Phylogenetic Branch Research Articles

A surface-exposed GH26 β-mannanase from Bacteroides ovatus: Structure, role, and phylogenetic analysis of BoMan26B

The galactomannan utilization locus (BoManPUL) of the human gut bacterium Bacteroides ovatus encodes BoMan26B, a cell-surface–exposed endomannanase whose functional and structural features have been unclear. Our study now places BoMan26B in context with related enzymes and reveals the structural basis for its specificity. BoMan26B prefers longer substrates and is less restricted by galactose side-groups than the mannanase BoMan26A of the same locus. Using galactomannan, BoMan26B generated a mixture of (galactosyl) manno-oligosaccharides shorter than mannohexaose. Three defined manno-oligosaccharides had affinity for the SusD-like surface–exposed glycan-binding protein, predicted to be implicated in saccharide transport. Co-incubation of BoMan26B and the periplasmic α-galactosidase BoGal36A increased the rate of galactose release by about 10-fold compared with the rate without BoMan26B. The results suggested that BoMan26B performs the initial attack on galactomannan, generating oligosaccharides that after transport to the periplasm are processed by BoGal36A. A crystal structure of BoMan26B with galactosyl-mannotetraose bound in subsites −5 to −2 revealed an open and long active-site cleft with Trp-112 in subsite −5 concluded to be involved in mannosyl interaction. Moreover, Lys-149 in the −4 subsite interacted with the galactosyl side-group of the ligand. A phylogenetic tree consisting of GH26 enzymes revealed four strictly conserved GH26 residues and disclosed that BoMan26A and BoMan26B reside on two distinct phylogenetic branches (A and B). The three other branches contain lichenases, xylanases, or enzymes with unknown activities. Lys-149 is conserved in a narrow part of branch B, and Trp-112 is conserved in a wider group within branch B.

Screening, characterization and molecular-genetical identification of a new bacterial strain Paenibacillus species

Bacterial variant PS-K-17 was isolated from wheat grain contaminated by polysaccharide-producing microbiota for further characterization. It was found that the isolate grown on agar slants and in submerged culture on media with specific substrates synthesized beta-galactosidase, amylase, protease, pectinase, cellulase, beta-glucanase, lipase (esterase), alginase, extracellular polysaccharides, and pigments, probably carotenoids. Based on cultural-morphological and physiological-biochemical properties and phylogenetic analysis of nucleotide sequences of 16S rRNA gene (access code MF443394 in GenBank) the bacterial culture was identified as Paenibacillus species PS-K-17. The studied isolate forms one phylogenetic branch with type strains Paenibacillus nicotianae (98.3 %), Paenibacillus hordei (98.2 %), Paenibacillus kyungheensis (97.9 %), holding wherein a separate position. Strain Paenibacillus sp. PS-K-17 may find use in biotechnology as a producer of extracellular polysaccharides and enzymes splitting plant polymeric substances as well as a component of microbial consortium-ingredient of a new complex feed additive.

Morphological innovation and the evolution of hadrosaurid dinosaurs

AbstractThe hadrosaurids were a successful group of herbivorous dinosaurs. During the Late Cretaceous, 100 to 66 million years ago, hadrosaurids had high diversity, rapid speciation rates, and wide geographic distribution. Most hadrosaurids were large bodied and had similar postcranial skeletons. However, they show important innovations in the skull, including disparate crests that functioned as socio-sexual display structures, and a complex feeding apparatus, with specialized jaws bearing dental batteries. Little is known about the macroevolutionary processes that produced these evolutionary novelties. Here we provide novel perspectives using evolutionary rate and disparity analyses. Our results show that hadrosaurid cranial evolution was complex and dynamic, but their postcranial skeleton and body size were conservative. High cranial disparity was achieved through multiple bursts of phenotypic innovation. We highlight contrasting evolutionary trends within hadrosaurids between the disparate facial skeleton and crests, which both showed multiple high-rate shifts, and the feeding apparatus, which had low variance and high rates on a single phylogenetic branch leading to the diverse Saurolophidae. We reveal that rapid evolutionary rates were important for producing the high disparity of exaggerated crests and present novel evidence that the hadrosaurid diversification was linked to both a key adaptive innovation in the feeding apparatus and multiple bursts of innovation in socio-sexual displays.

Detection and Molecular Characterization of Two Genotypes of Goose Parvoviruses Isolated from Growing Period Geese and Cherry Valley Ducks in China.

Goose parvovirus (GPV) is the etiologic pathogen of Derzsy's disease, causing great economic losses in the waterfowl industry. A novel GPV-related virus (NGPV), which caused short beak and dwarfism syndrome, has occurred in China since 2015. In this study, two GPV strains (RC45 and RC70) were isolated from diseased growing period geese (45 days old and 70 days old), and one NGPV strain GXN45 was isolated from a 45-day-old Cherry Valley duck in China. To better understand the genetic diversity between GPVs isolated from growing period waterfowls and other classical waterfowl parvoviruses, the complete genomes and main genes were sequenced and analyzed. Full-length genomic sequence alignments demonstrated that both RC45 and RC70 showed the highest identity with classical GPVs YZ99-6 and SHFX1201, whereas GXN45 shared the highest identity with NGPV SDLC01. Sequence alignment of the inverted terminal repeat region showed that GXN45, RC45, and RC70 had two 14-nucleotide (nt) deletions compared with the classical GPV virulent B strain and one 14-nt deletion compared with mule duck-origin NGPV M15 strain. Phylogenetic tree analysis of nonstructural and VP1 genes showed that GXN45 was clustered into a branch with NGPV QH15 strain except for the VP1 amino acid tree. Although both RC45 and RC70 formed one separate branch distinct from classic GPV isolates, they were in one large phylogenetic tree branch. This study will contribute to a better understanding of the genetic diversity and molecular characterization of three isolated parvoviruses and lay the foundation to further study the relationship between mutations of virus genome and viral pathogenicity.

Systematic Affiliation and Genome Analysis of Subtercola vilae DB165T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake.

Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number of isolates from various cold environments. Genomic evidence supports the separation of Agreia and Subtercola species. In order to gain insight into the ability of S. vilae to adapt to life in this extreme environment, we analyzed the genome with a particular focus on properties related to possible adaptation to a cold environment. General properties of the genome are presented, including carbon and energy metabolism, as well as secondary metabolite production. The repertoire of genes in the genome of S. vilae DB165T linked to adaptations to the harsh conditions found in Llullaillaco Volcano Lake includes several mechanisms to transcribe proteins under low temperatures, such as a high number of tRNAs and cold shock proteins. In addition, S. vilae DB165T is capable of producing a number of proteins to cope with oxidative stress, which is of particular relevance at low temperature environments, in which reactive oxygen species are more abundant. Most important, it obtains capacities to produce cryo-protectants, and to combat against ice crystal formation, it produces ice-binding proteins. Two new ice-binding proteins were identified which are unique to S. vilae DB165T. These results indicate that S. vilae has the capacity to employ different mechanisms to live under the extreme and cold conditions prevalent in Llullaillaco Volcano Lake.

Length heteroplasmy in the predominate mitochondrial DNA haplogroups in the Croatian population

Mitochondrial control region represents the most variable segment of the mitochondrial genome. The frequency and pattern of heteroplasmy has been described in several studies; however, none of the reports documented the Croatian population. In the present study, we screened the control region (1122 bp) of 95 individuals belonging to two predominant mitochondrial phylogenetic branches in the Croatian population, haplogroups H and U. Length heteroplasmy occurred in polycytosine (poly-C) tracts within three hypervariable segments of the control region with the following frequencies: HVSI - 26.3%, HVSII - 52.6% and HVSIII - 7.4%. Furthermore, the association between certain polymorphisms in HVSI and length heteroplasmy was investigated. Our results indicate that only polymorphisms located in the poly-C tract are associated with HVSI length heteroplasmy. The T to C transition at np 16189 is significantly associated with the occurrence of length heteroplasmy (p<0.0001). This effect was even stronger if the C insertion was present in the position 16193. The data support the hypothesis that an uninterrupted poly-C tract of more than eight cytosines leads to length heteroplasmy. Length heteroplasmy associated with the T to C substitution in np 16189 was predominantly found in haplogroup U.

Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus.

Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well–supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.

Characterization of the grapevine Shaker K+ channel VvK3.1 supports its function in massive potassium fluxes necessary for berry potassium loading and pulvinus-actuated leaf movements.

In grapevine, climate changes lead to increased berry potassium (K+ ) contents that result in must with low acidity. Consequently, wines are becoming 'flat' to the taste, with poor organoleptic properties and low potential aging, resulting in significant economic loss. Precise investigation into the molecular determinants controlling berry K+ accumulation during its development are only now emerging. Here, we report functional characterization by electrophysiology of a new grapevine Shaker-type K+ channel, VvK3.1. The analysis of VvK3.1 expression patterns was performed by qPCR and insitu hybridization. We found that VvK3.1 belongs to the AKT2 channel phylogenetic branch and is a weakly rectifying channel, mediating both inward and outward K+ currents. We showed that VvK3.1 is highly expressed in the phloem and in a unique structure located at the two ends of the petiole, identified as a pulvinus. From the onset of fruit ripening, all data support the role of the VvK3.1 channel in the massive K+ fluxes from the phloem cell cytosol to the berry apoplast during berry K+ loading. Moreover, the high amount of VvK3.1 transcripts detected in the pulvinus strongly suggests a role for this Shaker in the swelling and shrinking of motor cells involved in paraheliotropic leaf movements.

Analyses of four new Caulobacter Phicbkviruses indicate independent lineages.

Bacteriophages with genomes larger than 200 kbp are considered giant phages, and the giant Phicbkviruses are the most frequently isolated Caulobacter crescentus phages. In this study, we compare six bacteriophage genomes that differ from the genomes of the majority of Phicbkviruses. Four of these genomes are much larger than those of the rest of the Phicbkviruses, with genome sizes that are more than 250 kbp. A comparison of 16 Phicbkvirus genomes identified a 'core genome' of 69 genes that is present in all of these Phicbkvirus genomes, as well as shared accessory genes and genes that are unique for each phage. Most of the core genes are clustered into the regions coding for structural proteins or those involved in DNA replication. A phylogenetic analysis indicated that these 16 CaulobacterPhicbkvirus genomes are related, but they represent four distinct branches of the Phicbkvirus genomic tree with distantly related branches sharing little nucleotide homology. In contrast, pairwise comparisons within each branch of the phylogenetic tree showed that more than 80 % of the entire genome is shared among phages within a group. This conservation of the genomes within each branch indicates that horizontal gene transfer events between the groups are rare. Therefore, the Phicbkvirus genus consists of at least four different phylogenetic branches that are evolving independently from one another. One of these branches contains a 27-gene inversion relative to the other three branches. Also, an analysis of the tRNA genes showed that they are relatively mobile within the Phicbkvirus genus.

Comparative Study of Phylogenetic Analysis of S1 Gene of Infectious Bronchitis Virus Isolates from Iraq with the Selected Strains (genebank)

Recently 2018, four strains of infectious bronchitis virus (IBV) were isolated from vaccinated and non-vaccinated broiler flocks from different chicken farms in different cities in Iraq. The pathogenic characters were assessed for the four IBV strains. Test chickens were infected by the four strains releasing an immune response. Noticeable results showed by cross neutralization assays which revealed that strains antigenically distinct from classic IBV strains of H120, M41, Conn, and Gray. Compared to H120 vaccine strain, short insertion, point mutation, and deletion occurred at many positions in the S1 protein of the four strains. Two of the four strains had the motif (HRRRR), which was considered identical to that of the epidemic IBV strains in Iraq. Another two strains had new motifs (HRLRR and RRYRR) emerged in the isolated strains. These Four strains were also genetically different from the vaccine strains and non-Iraqi IBV strains but closely related to large numbers of USA and China, Singapore and India strains. The isolates and 14 reference IBV strains were clustered into three distinct groups (I-III). The four strains were categorized into groups III, forming a big phylogenetic branch, which is closely related to USA IBVs and Singapore IBVs whereas the vaccine strains belonging to group I and II are genetically distant from groups III. The results from this study indicate that different IBV strains circulate in the chicken population in Iraq.

A universal PCR assay amplifying the unique malic enzyme of phytoplasmas

Malic enzyme encoded by the gene scfA belongs to the core set of housekeeping genes encoded by phytoplasmas. It enables the conversion of malate to pyruvate, an essential step in the unique pathway of phytoplasmas resulting in the generation of ATP and acetate. Several studies have examined the functionality of this pathway and the phylogenetic origin back to its putative Gram-positive source. The current sequence information on the enzyme relies on available genome sequence data. Comparison of scfA gene sequences highlights a low number of conserved sites, even between closely related strains, thereby hampering the design of universal primer pairs for application in PCR. A primer set was designed that enables the amplification of this key gene in phytoplasma metabolism. Successful amplification was performed from strains covering the three main phylogenetic branches of phytoplasma, and, as such, the universal primers scfA115F/865R offer the ability to obtain additional data from closely and distantly related phytoplasmas.

Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment

Even closely related prokaryotes often show an astounding diversity in their ability to grow in different nutritional environments. It has been hypothesized that complex metabolic adaptations-those requiring the independent acquisition of multiple new genes-can evolve via selectively neutral intermediates. However, it is unclear whether this neutral exploration of phenotype space occurs in nature, or what fraction of metabolic adaptations is indeed complex. Here, we reconstruct metabolic models for the ancestors of a phylogeny of 53 Escherichia coli strains, linking genotypes to phenotypes on a genome-wide, macroevolutionary scale. Based on the ancestral and extant metabolic models, we identify 3,323 phenotypic innovations in the history of the E. coli clade that arose through changes in accessory genome content. Of these innovations, 1,998 allow growth in previously inaccessible environments, while 1,325 increase biomass yield. Strikingly, every observed innovation arose through the horizontal acquisition of a single DNA segment less than 30 kb long. Although we found no evidence for the contribution of selectively neutral processes, 10.6% of metabolic innovations were facilitated by horizontal gene transfers on earlier phylogenetic branches, consistent with a stepwise adaptation to successive environments. Ninety-eight percent of metabolic phenotypes accessible to the combined E. coli pangenome can be bestowed on any individual strain by transferring a single DNA segment from one of the extant strains. These results demonstrate an amazing ability of the E. coli lineage to adapt to novel environments through single horizontal gene transfers (followed by regulatory adaptations), an ability likely mirrored in other clades of generalist bacteria.

Genome-Wide Identification and Expression Analysis of the CrRLK1L Gene Family in Apple (Malus domestica)

It has been reported that members of the Catharanthus roseus receptor-like kinase1-like kinase (CrRLK1L) gene family detect cell wall integrity, cell-to-cell communication, and biotic and abiotic stress. We performed a comprehensive study including the genome-wide identification, characterization, and gene expression analysis of CrRLK1Ls in apple (Malus domestica). Sixty-seven M. domestica CrRLK1Ls (MdCrRLK1Ls) were identified based on their domain structure. Molecular weight and pI ranged from 52.36–141 kDa and 5.05–8.9, respectively. They were distributed across 16 of the 18 chromosomes and classified into five phylogenetic branches. Exon-intron structural analysis indicated a wide range of exon numbers. Collinearity analysis showed that both segmental-and tandem-duplication contributed to the expansion of this family. Cis-elements in the MdCrRLK1L promoter region responded mainly to light, circadian rhythm, phytohormones, and biotic or abiotic stress. Many members exhibited tissue-specific expression patterns and differentially expressed under biotic stresses, which may contribute to the different functional roles of MdCrRLK1Ls under physiological stress and/or pathological conditions. This study provides new insights into the CrRLK1Ls in Malus spp.

Species Composition, Distribution, and Environmental Ecology of Voles (Mammalia, Cricetidae, Microtus) Found in the Northwest Caucasus

Molecular genetic typing of voles from the vicinity of the Pslukh cordon (south of the Caucasian state reserve), Krasnaya Polyana, and from the Utrish reserve (the Abrau peninsula) has been carried out. Based on the nucleotide sequence of the mitochondrial cytochrome b gene, voles from Krasnaya Polyana and the Psulkh cordon should be attributed to Asia Minor voles (Chionomys roberti), and the animals from Utrish, to the Eastern European voles (Microtus rossiaemeridionalis). The Asia Minor voles belong to the North Caucasian phylogenetic branch of the species. The analysis of body measurements of voles from Krasnaya Polyana and Lazarevskii region (without molecular examination) showed that these animals also most likely belong to the Asia Minor voles (not to Gudaurskii, as was mistakenly considered earlier). Some information on the ecology of the Asia Minor voles in the region is given.

The first identification and characterization of a histidine-specific amino acid racemase, histidine racemase from a lactic acid bacterium, Leuconostoc mesenteroides subsp. sake NBRC 102480.

We expressed a histidine racemase from Leuconostoc mesenteroides subsp. sake NBRC 102480 (Lm-HisR) successively in a soluble fraction of Escherichia coli BL21 (DE3) and then highly purified it from the cell-free extract. Lm-HisR showed amino acid racemase activity on histidine specifically. This is the first example of an amino acid racemase specifically acting on histidine. Phylogenetic analysis of Lm-HisR showed that Lm-HisR was located far from the cluster of alanine racemases reported thus far and only in lactic acid bacteria of the genus Leuconostoc. Alignment of the primary structure of Lm-HisR with those of lysine and alanine racemases and alanine racemase homologs previously reported revealed that the PLP-binding lysine and catalytic tyrosine were completely conserved, and some residues that are unique to the phylogenetic branch of Lm-HisR, Phe44, Ser45, Thr174, Thr206, His286, Ser287, Phe292, Gly312, Val357, and Ala358 were identified. We determined the crystal structure of Lm-HisR complexed with PLP at a 2.1-Å resolution. The crystal structure contained four molecules (two dimers) in the asymmetric unit. When comparing the 3D structure of Lm-HisR with those of racemases from Geobacillus stearothermophilus and Oenococcus oeni, Met315 was completely conserved, but Val357 was not. In addition, two significant differences were observed between Lm-HisR and G. stearothermophilus alanine racemase. Phe44 and His286 in Lm-HisR corresponded to Tyr43 and Tyr284 in G. stearothermophilus alanine racemase, respectively. Based on the structural analysis, comparison with alanine racemase, and docking simulation, three significant residues, Phe44, His286, and Val357, were identified that may control the substrate specificity of Lm-HisR.

Morphometrics of Starch Granules From Sub-Saharan Plants and the Taxonomic Identification of Ancient Starch

The assumption that taxonomy can be ascertained by starch granule shape and size has persisted unchallenged since the late nineteenth and early twentieth century biochemistry. More recent work has established that granule morphological affinity is scattered throughout phylogenetic branches, morphotype proportions vary within the genus, granules from closely related genera can differ dramatically in shape, and size variations do not reflect phylogenetic relationships. This situation is confounded by polymorphism at the species and tissue level, resulting in redundancy and multiplicity. This paper classifies morphological features of starch granules from 77 species, 31 families, and 22 orders across three African ecoregions. This is the largest starch reference collection published to date, rendering the dataset uniquely well suited to explore i) the diagnostic power of unique morphometric classifiers and their frequency, ii) morphotypes that cut across taxonomic boundaries, and iii) issues surrounding the minimum counts needed to accurately reflect granule polymorphism, variability, and identification. In a collection of 23,100 granules, taxonomic identification occurred very rarely. In the instances it did, it was at the species level, with no occurrences of a single morphotype or complement identifying all species within a family or genus. Some families cannot be uniquely identified, and morphometric types are shared despite taxonomic distance for three quarters of the taxa. However, this reference collection boasts 98 unique identifiers located in the Arecaceae, Convolvulaceae, Cyperaceae, Dioscoreaceae, Fabaceae, Musaceae, Pedaliaceae, Poaceae, and Zamiaceae. Therefore, the identification of starch granules is possible in some cases only.

Assessing Genomic Admixture between Cryptic Plutella Moth Species following Secondary Contact.

Cryptic species are genetically distinct taxa without obvious variation in morphology and are occasionally discovered using molecular or sequence data sets of populations previously thought to be a single species. The world-wide Brassica pest, Plutella xylostella (diamondback moth), has been a problematic insect in Australia since 1882, yet a morphologically cryptic species with apparent endemism (P. australiana) was only recognized in 2013. Plutella xylostella and P. australiana are able to hybridize under laboratory conditions, and it was unknown whether introgression of adaptive traits could occur in the field to improve fitness and potentially increase pressure on agriculture. Phylogenetic reconstruction of 29 nuclear genomes confirmed P. xylostella and P. australiana are divergent, and molecular dating with 13 mitochondrial genes estimated a common Plutella ancestor 1.96 ± 0.175 Ma. Sympatric Australian populations and allopatric Hawaiian P. xylostella populations were used to test whether neutral or adaptive introgression had occurred between the two Australian species. We used three approaches to test for genomic admixture in empirical and simulated data sets including 1) the f3 statistic at the level of the population, 2) pairwise comparisons of Nei’s absolute genetic divergence (dXY) between populations, and 3) changes in phylogenetic branch lengths between individuals across 50-kb genomic windows. These complementary approaches all supported reproductive isolation of the Plutella species in Australia, despite their ability to hybridize. Finally, we highlight the most divergent genomic regions between the two cryptic Plutella species and find they contain genes involved with processes including digestion, detoxification, and DNA binding.

Population Structure, Taxonomy, and Genetic Features of Yersinia pestis Strains of the Central Asian Subspecies

On the basis of the data of phylogeographical analysis, strains of Yersinia pestis are divided into a number of phylogenetic branches, and in accordance with the traditionally used subspecies classification in the CIS countries, they are divided into five subspecies. We conducted a study of the population structure and genetic characteristics of strains belonging to the phylogenetic branch 0.PE4 and its strains of the Altai subspecies—0.PE4a (Russia, Mongolia), the Hissar subspecies—0.PE4h (Tajikistan), the Talas population—0.PE4t (Kyrgyzstan), and the microtus population—0.PE4m (China). The uniformity of phenotypic and genetic characteristics of strains of the 0.PE4 branch has been established and the necessity of their association into one subspecies, the Central Asian (Y. pestis subsp. central asiatica), has been substantiated. The dendrogram demonstrates the presence of four separate subclusters corresponding to four populations: 0.PE4a (Altai strains), 0.PE4h (Hissar strains), 0.PE4t (Talas strains), and 0.PE4m (microtus strains) in the composition of the 0.PE4 cluster, which we propose to allocate to four biovars of the Central Asian subspecies: Altai, Hissar, Talas, and Microtus. A number of mutations specific only to 0.PE4 strains were detected. A DNA target was found and a method for differentiating the Central Asian subspecies (strains avirulent for humans) from other strains of Y. pestis by Real-Time PCR was developed.

Genotypic analysis of S segment of Crimean-Congo hemorrhagic fever virus in Turkey.

The Crimean-Congo hemorrhagic fever (CCHF) virus (CCHFV) is a tick-borne virus, whose viral RNA consists of S, L, and M segments. The virus is migrating through the ticks with animals and migratory birds and the geographical distribution can be investigated based on genetic analysis. To better understand the connection between the seropositivity and the mortality rate, the key factor could be the temporal and spatial analysis of the different strains. In this study, serum samples (n = 26) were selected from CCHFV RNA-positive patients and subjected to sequence analysis of the gene regions encoding the S segments. According to the neighbor-joining analysis, the obtained partial sequences were linked to the European strain. The strains were closely related to Turkey-Kelkit06, Turkey 200310849 viruses, and viruses from Russia and Kosovo. The comparison with previously analyzed isolates from the GenBank showed 95%-99% sequence similarity. The isolates in phylogenetic branches were divided into two groups. AST, platelet, and APTT levels were found significantly higher in Group 2 compared to Group 1. Nucleotide differences can be prognostic factor in CCHF disease. Increasing CCHF cases not originating from local isolates were circulating strains imported from different neighboring countries of Turkey. The results show new evidence to the emerging threat of the CCHF disease.

Chromosome painting in Glyphorynchus spirurus (Vieillot, 1819) detects a new fission in Passeriformes.

Glyphorynchus spirurus (GSP), also called the Wedge-billed Woodcreeper (Furnariidae) has an extensive distribution in the Americas, including the Atlantic coast of Brazil. Nevertheless, there is no information about its karyotype or genome organization. To contribute to the knowledge of chromosomal evolution in Passeriformes we analysed the karyotype of Glyphorynchus spirurus by classic and molecular cytogenetics methods. We show that Glyphorynchus spirurus has a 2n = 80 karyotype with a fundamental number (FN) of 84, similar to the avian putative ancestral karyotype (PAK). Glyphorynchus spirurus pair 1 was heteromorphic in the Tapajós population whereby the short arms varied in sizes, possibly due to a pericentric inversion, as described in other Furnariidae birds. FISH with the Histone H5 probe revealed a signal in the pericentromeric region of G. spirurus chromosome 5 and rDNA 18S showed interstitial signal in GSP-1. Chromosome painting with Gallus gallus (GGA) macrochromosomes 1–9 probes showed disruption of chromosome syntenies of GGA-1, 2 and 4 by fission in Glyphorynchus spirurus. Our results confirm that the GGA1 centric fission is a synapomorphic character for the phylogenetic branch composed of Strigiformes, Passeriformes, Columbiformes and Falconiformes. On the other hand, the GGA-2 fission is reported here for the first time in Passeriformes. Chromosome painting with BOE whole chromosome probes confirmed these rearrangements in Glyphorynchus spirurus revealed by Gallus gallus 1–9 probes, in addition to enabling the establishment of genome-wide homology map.