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1.
Gene ; 711: 143932, 2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31202905

RESUMO

Hexokinase (HXK) is a multifunctional protein that serves as a sugar sensor for glucose signaling and a catalyst for glycolysis. It has been well studied in many species, however, there is far less information about this family in pear. To investigate the roles of HXK in the growth and development of pear fruit, we performed a genome-wide analysis and identified the HXK gene family members in pear. In addition, we functionally characterized a glucose sensor gene, PbHXK1, in P. bretschneideri. In total, 10 HXK genes were identified in pear, and a multiple sequence alignment and phylogenetic analysis showed that PbHXK1 is a Type B HXK that contains four conserved domains, phosphate 1 and 2, sugar binding and adenosine, which are specific to plant HXKs and essential for enzymatic functions. A qRT-PCR analysis revealed that the relative expression levels of PbHXK1 were negatively correlated with sugar content but significantly positively correlated with HXK activity during pear fruit development. Furthermore, the overexpression of PbHXK1 in tomatoes significantly enhanced the HXK activity and decreased the sugar content. In addition, the growth of transgenic tomato plants overexpressing PbHXK1 was inhibited, leading to shortened internodes and smaller leaves. Thus, in pear, PbHXK1 encodes HXK, which regulated the sugar content in fruit and affected the growth and development of plants.


Assuntos
Hexoquinase/genética , Hexoquinase/metabolismo , Pyrus/crescimento & desenvolvimento , Sequenciamento Completo do Genoma/métodos , Sítios de Ligação , Regulação Enzimológica da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Hexoquinase/química , Família Multigênica , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Ligação Proteica , Pyrus/enzimologia , Pyrus/genética , Açúcares/metabolismo
2.
J Microbiol ; 57(8): 655-660, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31187415

RESUMO

A Gram-negative, aerobic, short-rod-shaped, motile (with a terminal flagellum), non-spore-forming bacterium, designated strain 85T, was isolated from a surface-sterilized bark of Sonneratia caseolaris collected from Qinzhou in Guangxi, China and was analyzed using a polyphasic approach to determine its taxonomic position. Strain 85T grew optimally in the presence of 1-2% (w/v) NaCl at 30°C and pH 6.0-7.0. Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 85T belonged to the genus Fulvimarina and shared the highest 16S rRNA gene sequence similarity with Fulvimarina pelagi HTCC2506T (96.16%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and ubiquinone Q-10 was the predominant respiratory lipoquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, three unidentified phospholipids and six unidentified lipids. The major fatty acid was C18:1ω7c. The DNA G+C content of strain 85T was 65.4 mol%, and the average nucleotide identity and estimated DDH values between strain 85T and the type strain of Fulvimarina pelagi HTCC2506T were 77.3% and 21.7%, respectively. Based on the phylogenetic, phenotypic, and chemotaxonomic analyses, strain 85T should be considered as a novel species of the genus Fulvimarina with the proposed name Fulvimarina endophytica sp. nov., and its type strain is 85T (= KCTC 62717T = CGMCC 1.13665T).


Assuntos
Alphaproteobacteria/classificação , Endófitos/classificação , Lythraceae/microbiologia , Casca de Planta/microbiologia , Alphaproteobacteria/genética , Alphaproteobacteria/crescimento & desenvolvimento , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana/métodos , Composição de Bases , China , DNA Bacteriano/genética , Endófitos/genética , Endófitos/crescimento & desenvolvimento , Endófitos/isolamento & purificação , RNA Ribossômico 16S/genética , Sequenciamento Completo do Genoma/métodos
3.
J Microbiol ; 57(8): 676-687, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31201724

RESUMO

Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmic-phase culture, and elongated spirals during incubation with mitomycin or in aged culture. Growth characteristics of strain IMCC1322 were further evaluated based on genomic information; proteorhodopsin (PR), carbon monoxide dehydrogenase, and dimethylsulfoniopropionate (DMSP)-utilizing enzymes. IMCC1322 PR was characterized as a functional retinylidene protein that acts as a light-driven proton pump in the cytoplasmic membrane. However, the PR-dependent phototrophic potential of strain IMCC1322 was only observed under CO-inhibited and nutrient-limited culture conditions. A DMSP-enhanced growth response was observed in addition to cultures grown on C1 compounds like methanol, formate, and methane sulfonate. Strain IMCC1322 cultivation analysis revealed biogeochemical processes characteristic of the SAR116 group, a dominant member of the microbial community in euphotic regions of the ocean. The polyphasic taxonomy of strain IMCC1322 is given as Candidatus Puniceispirillum marinum, and was confirmed by chemotaxonomic tests, in addition to 16S rRNA phylogeny and cultivation analyses.


Assuntos
Alphaproteobacteria , RNA Ribossômico 16S/genética , Rodopsinas Microbianas , Água do Mar/microbiologia , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/crescimento & desenvolvimento , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana/métodos , DNA Bacteriano/genética , República da Coreia , Rodopsinas Microbianas/química , Rodopsinas Microbianas/metabolismo , Compostos de Sulfônio/metabolismo , Sequenciamento Completo do Genoma/métodos
4.
Nat Commun ; 10(1): 2313, 2019 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-31127121

RESUMO

DNA double-strand breaks (DSBs) are among the most lethal types of DNA damage and frequently cause genome instability. Sequencing-based methods for mapping DSBs have been developed but they allow measurement only of relative frequencies of DSBs between loci, which limits our understanding of the physiological relevance of detected DSBs. Here we propose quantitative DSB sequencing (qDSB-Seq), a method providing both DSB frequencies per cell and their precise genomic coordinates. We induce spike-in DSBs by a site-specific endonuclease and use them to quantify detected DSBs (labeled, e.g., using i-BLESS). Utilizing qDSB-Seq, we determine numbers of DSBs induced by a radiomimetic drug and replication stress, and reveal two orders of magnitude differences in DSB frequencies. We also measure absolute frequencies of Top1-dependent DSBs at natural replication fork barriers. qDSB-Seq is compatible with various DSB labeling methods in different organisms and allows accurate comparisons of absolute DSB frequencies across samples.


Assuntos
Biologia Computacional/métodos , Quebras de DNA de Cadeia Dupla , Sequenciamento Completo do Genoma/métodos , Linhagem Celular Tumoral , Replicação do DNA/genética , DNA Topoisomerases Tipo I/metabolismo , Genoma Fúngico/genética , Genoma Humano/genética , Humanos , Saccharomycetales/genética
5.
BMC Genomics ; 20(1): 356, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072326

RESUMO

BACKGROUND: Cadmium (Cd)-containing chemicals can cause serious damage to biological systems. In animals and plants, Cd exposure can lead to metabolic disorders or death. However, for the most part the effects of Cd on specific biological processes are not known. DNA methylation is an important mechanism for the regulation of gene expression. In this study we examined the effects of Cd exposure on global DNA methylation in a living organism by whole-genome bisulfite sequencing (WGBS) using Drosophila melanogaster as model. RESULTS: A total of 71 differentially methylated regions and 63 differentially methylated genes (DMGs) were identified by WGBS. A total of 39 genes were demethylated in the Cd treatment group but not in the control group, whereas 24 showed increased methylation in the former relative to the latter. In most cases, demethylation activated gene expression: genes such as Cdc42 and Mekk1 were upregulated as a result of demethylation. There were 37 DMGs that overlapped with differentially expressed genes from the digital expression library including baz, Act5C, and ss, which are associated with development, reproduction, and energy metabolism. CONCLUSIONS: DNA methylation actively regulates the physiological response to heavy metal stress in Drosophila in part via activation of apoptosis.


Assuntos
Cádmio/toxicidade , Metilação de DNA , Drosophila melanogaster/crescimento & desenvolvimento , Drosophila melanogaster/metabolismo , Regulação da Expressão Gênica , Genoma , Estresse Oxidativo , Animais , Drosophila melanogaster/efeitos dos fármacos , Feminino , Genômica , Sulfitos/química , Sequenciamento Completo do Genoma/métodos
6.
Arch Virol ; 164(8): 2183-2186, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31119477

RESUMO

Enterovirus C96 (EV-C96) is a newer member of the species Enterovirus C. In this study, we determined the complete genome sequences of three EV-C96 isolates, one recovered from domestic sewage in 2013 and the other two isolated during surveillance of acute flaccid paralysis cases in 1991 and 2009, respectively. The complete genome sequences of these isolates were 75.6-84.2% identical to each other, 75.1-81.8% identical to the prototype strain, and 75.0-91.5% identical to other previously reported strains. Phylogenetic analysis of VP1 sequences revealed a high degree of genetic divergence among currently available EV-C96 sequences in the GenBank database, with an overall mean p-distance of 0.176. It is interesting to note that the 1991 strain 127/SD/CHN/1991 is the earliest EV-C96 isolate so far. Although EV-C96 is not frequently isolated during enterovirus surveillance, its great genetic diversity and the above findings suggest that this serotype has been circulating in China for many years.


Assuntos
Enterovirus Humano C/genética , Enterovirus Humano C/isolamento & purificação , Infecções por Enterovirus/virologia , Genoma Viral/genética , China , Humanos , Filogenia , RNA Viral/genética , Análise de Sequência de DNA/métodos , Sequenciamento Completo do Genoma/métodos
7.
Arch Virol ; 164(8): 2031-2047, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31123963

RESUMO

Newcastle disease virus (NDV) has a wide avian host range and a high degree of genetic variability, and virulent strains cause Newcastle disease (ND), a worldwide concern for poultry health. Although NDV has been studied in Nigeria, genetic information about the viruses involved in the endemicity of the disease and the transmission that likely occurs at the poultry-wildlife interface is still largely incomplete. Next-generation and Sanger sequencing was performed to provide complete (n = 73) and partial genomic sequence data (n = 38) for NDV isolates collected from domestic and wild birds in Nigeria during 2002-2015, including the first complete genome sequences of genotype IV and subgenotype VIh from the African continent. Phylogenetic analysis revealed that viruses of seven different genotypes circulated in that period, demonstrating high genetic diversity of NDV for a single country. In addition, a high degree of similarity between NDV isolates from domestic and wild birds was observed, suggesting that spillovers had occurred, including to three species that had not previously been shown to be susceptible to NDV infection. Furthermore, the first spillover of a mesogenic Komarov vaccine virus is documented, suggesting a previous spillover and evolution of this virus. The similarities between viruses from poultry and multiple bird species and the lack of evidence for host adaptation in codon usage suggest that transmission of NDV between poultry and non-poultry birds occurred recently. This is especially significant when considering that some viruses were isolated from species of conservation concern. The high diversity of NDV observed in both domestic and wild birds in Nigeria emphasizes the need for active surveillance and epidemiology of NDV in all bird species.


Assuntos
Animais Selvagens/virologia , Aves/virologia , Doença de Newcastle/virologia , Vírus da Doença de Newcastle/genética , Animais , Variação Genética/genética , Genômica/métodos , Genótipo , Nigéria , Filogenia , Aves Domésticas/virologia , Sequenciamento Completo do Genoma/métodos
8.
BMC Genomics ; 20(1): 375, 2019 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-31088347

RESUMO

BACKGROUND: Plant non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are abundant in higher plants. They have been reported to play an important role in various plant physiological processes, such as lipid transfer, signal transduction, and pathogen defense. To date, a comprehensive analysis of the potato nsLTP gene family is still lacking after the completion of potato (Solanum tuberosum L.) genome sequencing. A genome-wide characterization, classification and expression analysis of the StnsLTP gene family was performed in this study. RESULTS: In this study, a total of 83 nsLTP genes were identified and categorized into eight types based on Boutrot's method. Multiple characteristics of these genes, including phylogeny, gene structures, conserved motifs, protein domains, chromosome locations, and cis-elements in the promoter sequences, were analyzed. The chromosome distribution and the collinearity analyses suggested that the expansion of the StnsLTP gene family was greatly enhanced by the tandem duplications. Ka/Ks analysis showed that 47 pairs of duplicated genes tended to undergo purifying selection during evolution. Moreover, the expression of StnsLTP genes in various tissues was analyzed by using RNA-seq data and verified by quantitative real-time PCR, revealing that the StnsLTP genes were mainly expressed in younger tissues. These results indicated that StnsLTPs may played significant and functionally varied roles in the development of different tissues. CONCLUSION: In this study, we comprehensively analyzed nsLTPs in potato, providing valuable information to better understand the functions of StnsLTPs in different tissues and pathways, especially in response to abiotic stress.


Assuntos
Proteínas de Transporte/genética , Análise de Sequência de RNA/métodos , Solanum tuberosum/metabolismo , Sequenciamento Completo do Genoma/métodos , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Mapeamento Cromossômico , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Metabolismo dos Lipídeos , Família Multigênica , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Domínios Proteicos , Seleção Genética , Solanum tuberosum/química , Solanum tuberosum/genética , Estresse Fisiológico
9.
BMC Genomics ; 20(1): 380, 2019 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-31092186

RESUMO

BACKGROUND: Aquaporins (AQPs) are a class of integral membrane proteins that facilitate the passive transport of water and other small solutes across biological membranes. Despite their importance, little information is available in cassava (Manihot esculenta), a perennial shrub of the Euphorbiaceae family that serves the sixth major staple crop in the world. RESULTS: This study presents a genome-wide analysis of the AQP gene family in cassava. The family of 42 members in this species could be divided into five subfamilies based on phylogenetic analysis, i.e., 14 plasma membrane intrinsic proteins (PIPs), 13 tonoplast intrinsic proteins (TIPs), nine NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and two small basic intrinsic proteins (SIPs). Best-reciprocal-hit-based sequence comparison and synteny analysis revealed 34 orthologous groups (OGs) present in the Euphorbiaceae ancestor, and nearly one-to-one or two-to-one orthologous relationships were observed between cassava with rubber/physic nut, reflecting the occurrence of one so-called ρ recent whole-genome duplication (WGD) in the last common ancestor of cassava and rubber. In contrast to a predominant role of the ρ WGD on family expansion in rubber, cassava AQP duplicates were derived from the WGD as well as local duplication. Species-specific gene loss was also observed in cassava, which includes the entire NIP4 group and/or six OGs. Comparison of conserved motifs and gene expression profiles revealed divergence of paralogs in cassava as observed in rubber. CONCLUSIONS: Our findings will not only improve our knowledge on family evolution in Euphorbiaceae, but also provide valuable information for further functional analysis of AQP genes in cassava and rubber.


Assuntos
Aquaporinas/genética , Duplicação Gênica , Genoma de Planta , Manihot/genética , Proteínas de Plantas/genética , Borracha/metabolismo , Sequenciamento Completo do Genoma/métodos , Regulação da Expressão Gênica de Plantas , Família Multigênica , Filogenia
10.
Arch Virol ; 164(6): 1733-1737, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30953204

RESUMO

High-throughput sequencing revealed a tentative new badnavirus infecting Codonopsis lanceolata, provisionally named Codonopsis vein clearing virus (CoVCV). The complete 8,112-nt CoVCV genomic DNA sequence (GenBank accession: MK044821) comprises three open reading frames (ORFs) encoding conserved domains, with typical features of badnaviruses. Additionally, BLASTn searches indicated the CoVCV genome sequence is most similar to the grapevine vein clearing virus (GVCV) genome (72% identity and 46% query coverage). Moreover, the polyprotein encoded in CoVCV ORF3 is most similar to the corresponding protein of GVCV, with 60% amino acid sequence identity (89% query coverage). These results suggest that CoVCV is a new member of the genus Badnavirus in the family Caulimoviridae.


Assuntos
Badnavirus/classificação , Codonopsis/virologia , Sequenciamento Completo do Genoma/métodos , Badnavirus/genética , Badnavirus/isolamento & purificação , Tamanho do Genoma , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Fases de Leitura Aberta , Filogenia , Folhas de Planta/virologia
11.
Genet Sel Evol ; 51(1): 15, 2019 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-30999842

RESUMO

BACKGROUND: Quantitative genetic studies suggest the existence of variation at the genome level that affects the ability of cattle to resist to parasitic diseases. The objective of the current study was to identify regions of the bovine genome that are associated with resistance to endo-parasites. METHODS: Individual cattle records were available for Fasciola hepatica-damaged liver from 18 abattoirs. Deregressed estimated breeding values (EBV) for F. hepatica-damaged liver were generated for genotyped animals with a record for F. hepatica-damaged liver and for genotyped sires with a least one progeny record for F. hepatica-damaged liver; 3702 animals were available. In addition, individual cow records for antibody response to F. hepatica on 6388 genotyped dairy cows, antibody response to Ostertagia ostertagi on 8334 genotyped dairy cows and antibody response to Neospora caninum on 4597 genotyped dairy cows were adjusted for non-genetic effects. Genotypes were imputed to whole-sequence; after edits, 14,190,141 single nucleotide polymorphisms (SNPs) and 16,603,644 SNPs were available for cattle with deregressed EBV for F. hepatica-damaged liver and cows with an antibody response to a parasitic disease, respectively. Association analyses were undertaken using linear regression on one SNP at a time, in which a genomic relationship matrix accounted for the relationships between animals. RESULTS: Genomic regions for F. hepatica-damaged liver were located on Bos taurus autosomes (BTA) 1, 8, 11, 16, 17 and 18; each region included at least one SNP with a p value lower than 10-6. Five SNPs were identified as significant (q value < 0.05) for antibody response to N. caninum and were located on BTA21 or 25. For antibody response to F. hepatica and O. ostertagi, six and nine quantitative trait loci (QTL) regions that included at least one SNP with a p value lower than 10-6 were identified, respectively. Gene set enrichment analysis revealed a significant association between functional annotations related to the olfactory system and QTL that were suggestively associated with endo-parasite phenotypes. CONCLUSIONS: A number of novel genomic regions were suggestively associated with endo-parasite phenotypes across the bovine genome and two genomic regions on BTA21 and 25 were associated with antibody response to N. caninum.


Assuntos
Doenças dos Bovinos/genética , Bovinos/genética , Interações Hospedeiro-Parasita/genética , Animais , Cruzamento , Fasciola hepatica/patogenicidade , Fertilidade/genética , Variação Genética/genética , Estudo de Associação Genômica Ampla/veterinária , Genótipo , Parasitos/genética , Parasitos/patogenicidade , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Sequenciamento Completo do Genoma/métodos
12.
PLoS Comput Biol ; 15(4): e1006953, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30986244

RESUMO

Determining the cancer type and molecular subtype has important clinical implications. The primary site is however unknown for some malignancies discovered in the metastatic stage. Moreover liquid biopsies may be used to screen for tumoral DNA, which upon detection needs to be assigned to a site-of-origin. Classifiers based on genomic features are a promising approach to prioritize the tumor anatomical site, type and subtype. We examined the predictive ability of causal (driver) somatic mutations in this task, comparing it against global patterns of non-selected (passenger) mutations, including features based on regional mutation density (RMD). In the task of distinguishing 18 cancer types, the driver mutations-mutated oncogenes or tumor suppressors, pathways and hotspots-classified 36% of the patients to the correct cancer type. In contrast, the features based on passenger mutations did so at 92% accuracy, with similar contribution from the RMD and the trinucleotide mutation spectra. The RMD and the spectra covered distinct sets of patients with predictions. In particular, introducing the RMD features into a combined classification model increased the fraction of diagnosed patients by 50 percentage points (at 20% FDR). Furthermore, RMD was able to discriminate molecular subtypes and/or anatomical site of six major cancers. The advantage of passenger mutations was upheld under high rates of false negative mutation calls and with exome sequencing, even though overall accuracy decreased. We suggest whole genome sequencing is valuable for classifying tumors because it captures global patterns emanating from mutational processes, which are informative of the underlying tumor biology.


Assuntos
Biologia Computacional/métodos , Neoplasias/classificação , Neoplasias/genética , Algoritmos , DNA de Neoplasias/classificação , DNA de Neoplasias/genética , Exoma/genética , Genômica , Humanos , Aprendizado de Máquina , Mutação/genética , Software , Sequenciamento Completo do Exoma/métodos , Sequenciamento Completo do Genoma/métodos
13.
An Acad Bras Cienc ; 91(1): e20180420, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30994767

RESUMO

Eugenia uniflora L. (Myrtaceae) is a tree species widely distributed in South America suffering the effects of the exploitation of natural populations. In this study, we employed low coverage sequencing of the E. uniflora genome for mining of SSR markers. The de novo assembly generated 2,601 contigs with an average length of 1139 bp and spans 3.15 Mb. A total of 76 dimer, 33 trimer and two compound SSR loci were identified. Twelve selected SSR loci were employed to genotype 30 individuals from two natural populations. A total of 73 alleles were detected (mean A= 6.1) were observed, the mean effective number of alleles was Ae = 3.91, mean Ho was 0.23 and mean HE was 0.70). The mean Wright's within population fixation index was FIS = 0.66 and significant deviation of HWE was observed in all loci, except one. The FST between populations equaled 0.27. The levels of genetic diversity and structure estimated with these 12 SSR markers are in accordance with data from genetics studies performed on other tree species of the Pampa biome, presenting moderate to high polymorphism and may be employed in studies of species conservation measures and breeding programs.


Assuntos
Eugenia/genética , Repetições de Microssatélites , Sequenciamento Completo do Genoma/métodos , Análise de Variância , Sequência de Bases , Loci Gênicos , Marcadores Genéticos , Variação Genética , Valores de Referência
14.
BMC Bioinformatics ; 20(1): 207, 2019 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-31014244

RESUMO

BACKGROUND: Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows. RESULTS: We introduce a novel method to detect introgression by combining two widely used statistics: pairwise nucleotide diversity dxy and Patterson's D. The resulting statistic, the distance fraction (df), accounts for genetic distance across possible topologies and is designed to simultaneously detect and quantify introgression. We also relate our new method to the recently published fd and incorporate these statistics into the powerful genomics R-package PopGenome, freely available on GitHub (pievos101/PopGenome) and the Comprehensive R Archive Network (CRAN). The supplemental material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework. CONCLUSION: We present a new distance based statistic df that avoids the pitfalls of Patterson's D when applied to small genomic regions and accurately quantifies the fraction of introgression (f) for a wide range of simulation scenarios.


Assuntos
Genômica/métodos , Hibridização Genética/genética , Modelos Genéticos , Sequenciamento Completo do Genoma/métodos , Bases de Dados Genéticas , Fluxo Gênico , Modelos Estatísticos , Polimorfismo de Nucleotídeo Único
15.
PLoS Comput Biol ; 15(4): e1006967, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30958827

RESUMO

Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics.


Assuntos
Metagenômica/métodos , Microbiota/genética , Análise de Sequência de DNA/métodos , Algoritmos , Big Data , Biologia Computacional/métodos , Contaminação por DNA , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Internet , Metagenoma , Software , Sequenciamento Completo do Genoma/métodos
16.
J Microbiol Biotechnol ; 29(5): 794-808, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31030454

RESUMO

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.


Assuntos
Bacillus/genética , Genes Bacterianos/genética , Sequenciamento Completo do Genoma/métodos , Bacillus/classificação , Bacillus/isolamento & purificação , Sequência de Bases , China , Mapeamento Cromossômico , DNA Bacteriano/análise , DNA Bacteriano/genética , Variação Genética , Genoma Bacteriano , Família Multigênica , Musa/microbiologia , Mutação , Filogenia , Desenvolvimento Vegetal , Doenças das Plantas/microbiologia , Polimorfismo de Nucleotídeo Único , Metabolismo Secundário/genética , Análise de Sequência de DNA
17.
Methods Mol Biol ; 1979: 319-362, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31028647

RESUMO

The simultaneous examination of a single cell's genome and transcriptome presents scientists with a powerful tool to study genetic variability and its effect on gene expression. In this chapter, we describe the library generation method for combined genome and transcriptome sequencing (G&T-seq) originally described by Macaulay et al. (Nat Protoc 11(11):2081-2103, 2016; Nat Methods 12(6):519-522, 2015). This includes some alterations we made to improve robustness of this process for both the novice user and laboratories that want to deploy this method at scale. Using this method, genomic DNA and full-length mRNA from single cells are separated, amplified, and converted into Illumina sequencer-compatible sequencing libraries.


Assuntos
Perfilação da Expressão Gênica/métodos , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Célula Única/métodos , DNA/genética , Variações do Número de Cópias de DNA , Biblioteca Gênica , Humanos , RNA Mensageiro/genética , Análise de Sequência de DNA/métodos , Transcriptoma , Sequenciamento Completo do Genoma/métodos
18.
Mol Ecol Resour ; 19(4): 877-892, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30934146

RESUMO

Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference-based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide-distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large-scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.


Assuntos
Fraxinus/classificação , Fraxinus/genética , Olea/classificação , Olea/genética , Filogenia , Sequenciamento Completo do Genoma/métodos , Polimorfismo de Nucleotídeo Único
19.
Cytogenet Genome Res ; 157(4): 197-202, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30991391

RESUMO

Uniparental disomy (UPD) is a rare type of chromosomal aberration that has sometimes been detected in paternity testing. We examined a 3-person family (father, mother, daughter) first by using short tandem repeat markers, which revealed 4 markers, TPOX, D2S1338, D2S1772, and D2S441, on chromosome 2 that were not transmitted in a Mendelian style. We then performed whole genome sequencing (WGS) to determine the range of the UPD. Chromosome 2 in the daughter showed a complete paternal UPD. To the best of our knowledge, this is the 4th case of complete paternal UPD of chromosome 2 with no clinical phenotype. Our study suggests that WGS, when performed to enhance the accuracy and reliability of parentage testing, can provide a powerful method to detect an UPD.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Repetições de Microssatélites , Dissomia Uniparental/diagnóstico , Sequenciamento Completo do Genoma/métodos , Adolescente , Cromossomos Humanos Par 2/genética , Pai , Feminino , Humanos , Masculino , Mães , Linhagem , Dissomia Uniparental/genética
20.
J Microbiol ; 57(8): 661-667, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31012058

RESUMO

A Gram-stain-negative, rod-shaped, obligately aerobic, chemoheterotrophic bacterium which is motile by means of a single polar flagellum, designated SAORIC-263T, was isolated from deep seawater of the Pacific Ocean. Phylogenetic analyses based on 16S rRNA gene sequences and genomebased phylogeny revealed that strain SAORIC-263T belonged to the genus Sulfitobacter and shared 96.1-99.9% 16S rRNA gene sequence similarities with Sulfitobacter species. Wholegenome sequencing of strain SAORIC-263T revealed a genome size of 3.9Mbp and DNA G+C content of 61.3 mol%. The SAORIC-263T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 79.1-88.5% and 18.9-35.0%, respectively, with other Sulfitobacter genomes. The SAORIC-263T genome contained the genes related to benzoate degradation, which are frequently found in deep-sea metagenome. The strain contained summed feature 8 (C18:1ω7c), C18:1ω7c 11-methyl, and C16:0 as the predominant cellular fatty acids as well as ubiquinone-10 (Q-10) as the major respiratory quinone. The major polar lipids of the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and aminolipid. On the basis of taxonomic data obtained in this study, it is suggested that strain SAORIC-263T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter profundi sp. nov. is proposed. The type strain is SAORIC-263T (= KACC 21183T = NBRC 113428T).


Assuntos
Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana/métodos , Composição de Bases , DNA Bacteriano/genética , Oceano Pacífico , RNA Ribossômico 16S/genética , Rhodobacteraceae/genética , Rhodobacteraceae/crescimento & desenvolvimento , Rhodobacteraceae/isolamento & purificação , Sequenciamento Completo do Genoma/métodos
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