The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across ...millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
•High Throughput Sequencing techniques have revolutionized many fields of Biology, including Virology.•More and easier access to sequence information provides new possibilities for analyzing virus populations.•For RNA viruses, mutation rates are of similar magnitude than error rates in HTS technologies.•There are many computer programs specifically designed for analyzing HTS data of virus populations.•We review analytical and methodological advances and some major applications of HTS of virus populations.
Although the widespread use of nanoparticles has been reported in various fields, the toxic mechanisms of molecular regulation involved in the alfalfa treated by nanomaterials is still in the ...preliminary research stage. In this study, Bara 310 SC (Bara, tolerant genotype) and Gold Empress (Gold, susceptible genotype) were used to investigate how the leaves of alfalfa interpret the physiological responses to graphene stress based on metabolome and transcriptome characterizations. Herein, graphene at different concentrations (0, 1% and 2%, w/w) were selected as the analytes. Physiological results showed antioxidant defence system and photosynthesis was significantly disturbed under high environmental concentration of graphene. With Ultra high performance liquid chromatography electrospray tandem mass spectrometry (UPLC-ESI-MS/MS), 406 metabolites were detected and 62/13 and 110/58 metabolites significantly changed in the leaves of Gold/Bara under the 1% and 2%-graphene treatments (w/w), respectively. The most important metabolites which were accumulated under graphene stress includes amino acids, flavonoids, organic acids and sugars. Transcriptomic analysis reveals 1125 of core graphene-responsive genes in alfalfa that was robustly differently expressed in both genotypes. And differential expression genes (DEGs) potentially related to photosynthetic enzymes, antioxidant enzymes, amino acids metabolism, and sucrose and starch metabolic which finding was supported by the metabolome study. Gold was more disturbed by graphene stress at both transcriptional and metabolic levels, since more stress-responsive genes/metabolites were identified in Gold. A comprehensive analysis of transcriptomic and metabolomic data highlights the important role of amino acid metabolism and nicotinate and nicotinamide metabolism pathways for graphene tolerance in alfalfa. Our study provide necessary information for better understanding the phytotoxicity molecular mechanism underlying nanomaterials tolerance of plant.
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•Data on the phytotoxicity of graphene to alfalfa in soil were provided.•Integrating omics results revealed molecular mechanisms underlying plant response.•Results provide accurately characterize the risk of these materials in the environment.•These findings help to find sustainable nano-enabled plant protection strategies.
Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups.
, a species of Corbiculidae, plays an important role in mangrove ecology. It is ...highly adaptable and can withstand environmental pollution and microbial infections. However, there is no reference genome or full-length transcriptome available for
. This impedes the study of the biological functions of its different tissues because transcriptome research requires reference genome or full-length transcriptome as a reference to improve accuracy. In this study, we applied a combination of Illumina and PacBio single-molecule real-time sequencing technologies to sequence the full-length transcriptomes of
tissues. Transcriptomes of nine samples obtained from three tissues (hepatopancreas, gill, and muscle) were sequenced using Illumina. Furthermore, we obtained 87,310 full-length reads non-chimeric sequences. After removing redundancy, 22,749 transcripts were obtained. The average Q score of 30 was 94.48%. In total, 271 alternative splicing events were predicted. There were 14,496 complete regions and 3,870 lncRNAs. Differential expression analysis revealed tissue-specific physiological functions. The gills mainly express functions related to filtration, metabolism, identifying pathogens and activating immunity, and neural activity. The hepatopancreas is the main tissue related to metabolism, it also involved in the immune response. The muscle mainly express functions related to muscle movement and control, it contains more energy metabolites that gill and hepatopancreas. Our research provides an important reference for studying the gene expression of
under various environmental stresses. Moreover, we present a reliable sequence that will provide an excellent foundation for further research on
We present evidence that both corepressors SMRT and N‐CoR exist in large protein complexes with estimated sizes of 1.5–2 MDa in HeLa nuclear extracts. Using a combination of conventional and ...immunoaffinity chromatography, we have successfully isolated a SMRT complex and identified histone deacetylase 3 (HDAC3) and transducin (β)‐like I (TBL1), a WD‐40 repeat‐containing protein, as the subunits of the purified SMRT complex. We show that the HDAC3‐containing SMRT and N‐CoR complexes can bind to unliganded thyroid hormone receptors (TRs) in vitro. We demonstrate further that in Xenopus oocytes, both SMRT and N‐CoR also associate with HDAC3 in large protein complexes and that injection of antibodies against HDAC3 or SMRT/N‐CoR led to a partial relief of repression by unliganded TR/RXR. These findings thus establish both SMRT and N‐CoR complexes as bona fide HDAC‐containing complexes and shed new light on the molecular pathways by which N‐CoR and SMRT function in transcriptional repression.
is an essential timber species that provide 20%-30% raw materials for China's timber industry. Although a few transcriptomes have been published in
, full-length mRNA transcripts and regulatory ...mechanisms behind the cellulose and lignin biosynthesis have not been thoroughly investigated. Here, PacBio Iso-seq and RNA-seq analyses were adapted to identify the full-length and differentially expressed transcripts along a developmental gradient from apex to base of
shoots. A total of 48,846 high-quality full-length transcripts were obtained, of which 88.0% are completed transcriptome based on benchmarking universal single-copy orthologs (BUSCO) assessment. Along stem developmental gradient, 18,714 differentially expressed genes (DEGs) were detected. Further, 28 and 125 DEGs were identified as enzyme-coding genes of cellulose and lignin biosynthesis, respectively. Moreover, 57 transcription factors (TFs), including
and
, were identified to be involved in the regulatory network of cellulose and lignin biosynthesis through weighted gene co-expression network analysis (WGCNA). These TFs are composed of a comparable regulatory network of secondary cell wall formation in angiosperms, revealing a similar mechanism may exist in gymnosperms. Further, through qRT-PCR, we also investigated eight specific TFs involved in compression wood formation. Our findings provide a comprehensive and valuable source for molecular genetics breeding of
and will be beneficial for molecular-assisted selection.
Summary
Following earlier incomplete and fragmented versions of a genome sequence for the grey mould Botrytis cinerea, a gapless, near‐finished genome sequence for B. cinerea strain B05.10 is ...reported. The assembly comprised 18 chromosomes and was confirmed by an optical map and a genetic map based on approximately 75 000 single nucleotide polymorphism (SNP) markers. All chromosomes contained fully assembled centromeric regions, and 10 chromosomes had telomeres on both ends. The genetic map consisted of 4153 cM and a comparison of the genetic distances with the physical distances identified 40 recombination hotspots. The linkage map also identified two mutations, located in the previously described genes Bos1 and BcsdhB, that conferred resistance to the fungicides boscalid and iprodione. The genome was predicted to encode 11 701 proteins. RNAseq data from >20 different samples were used to validate and improve gene models. Manual curation of chromosome 1 revealed interesting features, such as the occurrence of a dicistronic transcript and fully overlapping genes in opposite orientations, as well as many spliced antisense transcripts. Manual curation also revealed that the untranslated regions (UTRs) of genes can be complex and long, with many UTRs exceeding lengths of 1 kb and possessing multiple introns. Community annotation is in progress.
SUMMARY
The assembly and scaffolding of plant crop genomes facilitate the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato (Solanum lycopersicum) has been ...improved through the introgression of genetic material from related wild species, including resistance to pandemic strains of tobacco mosaic virus (TMV) from Solanum peruvianum. Here we applied PacBio HiFi and ONT Nanopore sequencing to develop independent, highly contiguous and complementary assemblies of an inbred TMV‐resistant tomato variety. We show specific examples of how HiFi and ONT datasets can complement one another to improve assembly contiguity. We merged the HiFi and ONT assemblies to generate a long‐read‐only assembly where all 12 chromosomes were represented as 12 contiguous sequences (N50 = 68.5 Mbp). This chromosome scale assembly did not require scaffolding using an orthogonal data type. The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato genome assemblies that made use of genetic maps and Hi‐C for scaffolding. Our long‐read‐only assembly reveals that a complex series of structural variants linked to the TMV resistance gene likely contributed to linkage drag of a 64.1‐Mbp region of the S. peruvianum genome during tomato breeding. Through marker studies and ONT‐based comprehensive haplotyping we show that this minimal introgression region is present in six cultivated tomato hybrid varieties developed in three commercial breeding programs. Our results suggest that complementary long read technologies can facilitate the rapid generation of near‐complete genome sequences.
Significance Statement
Modern cultivated tomato (Solanum lycopersicum) hybrids are resistant to economically devastating pandemic strains of tobacco mosaic virus (TMV), due to an introgressed resistance gene from Solanum peruvianum. Our ‘long‐read‐only’ tomato genome assembly reveals, for the first time, that a complex series of structural variants in the TMV resistance locus likely contributed to a massive linkage drag of a 64.1‐Mbp region of ‘wild DNA’ from S. peruvianum during tomato breeding.
Abstract
The Silencing Mediator of Retinoid and Thyroid Hormone Receptors (SMRT) is a nuclear corepressor, regulating the transcriptional activity of many transcription factors critical for metabolic ...processes. While the importance of the role of SMRT in the adipocyte has been well-established, our comprehensive understanding of its in vivo function in the context of homeostatic maintenance is limited due to contradictory phenotypes yielded by prior generalized knockout mouse models. Multiple such models agree that SMRT deficiency leads to increased adiposity, although the effects of SMRT loss on glucose tolerance and insulin sensitivity have been variable. We therefore generated an adipocyte-specific SMRT knockout (adSMRT-/-) mouse to more clearly define the metabolic contributions of SMRT. In doing so, we found that SMRT deletion in the adipocyte does not cause obesity—even when mice are challenged with a high-fat diet. This suggests that adiposity phenotypes of previously described models were due to effects of SMRT loss beyond the adipocyte. However, an adipocyte-specific SMRT deficiency still led to dramatic effects on systemic glucose tolerance and adipocyte insulin sensitivity, impairing both. This metabolically deleterious outcome was coupled with a surprising immune phenotype, wherein most genes differentially expressed in the adipose tissue of adSMRT-/- mice were upregulated in pro-inflammatory pathways. Flow cytometry and conditioned media experiments demonstrated that secreted factors from knockout adipose tissue strongly informed resident macrophages to develop a pro-inflammatory, MMe (metabolically activated) phenotype. Together, these studies suggest a novel role for SMRT as an integrator of metabolic and inflammatory signals to maintain physiological homeostasis.
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