The complete chloroplast genome sequence of Quercus ningangensis and its phylogenetic implication

Quercus ningangensis is an economically and ecologically important tree species belonging to the family Fagaceae. In this study, the complete chloroplast (cp) genome of Q. ningangensis was sequenced and assembled, and 18 published cp genomes of Quercus were retrieved for genomic analyses (including sequence divergence, repeat elements, and structure) and phylogenetic inference. With this study, we found that complete cp genomes in Quercus are conserved, and we discovered a codon composition bias, which may be related to genomic content and genetic characteristics. In addition, we detected considerable structural variations in the expansion and contraction of inverted repeat regions. Six regions with relatively high variable (matK-rps16, psbC, ycf3 intron, rbcL, petA-psbJ, and ycf1) were detected by conducting a sliding window analysis, which has a high potential for developing effective genetic markers. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods resulted in a robust phylogenetic tree of Quercus with high resolution for nearly all identified nodes. The phylogenetic relationships showed that the phylogenetic position of Q. ningangensis was located between Q. sichourensis and Q. acuta. The results of this study contribute to future research into the phylogenetic evolution of Quercus section Cyclobalanopsis (Fagaceae).

Hot Spots of Phytoene Desaturase from Rhodobacter Sphaeroides Influencing the Desaturation of Phytoene

Phytoene desaturase (CrtI, E.C. 1.3.99.31) shows variable desaturation activity, thereby introducing different numbers of conjugated double bonds (CDB) into the substrate phytoene. In particular, Rhodobacter sphaeroides CrtI is known to introduce additional 6 CDBs into the phytoene with 3 CDBs, generating neurosporene with 9 CDBs. Although in-depth studies have been conducted on the function and phylogenetic evolution of CrtI, little information exists on its range of CDB-introducing capabilities. We investigated the relationship between the structure and CDB-introducing capability of CrtI. CrtI of R. sphaeroides KCTC 12085 was randomly mutagenized to produce carotenoids of different CDBs (neurosporene for 9 CDBs, lycopene for 11 CDBs, and 3,4-didehydrolycopene for 13 CDBs). From six CrtI mutants producing different ratios of neurosporene/lycopene/3,4-didehydrolycopene, three amino acids (Leu163, Ala171, and Ile454) were identified that significantly determined carotenoid profiles. While the L163P mutation was responsible for producing neurosporene as a major carotenoid, A171P and I454T produced lycopene as the major product. Finally, according to the in silico model, the mutated amino acids are gathered in the membrane-binding domain of CrtI, which could distantly influence the FAD binding region and consequently the degree of desaturation in phytoene.

Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes

An adult Sinocyclocheilus maitianheensis, a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were annotated. Based on a comparative phylogenetic analysis of five Sinocyclocheilus species and other five representative vertebrates with published genome sequences, we found that S. maitianheensis is close to Sinocyclocheilus anophthalmus (a cave-restricted species with similar locality). Moreover, the assembled genomes of S. maitianheensis and other four Sinocyclocheilus counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted Sinocyclocheilus species. In summary, we report the first genome assembly of S. maitianheensis, which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish.

Association of Sequence types, Antimicrobial Resistance and Virulence Genes in India isolates of Klebsiella pneumoniae: A Comparative Genomics Study

Klebsiella pneumoniae is an important ESKAPE pathogen that causes sepsis, urinary tract infections, peritonitis, intraabdominal abscesses and upper respiratory infections. The strains exhibiting multidrug resistance and hypervirulence are priority pathogens for which immediate treatment and dissemination prevention strategies are required. The hypervirulent drug resistant K. pneumoniae is associated with high mortality rates. Numbers of environmental strains also have acquired virulence genes. Hence to gain a better understanding of the spread of antimicrobial resistant genes across the country over 10 years and to delineate environmental and clinical K. pneumoniae, a comparative genomics investigation was made. This is the first comparative genomic study using India isolates of K. pneumoniae, which includes publicly available WGS of 144 clinical and 9 environmental strains collected during 2010–2020. The blaCTX-M-15 was widely distributed in clinical isolates since 2013 and increased over time from 5 % to 30 %. The co-existence of blaNDM and blaOXA was observed in 22 % of clinical strains. Diverse serotypes were found among the 153 K. pneumoniae isolates, of which, K51 (28%) and K64 (21.56%) were majorly found. Most of the K51 isolates belong to ST231 (93.02 %). And more than 50% of KL51 strains were found to have both rmpA and magA. The number of associated virulence genes (rmpA, magA, entB, ybtS, iutA, alls,) appeared to be higher in ST231-KL51 and ST23-KL1 isolates. Of greatest concern, these virulence genes are observed in environmental strains aswell. More than 97% of clinical strains have ybtS, iutA genes. Importantly, 98% of ESBL and 62% of carbapenamase isolates harbored ybtS, iutA and rmpA, magA respectively. The IncF conjugative plasmids are predominant in K. pneumoniae, which contribute to the spread of antimicrobial resistant and virulence genes. The increasing trend in hypervirulent strains was observed from 2017. The phylogenetic analysis separates the environmental from clinical strains and is characterized by uncommon STs and serotypes. Thus, the study illustrates the K. pneumoniae genomic surveillance in India representing the phylogenetic evolution, STs, AMR, virulence, serotype to provide more attention for immediate treatment and preventing the dissemination of K. pneumoniae.

Association of Sequence types, Antimicrobial Resistance and Virulence Genes in India isolates of Klebsiella pneumoniae: A Comparative Genomics Study

Klebsiella pneumoniae is an important ESKAPE pathogen that causes sepsis, urinary tract infections, peritonitis, intraabdominal abscesses and upper respiratory infections. The strains exhibiting multidrug resistance and hypervirulence are priority pathogens for which immediate treatment and dissemination prevention strategies are required. The hypervirulent drug resistant K. pneumoniae is associated with high mortality rates. Numbers of environmental strains also have acquired virulence genes. Hence to gain a better understanding of the spread of antimicrobial resistant genes across the country over 10 years and to delineate environmental and clinical K. pneumoniae, a comparative genomics investigation was made. This is the first comparative genomic study using India isolates of K. pneumoniae, which includes publicly available WGS of 144 clinical and 9 environmental strains collected during 2010–2020. The blaCTX-M-15 was widely distributed in clinical isolates since 2013 and increased over time from 5 % to 30 %. The co-existence of blaNDM and blaOXA was observed in 22 % of clinical strains. Diverse serotypes were found among the 153 K. pneumoniae isolates, of which, K51 (28%) and K64 (21.56%) were majorly found. Most of the K51 isolates belong to ST231 (93.02 %). And more than 50% of KL51 strains were found to have both rmpA and magA. The number of associated virulence genes (rmpA, magA, entB, ybtS, iutA, alls,) appeared to be higher in ST231-KL51 and ST23-KL1 isolates. Of greatest concern, these virulence genes are observed in environmental strains aswell. More than 97% of clinical strains have ybtS, iutA genes. Importantly, 98% of ESBL and 62% of carbapenamase isolates harbored ybtS, iutA and rmpA, magA respectively. The IncF conjugative plasmids are predominant in K. pneumoniae, which contribute to the spread of antimicrobial resistant and virulence genes. The increasing trend in hypervirulent strains was observed from 2017. The phylogenetic analysis separates the environmental from clinical strains and is characterized by uncommon STs and serotypes. Thus, the study illustrates the K. pneumoniae genomic surveillance in India representing the phylogenetic evolution, STs, AMR, virulence, serotype to provide more attention for immediate treatment and preventing the dissemination of K. pneumoniae.

Association of Sequence types, Antimicrobial Resistance and Virulence Genes in India isolates of Klebsiella pneumoniae: A Comparative Genomics Study

Klebsiella pneumoniae is an important ESKAPE pathogen that causes sepsis, urinary tract infections, peritonitis, intraabdominal abscesses and upper respiratory infections. The strains exhibiting multidrug resistance and hypervirulence are priority pathogens for which immediate treatment and dissemination prevention strategies are required. The hypervirulent drug resistant K. pneumoniae is associated with high mortality rates. Numbers of environmental strains also have acquired virulence genes. Hence to gain a better understanding of the spread of antimicrobial resistant genes across the country over 10 years and to delineate environmental and clinical K. pneumoniae, a comparative genomics investigation was made. This is the first comparative genomic study using India isolates of K. pneumoniae, which includes publicly available WGS of 144 clinical and 9 environmental strains collected during 2010–2020. The blaCTX-M-15 was widely distributed in clinical isolates since 2013 and increased over time from 5 % to 30 %. The co-existence of blaNDM and blaOXA was observed in 22 % of clinical strains. Diverse serotypes were found among the 153 K. pneumoniae isolates, of which, K51 (28%) and K64 (21.56%) were majorly found. Most of the K51 isolates belong to ST231 (93.02 %). And more than 50% of KL51 strains were found to have both rmpA and magA. The number of associated virulence genes (rmpA, magA, entB, ybtS, iutA, alls,) appeared to be higher in ST231-KL51 and ST23-KL1 isolates. Of greatest concern, these virulence genes are observed in environmental strains aswell. More than 97% of clinical strains have yersinibactin (ybtS), aerobactin (iutA) genes. Importantly, 98% of ESBL and 62% of carbapenamasen isolates harboured ybtS, iutA and rmpA, magA respectively. The IncF conjugative plasmids are predominant in K. pneumoniae, which contribute to the spread of AMR, and virulence genes. The increasing trend in hypervirulent strains was observed from 2017. The phylogenetic analysis separates the environmental from clinical strains and is characterized by uncommon STs and serotypes. Thus, the study illustrates the K. pneumoniae genomic surveillance in India representing the phylogenetic evolution, STs, AMR, virulence, serotype to provide more attention for immediate treatment and preventing the dissemination of K. pneumoniae.

The late Berriasian early evolutionary burst of the Orbitolinidae: New insights into taxonomy, origin, diversification and phylogeny of the family based on data from eastern Serbia

New data from the Carpatho-Balkanides of eastern Serbia evidence the more or less near-simultaneous "explosive" first appearances of several genera of the Orbitolinidae in the late Berriasian. Most of the observed taxa were previously recorded from strata not older than the Late Hauterivian (= classical Urgonian of southeastern France), evidence that these ages refer to local first appearance data. The diversified assemblage from Serbia includes representatives of the subfamilies Dictyoconinae: genera Cribellopsis ARNAUD-VANNEAU, Montseciella CHERCHI & SCHROEDER, Orbitolinopsis HENSON, Urgonina FOURY & MOULLADE, Valserina SCHROEDER & CONRAD, Vanneauina SCHLAGINTWEIT, and Dictyorbitolininae: genus Paracoskinolina MOULLADE. Representatives of the Orbitolininae (with complex embryo) have not been observed. They appeared later in the fossil record seemingly during the Late Hauterivian-early Barremian. All together 17 taxa are reported, of which three in open nomenclature. A new species is described as Cribellopsis sudari n. sp. The majority of the observed species display medium- to high-conical tests and a rather simple exoskeleton lacking horizontal partitions (rafters). The new data contradict a phylogenetic evolution of distinct genera displaying different internal test structures one after the other in time (= ancestor-descendant relationships) as postulated by some authors. The explosive radiation ("early burst") of the Orbitolinidae in the late Berriasian is accompanied by the first appearance date of several other large benthic foraminifera including mostly agglutinating (e.g., Ammocycloloculina, Choffatella, Drevennia, Eclusia, Moulladella, Pfenderina, Pseudotextulariella) but also complex porcelaneous taxa (Pavlovcevina) providing evidence for a bioevent in this time period that exceeds the number of taxa originating in the previous (Tithonian) and the following stage (Valanginian). The early evolutionary history of the Orbitolinidae can be considered a classical example of adaptive radiation within the clade's history.

Architecture Insight of Bifidobacterial α-L-Fucosidases

Fucosylated carbohydrates and glycoproteins from human breast milk are essential for the development of the gut microbiota in early life because they are selectively metabolized by bifidobacteria. In this regard, α-L-fucosidases play a key role in this successful bifidobacterial colonization allowing the utilization of these substrates. Although a considerable number of α-L-fucosidases from bifidobacteria have been identified by computational analysis, only a few of them have been characterized. Hitherto, α-L-fucosidases are classified into three families: GH29, GH95, and GH151, based on their catalytic structure. However, bifidobacterial α-L-fucosidases belonging to a particular family show significant differences in their sequence. Because this fact could underlie distinct phylogenetic evolution, here extensive similarity searches and comparative analyses of the bifidobacterial α-L-fucosidases identified were carried out with the assistance of previous physicochemical studies available. This work reveals four and two paralogue bifidobacterial fucosidase groups within GH29 and GH95 families, respectively. Moreover, Bifidobacterium longum subsp. infantis species exhibited the greatest number of phylogenetic lineages in their fucosidases clustered in every family: GH29, GH95, and GH151. Since α-L-fucosidases phylogenetically descended from other glycosyl hydrolase families, we hypothesized that they could exhibit additional glycosidase activities other than fucosidase, raising the possibility of their application to transfucosylate substrates other than lactose in order to synthesis novel prebiotics.

Next-Generation Sequencing (NGS) in COVID-19: A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology

This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.

Intraspecific Genetic Distance and Phylogenetic Evolution of Schizothorax Plagiostomus Inferred from Mitochondrial D-Loop Sequences

The fish in the genus Schizothorax from the Cyprinidae family live in high-altitude Rivers andstreams, are threatened by various anthropogenic stressors. This study aims to characterize S. plagiostomus across Pakistan and throughout the world available on NCBI using the mitochondrial D-loop region, and in particular, to assess the degree of intra-specific pairwise distance among these sequences, as well as to establish their phylogenetic relationships. The percent overall nucleotide composition was 32.6% (A), 33.6% (T), 19.8% (C), and 14.0% (G), which infers that S. plagiostomus control regions is AT-rich (66.2%) and poor in G contents. The mean pair-wise intra-specific nucleotide diversity (Pi)of all the S. plagiostomus was 0.022. While, the inter-specific nucleotide diversity of all the Schizothorax species was 0.049. D-loop sequences for intra-specific variations revealed 765 sites were invariable and 10 were variable, 8 parsimony informative sites and only 2 were singletons. The overall transition/transversion ratio is R = 7.135. Three domains in S. plagiostomus were observed, namely, the termination associated sequence (TAS) domain, the central conserved sequence block (CSB) domain, and the conserved sequence block (CSB) domain. No substitution saturation was detected as an Iss value was significantly (𝑃< 0.001) lower than the Iss.c in all cases indicating the suitability of the data for phylogenetic analysis. This study signifies the importance of the control region for the genetic analysis of S. plagiostomus and also provides a hypothesis of their phylogenetic relationships.