostratigraphic correlation with one of the sub-divisions already proposed for the Hyperodapedon AZ, the Exaeretodon Subzone, interpreted as the top of this AZ. Despite the abundance of sauropodomorphs in Rio Grande do Sul, this record confirms the occurrence of this clade at the Hyperodapedon AZ in the Candelária region.

Streptococcus hohhotensis sp. nov., isolated from the breast milk of a healthy woman.

Human breast milk contains lactic acid bacteria (LAB), which have an important influence on the composition of the intestinal microbia of infants. In this study, one strain of an α-hemolytic species of the genus Streptococcus, IMAU99199T, isolated from the breast milk of a healthy nursing mother in Hohhot city PR China, was studied to characterise its taxonomic status using phenotypic and molecular taxonomic methods. The results indicated that it represented a member of the mitis-suis clade, pneumoniae subclade of the genus Streptococcus. It is a Gram-stain-positive, catalase-negative and oxidase-negative bacterium, and the cells are globular, paired or arranged in short chains. The results of a phylogenetic analysis of its 16S rRNA gene and two housekeeping genes (gyrB and rpoB) placed it in the genus Streptococcus. A phylogenetic tree based on 135 single-copy genes sequences indicated that IMAU99199T formed a closely related branch well separated from 'Streptococcus humanilactis' IMAU99125, 'Streptococcus bouchesdurhonensis' Marseille Q6994, Streptococcus mitis NCTC 12261T, 'Streptococcus vulneris' DM3B3, Streptococcus toyakuensis TP1632T, Streptococcus pseudopneumoniae ATCC BAA-960T and Streptococcus pneumoniae NCTC 7465T. IMAU99199T and 'S. humanilactis' IMAU99125 had the highest average nucleotide identity (93.7 %) and digital DNA-DNA hybridisation (55.3 %) values, which were below the accepted thresholds for novel species. The DNA G+C content of the draft genome of IMAU99199T was 39.8 %. The main cellular fatty acids components of IMAU99199T were C16 : 0 and C16 : 1ω7. It grew at a temperature range of 25-45 °C (the optimum growth temperature was 37 °C) and a pH range of 5.0-8.0 (the optimum growth pH was 7.0). These data indicate that strain IMAU99199T represents a novel species in the genus Streptococcus, for which the name Streptococcus hohhotensis sp. nov. is proposed. The type strain is IMAU99199T (=GDMCC 1.1874T=KCTC 21155T).

A giant bowfin from a Paleocene hothouse ecosystem in North America

Abstract Aquatic biodiversity changed dramatically at the start of the Paleogene. Although comparatively little is known about global freshwater ecosystems that appeared just after the Cretaceous–Paleogene mass extinction, available data suggest that they were buffered from the worst effects of the extinction event. Here, we describe a nearly complete skeleton of a large-bodied ray-finned fish from a wetland ecosystem that existed fewer than 10 Myr after the end-Cretaceous extinction in western North America. With a maximum length likely exceeding 2 m, †Amia basiloides sp. nov. is one of the largest species in Holostei, a once species-rich clade of ray-finned fishes now survived by the nine living species of gars and bowfins. High-resolution computed tomography scans illuminate the anatomy of †A. basiloides and suggest it was an analogue of living large-bodied, piscivorous freshwater fishes found in the Southern Hemisphere and southern North America. When considered in a phylogenetic context, †A. basiloides shows that close relatives of living bowfins rapidly achieved gigantism in the Early Paleogene of North America after the largest members of an ancient clade closely related to bowfins went extinct. Although the Cretaceous–Paleogene boundary likely induced turnover of freshwater vertebrate predatory guilds, holostean faunas remained ecologically comparable across the extinction due to exceptionally fast episodes of convergence.

Two new nocturnal species of South Asian Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) of the wynadensis clade from the southern Western Ghats, India

We describe two new medium-bodied, nocturnal species of South Asian Cnemaspis from the southern Western Ghats, Tamil Nadu, India in an integrative taxonomic framework. The two new species are phylogenetically and morphologically allied to the wynadensis clade and can be distinguished from other species of the wynadensis clade and each other by a combination of nonoverlapping morphological characters including body size, homogeneous dorsal pholidosis, the number of femoral pores and poreless scales separating these series, the number of ventral scales across the midbody and longitudinal scales from mental to cloaca, the number of dorsal granules around the body; and an uncorrected pairwise ND2 sequence divergence of 8.2–22.9 % (16S 4.2–12.2 %) from all other members in the clade. These are the first members of the wynadensis clade known from south of the Palghat Gap apart from C. bireticulata, a putative junior synonym of C. sisparensis that is likely to be distinct owing to morphological differences and geographic distance. Cnemaspis sanctus sp. nov. is from low coastal hills in Kanyakumari District at the southern tip of the Western Ghats and Cnemaspis persephone sp. nov. is from the Anaimalais, Anaimalai Tiger Reserve. Many more undescribed species of the wynadensis clade and South Asian Cnemaspis are likely to be found across the southern Western Ghats.

Tooth replacement in the early-diverging neornithischian Jeholosaurus shangyuanensis and implications for dental evolution and herbivorous adaptation in Ornithischia

BackgroundTooth replacement patterns of early-diverging ornithischians, which are important for understanding the evolution of the highly specialized dental systems in hadrosaurid and ceratopsid dinosaurs, are poorly known. The early-diverging neornithischian Jeholosaurus, a small, bipedal herbivorous dinosaur from the Early Cretaceous Jehol Biota, is an important taxon for understanding ornithischian dental evolution, but its dental morphology was only briefly described previously and its tooth replacement is poorly known.ResultsCT scanning of six specimens representing different ontogenetic stages of Jeholosaurus reveals significant new information regarding the dental system of Jeholosaurus, including one or two replacement teeth in nearly all alveoli, relatively complete tooth resorption, and an increase in the numbers of alveoli and replacement teeth during ontogeny. Reconstructions of Zahnreihen indicate that the replacement pattern of the maxillary dentition is similar to that of the dentary dentition but with a cyclical difference. The maxillary tooth replacement rate in Jeholosaurus is probably 46 days, which is faster than that of most other early-diverging ornithischians. During the ontogeny of Jeholosaurus, the premaxillary tooth replacement rate slows from 25 days to 33 days with similar daily dentine formation.ConclusionsThe tooth replacement rate exhibits a decreasing trend with ontogeny, as in Alligator. In a phylogenetic context, fast tooth replacement and multi-generation replacement teeth have evolved at least twice independently in Ornithopoda, and our analyses suggest that the early-diverging members of the major ornithischian clades exhibit different tooth replacement patterns as an adaption to herbivory.

A rice GT61 glycosyltransferase possesses dual activities mediating 2-O-xylosyl and 2-O-arabinosyl substitutions of xylan.

A member of the rice GT61 clade B is capable of transferring both 2-O-xylosyl and 2-O-arabinosyl residues onto xylan and another member specifically catalyses addition of 2-O-xylosyl residue onto xylan. Grass xylan is substituted predominantly with 3-O-arabinofuranose (Araf) as well as with some minor side chains, such as 2-O-Araf and 2-O-(methyl)glucuronic acid [(Me)GlcA]. 3-O-Arabinosylation of grass xylan has been shown to be catalysed by grass-expanded clade A members of the glycosyltransferase family 61. However, glycosyltransferases mediating 2-O-arabinosylation of grass xylan remain elusive. Here, we performed biochemical studies of two rice GT61 clade B members and found that one of them was capable of transferring both xylosyl (Xyl) and Araf residues from UDP-Xyl and UDP-Araf, respectively, onto xylooligomer acceptors, whereas the other specifically catalysed Xyl transfer onto xylooligomers, indicating that the former is a xylan xylosyl/arabinosyl transferase (named OsXXAT1 herein) and the latter is a xylan xylosyltransferase (named OsXYXT2). Structural analysis of the OsXXAT1- and OsXYXT2-catalysed reaction products revealed that the Xyl and Araf residues were transferred onto O-2 positions of xylooligomers. Furthermore, we demonstrated that OsXXAT1 and OsXYXT2 were able to substitute acetylated xylooligomers, but only OsXXAT1 could xylosylate GlcA-substituted xylooligomers. OsXXAT1 and OsXYXT2 were predicted to adopt a GT-B fold structure and molecular docking revealed candidate amino acid residues at the predicted active site involved in binding of the nucleotide sugar donor and the xylohexaose acceptor substrates. Together, our results establish that OsXXAT1 is a xylan 2-O-xylosyl/2-O-arabinosyl transferase and OsXYXT2 is a xylan 2-O-xylosyltransferase, which expands our knowledge of roles of the GT61 family in grass xylan synthesis.