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Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ—trnG-GCC, rbcL—accD, and rpl32—trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.

Diverse candidate antibodies are needed to successfully identify therapeutic and diagnostic applications. The variable domain of IgNAR (VNAR), a shark single-domain antibody, has attracted attention owing to its favorable physicochemical properties. The phage display method used to screen for optimal VNARs loses sequence diversity because of the bias caused by the differential ease of protein expression in Escherichia coli. Here, we investigated a VNAR selection method that combined panning with various selection pressures and next-generation sequencing (NGS) analyses to obtain additional candidates. Drawing inspiration from the physiological conditions of sharks and the physicochemical properties of VNARs, we examined the effects of NaCl and urea concentrations, low temperature, and preheating at the binding step of panning. VNAR phage libraries generated from Japanese topeshark (Hemitriakis japanica) were enriched under these conditions. We then performed NGS analysis and attempted to select clones that were specifically enriched under each panning condition. The identified VNARs exhibited higher reactivity than those obtained by panning without selection pressure. Additionally, they possess physicochemical properties that reflect their respective selection pressures. These results can greatly enhance our understanding of VNAR properties and offer guidance for the screening of high-quality VNAR clones that are present at low frequencies.

Caladiums are promising colorful foliage plants due to their dazzling colors of the leaves, veins, stripes, and patches, which are often cultivated in pots or gardens as decorations. Four wild species, including C. bicolor, C. humboldtii, C. praetermissum, and C. lindenii, were employed in this study, where their chloroplast (cp) genomes were sequenced, assembled, and annotated via high-throughput sequencing. The whole cp genome size ranged from 162,776 bp to 168,888 bp, and the GC contents ranged from 35.09% to 35.91%. Compared with the single large copy (LSC) and single small copy (SSC) regions, more conserved sequences were identified in the inverted repeat regions (IR). We further analyzed the different region borders of nine species of Araceae and found the expansion or contraction of IR/SSC regions might account for the cp genome size variation. Totally, 131 genes were annotated in the cp genomes, including 86 protein-coding genes (PCGs), 37 tRNAs, and eight rRNAs. The effective number of codons (ENC) values and neutrality plot analyses provided the foundation that the natural selection pressure could greatly affect the codon preference. The GC3 content was significantly lower than that of GC1 and GC2, and codons ending with A/U had higher usage preferences. Finally, we conducted phylogenetic relationship analysis based on the chloroplast genomes of twelve species of Araceae, in which C. bicolor and C. humboldtii were grouped together, and C. lindenii was furthest from the other three Caladium species occupying a separate branch. These results will provide a basis for the identification, development, and utilization of Caladium germplasm.

Dengue virus (DENV) is an arbovirus whose transmission cycle involves disparate hosts: humans and mosquitoes. The error-prone nature of viral RNA replication drives the high mutation rates, and the consequently high genetic diversity affects viral fitness over this transmission cycle. A few studies have been performed to investigate the intrahost genetic diversity between hosts, although their mosquito infections were performed artificially in the laboratory setting. Here, we performed whole-genome deep sequencing of DENV-1 (n = 11) and DENV-4 (n = 13) derived from clinical samples and field-caught mosquitoes from the houses of naturally infected patients, in order to analyze the intrahost genetic diversity of DENV between host types. Prominent differences in DENV intrahost diversity were observed in the viral population structure between DENV-1 and DENV-4, which appear to be associated with differing selection pressures. Interestingly, three single amino acid substitutions in the NS2A (K81R), NS3 (K107R), and NS5 (I563V) proteins in DENV-4 appear to be specifically acquired during infection in Ae. aegypti mosquitoes. Our in vitro study shows that the NS2A (K81R) mutant replicates similarly to the wild-type infectious clone-derived virus, while the NS3 (K107R), and NS5 (I563V) mutants have prolonged replication kinetics in the early phase in both Vero and C6/36 cells. These findings suggest that DENV is subjected to selection pressure in both mosquito and human hosts. The NS3 and NS5 genes may be specific targets of diversifying selection that play essential roles in early processing, RNA replication, and infectious particle production, and they are potentially adaptive at the population level during host switching.

Canine parvovirus (CPV) is a major pathogen in canines, with a high mortality rate in unvaccinated puppies. CPV is traditionally classified into three antigenic variants (CPV-2a, CPV-2b and CPV-2c) based on the amino acid sequence of the VP2 protein. Currently, various mutations are described in the receptor-binding area or in the regions of greatest antigenicity of the VP2 protein, giving rise to new viral variants that are capable of immunological escape, affecting the protective immunity of traditional vaccines. In the present study, a molecular characterization of the VP2 gene was performed, which included phylogenetic analysis, amino acid characterization and determination of selection pressures. Blood samples were initially collected from canine patients with clinical signs of gastrointestinal infection, of which 69 were positive for CPV as measured by means of PCR and 18 samples were selected for the amplification of the complete VP2 gene. The analysis revealed a higher rate of CPV-2c-positive patients compared to CPV-2b. Furthermore, the amino acid characterization of VP2 indicated mutations in the regions of highest antigenicity previously described in the literature (CPV-2b: 297 and 324; CPV-2c: 440), as well as others not previously documented (CPV-2b: 514; CPV-2c: 188, 322, 379, 427 and 463). Our analysis of selection pressure showed that the VP2 gene is under negative selection. However, positive selection point sites were identified, both in CPV-2c (324, 426 and 440) and CPV-2b (297 and 324), at sites that have been associated with evasion of the immune response via antigenic drift, which possibly has implications for the protective immunity generated by traditional vaccines.

Blood typing has revolutionized the field of medical science since its discovery about a century ago. Besides its established role in life-saving blood transfusions, researchers have always been curious about the relationship between blood groups and human ailments. The effect of blood groups on disease outcomes, susceptibility, and mortality has been widely explored. According to a particular school of thought, the endemicity of diseases shapes the distribution of blood group frequency in human populations and exert selection pressure favoring one blood type over another. Here we discuss the scope and association of different blood groups in the context of malaria.

The present study reports the detection and molecular characterisation of rotavirus C (RVC) in sloth bears (Melursus ursinus) rescued from urban areas in India. Based on an RVC VP6 gene-targeted diagnostic RT-PCR assay, 48.3% (42/87) of sloth bears tested positive for RVC infection. The VP6, VP7, and NSP4 genes of three sloth bear RVC isolates (UP-SB19, 21, and 37) were further analysed. The VP6 genes of RVC UP-SB21 and 37 isolates were only 37% identical. The sequence identity, TM-score from structure alignment, and selection pressure (dN/dS) of VP6 UP-SB37 with pig and human RVCs isolates were (99.67%, 0.97, and 1.718) and (99.01%, 0.93, and 0.0340), respectively. However, VP6 UP-SB21 has an identity, TM-score, and dN/dS of (84.38%, 1.0, and 0.0648) and (99.63%, 1.0, and 3.7696) with human and pig RVC isolates, respectively. The VP7 genes from UP-SB19 and 37 RVC isolates were 79.98% identical and shared identity, TM-score, and dN/dS of 88.4%, 0.76, and 5.3210, along with 77.98%, 0.77, and 4.7483 with pig and human RVC isolates, respectively. The NSP4 gene of UP-SB37 RVC isolates has an identity, TM-score, and dN/dS of 98.95%, 0.76, and 0.2907, along with 83.12%, 0.34, and 0.2133 with pig and human RVC isolates, respectively. Phylogenetic analysis of the nucleotide sequences of the sloth bear RVC isolates assigned the isolate UP-SB37 to genotype G12, I2 for RVC structural genes VP7 and VP6, and E1 for NSP4 genes, respectively, while isolates UP-SB19 and UP-SB21 were classified as genotype G13 and GI7 based on the structural gene VP7, respectively. The study suggests that the RVCs circulating in the Indian sloth bear population are highly divergent and might have originated from pigs or humans, and further investigation focusing on the whole genome sequencing of the sloth bear RVC isolate may shed light on the virus origin and evolution.

Sugarcane mosaic virus (SCMV) one of the causative viruses of mosaic disease in sugarcane occurs in sugarcane growing countries worldwide. India is the second largest sugarcane producing country and genome of SCMV from India has not been characterized so far. Hence detailed studies were carried out to characterize the virus isolates based on its complete genome. Comparative genome analyses of five new isolates were performed with previously reported SCMV full genome sequences of isolates infecting sugarcane, maize, sorghum and Canna. Sequence identity matrix and phylogenetic analyses clearly represented that Indian isolates are closely related to sugarcane infecting isolates reported from Australia, Argentina, China and Iran and they diverged as a separate subgroup from other reported maize infecting isolates from Mexico, China, Ohio, Spain, Germany, Iran, Ethiopia, Kenya and Eucador. Selection pressure analysis clearly depicted the predomination of strong purifying selection throughout the viral genome, and strongest in CI and HC-Pro gene. Evidence for few positively selected sites was identified in all the cistrons except in 6 K1 and Nib rep. Among the genomic region, CI gene has exhibited comparatively more recombination hotspots followed by HC-Pro unlike other reported isolates. As the cultivation of sugarcane first originated in India, our results from the recombination events strongly suggest that Indian SCMV populations contribute for the emergence of upcoming new recombinant SCMV isolates not only within the sugarcane isolates but also with maize infecting isolates of SCMV in other countries irrespective of geographic origin and host type.

• Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. • Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. • Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. • Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.

Background The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. Results We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events—transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. Conclusions We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.