Journal of Genomics最新文献

Genotyping array is the most economical approach for conducting large-scale genome-wide genetic association studies. Thorough quality control is key to generating high integrity genotyping data and robust results. Quality control of genotyping array is generally a complicated process, as it requires intensive manual labor in implementing the established protocols and curating a comprehensive quality report. There is an urgent need to reduce manual intervention via an automated quality control process. Based on previously established protocols and strategies, we developed an R package GTQC (GenoTyping Quality Control) to automate a majority of the quality control steps for general array genotyping data. GTQC covers a comprehensive spectrum of genotype data quality metrics and produces a detailed HTML report comprising tables and figures. Here, we describe the concepts underpinning GTQC and demonstrate its effectiveness using a real genotyping dataset. R package GTQC streamlines a majority of the quality control steps and produces a detailed HTML report on a plethora of quality control metrics, thus enabling a swift and rigorous data quality inspection prior to downstream GWAS and related analyses. By significantly cutting down on the time on genotyping quality control procedures, GTQC ensures maximum utilization of available resources and minimizes waste and inefficient allocation of manual efforts. GTQC tool can be accessed at https://github.com/slzhao/GTQC.

Antibiotic resistance continues to be a significant public health challenge. Soil bacteria represent a potential source of yet to be discovered antimicrobials. The screening of Iowa (United States) soils yielded the identification of a strain of Pantoea ananatis (MMB-1), which displayed an antimicrobial-producing phenotype against a bacterium (Bacillus subtilis) representative of Gram-positive bacteria. Crude, organic, extracts of MMB-1 retained the anti-microbial activity. The draft genome of strain MMB-1 contains a total of 4,634,340 bp, and 4,624 protein-encoding genes. Consistent with phenotypic observation, the genome of MMB-1 encodes for a number of putative secondary metabolite biosynthetic gene clusters, including those known to be involved in the production of the antibiotics lankacidin C and bottromycin. This study increases our overall understanding of Panteoa as a group, and is also consistent with the notion that members of this genus have significant potential as useful natural product producers.

Background: Cervical cancer (CC) is one of the most common female malignancies worldwide. An increasing body of evidence suggests that circular RNAs (circRNAs) participate in the pathogenesis of various cancers, including CC. However, the expression profile and underlying molecular mechanisms remain largely unknown. Methods: In this study, high throughput sequencing was applied to identify circRNA in HPV-16 positive CC tissues. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression in CC tissues and cell lines. RNase R treatment, gel-electrophoresis, and RNA fluorescent in situ hybridization (FISH) were used to characterize the circRNAs. Subsequently, the Cell Counting Kit-8 assay (CCK8), transwell and wound healing assays were performed to assess circRNA function. Meanwhile, dual-luciferase reporter and western blot were used to clarify the associated molecular mechanisms. Results: Circ0036602 was upregulated in HPV-16 positive CC and correlated with a poor prognosis. Moreover, circ0036602 expression significantly correlated with the clinicopathologic characteristics. Knockdown of circ0036602 inhibited CC cell proliferation, migration, and invasion. Further studies showed that circ0036602 could bind to miR-34-5p and miR-431-5p to regulate the expression of the target gene HMGB1. Conclusions: Taken together, our findings suggest that circ0036602 is a tumor-promoting circRNA that promotes CC cells by sponging miR-34-5p and miR-431-5p to regulate HMGB1. Circ0036602 has huge prospects as a potential therapeutic target for CC patients.

Aim of study was comparative analysis of mRNA transcripts of HT-29 cell line, expressed in identical quantities for the combination of pathogenic and non-pathogenic Escherichia coli strains. HT-29 confluent monolayers infection with two pathogenic E. coli strains UM146 and UM147 resulted in two sets of mRNA transcripts that were identical with RNA transcripts obtained for non-pathogenic one strain E. coli Nissle 1917. In this study genome-wide experiments were conducted using expression microarray-system. Only one common mRNA transcript coding for CCDC65 gene was equally expressed by HT-29 cells after incubation challenge with three different E. coli strains used. This gene and its bacterial analogue are important in the ciliary or flagellar motility, respectively. Altogether, 78 and 81 HT-29 mRNA transcripts for E. coli UM146 and E. coli UM147 had identical RNA quantity in comparison to the response obtained for non-pathogenic E. coli Nissle 1917 interactions with HT-29 monolayers. Specific analysis using REACTOME and agriGO terms enrichment data-mining tools as well as word-cloud analysis allowed for identification the most important processes characteristic during HT-29 cell line infections for each pathogenic E. coli strain used. The importance of results may contribute to recognition of those processes during bacterial infections that are identical with processes arising from human interaction with non-pathogenic strains that belong to the same bacterial species.

Wheat (Triticum aestivum L.) flour mixing properties are essential quality parameters in the dough development process. Limited research on superior alleles for mixing properties has restricted their molecular improvement, and other factors related to the complex traits have been ignored. A molecular map of 9576 polymorphic markers in the RIL population (F_8:9) (Shannong01-35/Gaocheng9411) was constructed to evaluate mixing property effects in three environments. The parents were selected with markedly distinct high-molecular-weight glutenin subunits (HMW-GS). This study not only evaluated mixing properties using conventional unconditional QTL mapping but also evaluated the relationships between protein-related traits using conditional QTL mapping. The analyses identified most additive QTLs for major mixing properties on chromosomes 1A, 1B, and 1D. Two major loci (1A.1-15 and 1D-1) associated with mixing properties have confirmed the important contributions of Glu-A1 and Glu-D1 to wheat quality at the QTL level, which were mainly affected by the gluten index. Another important locus, 1B.1-24 (associated with midline peak value and midline peak width, with high phenotypic variations explained), might represent a new variation distinct from Glu-B1. The favored alleles came from Gaocheng9411. Several mixing properties shared the same QTLs (1B.1-6 and 1A.1-15), indicating tight linkage or pleiotropism. Genotype-by-environment (G×E) interactions were also investigated in the present study. The QTL results in our study may improve our understanding of the genetic interrelationships between mixing properties and protein-related traits.

In this study, we describe the genomes of two novel candidate species of non-nitrogen fixing Frankia that were isolated from the root nodules of Coriaria nepalensis and Alnus glutinosa, genospecies CN and Ag, respectively. Comparative genomic analyses revealed that both genospecies lack genes essential for nitrogen-fixation and possess genes involved in the degradation of plant cell walls. Additionally, we found distinct biosynthetic gene clusters in each genospecies. The availability of these genomes will contribute to the study of the taxonomy and evolution of actinorhizal symbioses.

Cold-tolerant bacteria are known to contaminate and cause defects in refrigerated foods. Defects in food products can be observed as changes in appearance, texture, and/or flavor that detract from the product's intended look, feel, or taste. Two distinct organisms were cultured from blue pigmented soymilk and tofu that had been left opened and expired in a home refrigerator. The blue coloration was reproduced when isolates were cultured in fresh, sterile soymilk. These strains also produced a variety of colony color morphologies when cultured on different media types. We report two draft genome sequences of the potential causative agents of blue discoloration of soy foods, Pseudomonas carnis strains UCD_MED3 and UCD_MED7 as well as the 16S rRNA gene sequences of co-occurring strains isolated from the defective soy samples but that did not cause blue discoloration when cultured in fresh soymilk; Serratia liquefaciens strains UCD_MED2 and UCD_MED5.

Pathogenic variants (PVs) in BRCA genes have been mainly associated with an increasing risk of triple negative breast cancer (TNBC). The contribution of PVs in non-BRCA genes to TNBC seems likely since the processing of homologous recombination repair of double-strand DNA breaks involves several genes. Here, we investigate the susceptibility of genetic variation of the BRCA and non-BRCA genes in 30 early-onset Moroccan women with TNBC. Methods: Targeted capture-based next generation sequencing (NGS) method was performed with a multigene panel testing (MGPT) for variant screening. Panel sequencing was performed with genes involved in hereditary predisposition to cancer and candidate genes whose involvement remains unclear using Illumina MiSeq platform. Interpretation was conducted by following the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) criteria. Results: PVs were identified in 20% (6/30) of patients with TNBC. Of these, 16.7% (5/30) carried a BRCA PV [10% (3/30) in BRCA1, 6.7% (2/30) in BRCA2] and 6.6% (2/30) carried a non-BRCA PV. The identified PVs in BRCA genes (BRCA1 c.798_799delTT, BRCA1 c.3279delC, BRCA2 c.1310_1313del, and BRCA2 c.1658T>G) have been reported before and were classified as pathogenic. The identified founder PVs BRCA1 c.798_799del and BRCA2 c.1310_1313delAAGA represented 10% (3/30). Our MGPT allowed identification of several sequence variations in most investigated genes, among which we found novel truncating variations in PALB2 and BARD1 genes. The PALB2 c.3290dup and BARD1 c.1333G>T variants are classified as pathogenic. We also identified 42 variants of unknown/uncertain significance (VUS) in 70% (21/30) of patients with TNBC, including 50% (21/42) missense variants. The highest VUS rate was observed in ATM (13%, 4/30). Additionally, 35.7% (15/42) variants initially well-known as benign, likely benign or conflicting interpretations of pathogenicity have been reclassified as VUS according to ACMG-AMP. Conclusions: PALB2 and BARD1 along with BRCA genetic screening could be helpful for a larger proportion of early-onset TNBC in Morocco.

Objectives: Pertussis is a highly contagious disease of the respiratory tract caused by Bordetella pertussis, a bacterium that lives in the mouth, nose, and throat. Current study reports the highly accurate complete genomes of two clinical B. pertussis strains from India for the first time. Methods: Complete genome sequencing was performed for two B. pertussis strains using Ion Torrent PGM and Oxford nanopore sequencing method. Data was assembled de novo and the sequence annotation was performed through PATRIC and NCBI server. Downstream analyses of the isolates were performed using CGE server databases for antimicrobial resistance genes, plasmids, and sequence types. The phylogenetic analysis was performed using Roary. Results: The analysis revealed insertional elements flanked by IS481, which has been previously regarded as the important component for bacterial evolution. The two B. pertussis clinical strains exhibited diversity through genome degradation when compared to whole-cell vaccine reference strains of India. These isolates harboured multiple genetic virulence traits and toxin subunits, which belonged to sequence type ST2. Conclusion: The genome information of Indian clinical B. pertussis strains will serve as a baseline data to decipher more information on the genome evolution, virulence factors and their role in pathogenesis for effective vaccine strategies.

Here, we report high-quality annotated draft genomes of eight coagulase-negative staphylococci (CoNS) isolates obtained from South Africa and Nigeria. We explored the prevalence of antibiotic resistance and virulence genes, their association with mobile genetic elements. The pan-genomic analysis highlighted the environmentally driven heterogeneity of the isolates. Isolates from Nigeria had at least one gene for cadmium resistance/tolerance, these genes were not detected in isolates from South Africa. In contrast, isolates from South Africa had a tetM gene, which was not detected among the isolates from Nigeria. The observed genomic heterogeneity correlates with anthropogenic activities in the area where the isolates were collected. Moreover, the isolates used in this study possess an open pan-genome, which could easily explain the environmentally driven heterogeneity.