Journal of Genomics最新文献_第10页

Permanent Draft Genome sequence for Frankia sp. strain CcI49, a Nitrogen-Fixing Bacterium Isolated from Casuarina cunninghamiana that Infects Elaeagnaceae. 从木麻黄中分离的固氮细菌Frankia sp.菌株CcI49的永久基因组序列草图。

Journal of Genomics Pub Date : 2017-09-12 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.22138

Samira Mansour, Erik Swanson, Zakkary McNutt, Céline Pesce, Kelsey Harrington, Feseha Abebe-Alele, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Louis S Tisa

引用次数: 6

Small Non-coding RNA Abundance in Adrenocortical Carcinoma: A Footprint of a Rare Cancer. 肾上腺皮质癌中的小非编码 RNA 丰度：罕见癌症的足迹

Journal of Genomics Pub Date : 2017-09-08 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.22060

Srinivas V Koduru, Ashley N Leberfinger, Dino J Ravnic

{"title":"Small Non-coding RNA Abundance in Adrenocortical Carcinoma: A Footprint of a Rare Cancer.","authors":"Srinivas V Koduru, Ashley N Leberfinger, Dino J Ravnic","doi":"10.7150/jgen.22060","DOIUrl":"10.7150/jgen.22060","url":null,"abstract":"BACKGROUND: Adrenocortical carcinoma (ACC) is a relatively rare, but aggressive type of cancer, which affects both children and adults. OBJECTIVE: Small non-coding RNAs (sncRNAs) play important roles and may serve as biomarkers for disease diagnosis, prognosis and treatment. METHODS: In our study, we sought to identify sncRNAs associated with malignant adrenal tumors. We obtained publicly available, small RNA sequencing data derived from 45 ACC and 30 benign tumors arising from the cortex of the adrenal gland, adrenocortical adenomas (ACA), and compared their sncRNA expression profiles. RESULTS: First, we remapped small RNA-seq to miRBase version 21 to check expression of miRNAs and found 147 miRNAs were aberrantly expressed (p<0.05) in ACC samples compared to ACA samples. Pathway analysis of differentially expressed miRNAs revealed p53 signaling pathways to be profoundly affected in ACC samples. Further examination for other types of small RNAs revealed 16 piRNAs, 48 lncRNAs and 19 sn/snoRNAs identified in ACC samples. Conclusions: Our data analysis suggests that publically available resources can be mined for biomarker development and improvements in-patient care; however, further research must be performed to correlate tumor grade with gene expression.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"5 ","pages":"99-118"},"PeriodicalIF":0.0,"publicationDate":"2017-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ec/22/jgenv05p0099.PMC5607708.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35442248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome Comparison of Pseudomonas fluorescens UM270 with Related Fluorescent Strains Unveils Genes Involved in Rhizosphere Competence and Colonization. 荧光假单胞菌UM270与相关荧光菌株的基因组比较揭示了参与根际能力和定植的基因。

Journal of Genomics Pub Date : 2017-08-24 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.21588

Julie E Hernández-Salmerón, Gabriel Moreno-Hagelsieb, Gustavo Santoyo

{"title":"Genome Comparison of Pseudomonas fluorescens UM270 with Related Fluorescent Strains Unveils Genes Involved in Rhizosphere Competence and Colonization.","authors":"Julie E Hernández-Salmerón, Gabriel Moreno-Hagelsieb, Gustavo Santoyo","doi":"10.7150/jgen.21588","DOIUrl":"https://doi.org/10.7150/jgen.21588","url":null,"abstract":"Pseudomonas fluorescens UM270 is a rhizosphere-colonizing bacterium that produces multiple diffusible and volatile compounds involved in plant growth-promoting activities. Strain UM270 exhibits excellent biocontrol capacities against diverse fungal pathogens . In a previous study, the general UM270 genome characteristics were published. Here, we report a deeper analysis of its gene content and compare it to other P. fluorescens strains to unveil the genetic elements that might explain UM270's great colonizing and plant growth-promoting capabilities. Our analyses found high variation in genome size and gene content among the eight Pseudomonas genomes analyzed (strains UM270, Pf0-1, A506, F113, SBW25, PICF-7, UK4 and UW4). A core genome of 3,039 coding DNA sequences (CDSs) was determined, with 599 CDSs present only in the UM270 genome. From these unique UM270 genes, a set of 192 CDSs was found to be involved in signaling, rhizosphere colonization and competence, highlighted as important traits to achieve an effective biocontrol and plant growth promotion.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"5 ","pages":"91-98"},"PeriodicalIF":0.0,"publicationDate":"2017-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.21588","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35442247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Draft genome and SNPs associated with carotenoid accumulation in adductor muscles of bay scallop (Argopecten irradians). 与海湾扇贝（Argopecten irradians）内收肌类胡萝卜素积累相关的基因组草案和 SNPs。

Journal of Genomics Pub Date : 2017-07-18 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.19146

Xuedi Du, Kai Song, Jinpeng Wang, Rihao Cong, Li Li, Guofan Zhang

{"title":"Draft genome and SNPs associated with carotenoid accumulation in adductor muscles of bay scallop (Argopecten irradians).","authors":"Xuedi Du, Kai Song, Jinpeng Wang, Rihao Cong, Li Li, Guofan Zhang","doi":"10.7150/jgen.19146","DOIUrl":"10.7150/jgen.19146","url":null,"abstract":"Carotenoids are commonly deposited in the gonads of marine bivalves but rarely in their adductor muscles. An orange-adductor variant was identified in our breeding program for the bay scallop Argopecten irradians. In the present study, bay scallop genome survey sequencing was conducted, followed by genotyping by sequencing (GBS)-based case-control association analysis in a selfing family that exhibited segregation in adductor color. K-mer analysis (K=17) revealed that the bay scallop genome is about 990 Mb in length. De novo assembly produced 217,310 scaffold sequences, which provided 72.1% coverage of the whole genome and covered 72,187 transcripts, thereby yielding the most informative sequence resource for bay scallop to date. The average carotenoid content of the orange-adductor progenies was significantly higher than that of the white-adductor progenies. Thus, 20 individuals of each subgroup were sampled for case-control analysis. As many as 15,224 heterozygous loci were identified in the parent, among which 9280 were genotyped in at least 10 individuals of each of the two sub-groups. Association analysis indicated that 126 SNPs were associated with carotenoid accumulation in the adductor muscle and that 88 of these were significantly enriched on 28 scaffolds (FDR controlled P < 0.05). The SNPs and genes located on these scaffolds can serve as valuable candidates for further research into the mechanisms by which marine bivalves accumulate carotenoids in their adductor muscles.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"5 ","pages":"83-90"},"PeriodicalIF":0.0,"publicationDate":"2017-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b9/74/jgenv05p0083.PMC5535694.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35381166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A glimpse into the genetic basis of symbiosis between Hydrogenophaga and their helper strains in the biodegradation of 4-aminobenzenesulfonate. 食氢菌及其辅助菌共生降解4-氨基苯磺酸的遗传基础

Journal of Genomics Pub Date : 2017-07-10 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.20216

Kangsan Kim, Han Ming Gan

{"title":"A glimpse into the genetic basis of symbiosis between Hydrogenophaga and their helper strains in the biodegradation of 4-aminobenzenesulfonate.","authors":"Kangsan Kim, Han Ming Gan","doi":"10.7150/jgen.20216","DOIUrl":"https://doi.org/10.7150/jgen.20216","url":null,"abstract":"We report the whole genome sequences of Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2, the first reported bacterial co-culture capable of degrading 4-aminobenzenesulfonate (4-ABS), a recalcitrant industrial waste product. To gain insights into the genetic basis for the syntrophic interaction between this symbiotic pair and also another recently reported Hydrogenophaga associated co-culture, Hydrogenophaga sp. PBC and Ralstonia sp. PBA, we performed detailed genetic analysis of these four strains focusing on the metabolic pathways associated with biotin, para-aminobenzoic acid (pABA), and protocatechuate metabolism. Both assembled Hydrogenophaga draft genomes are missing a majority of the genetic components associated in the biosynthetic pathway of pABA and biotin. Interestingly, a fused pABA synthase was found in R. sp PBA but not in A. radiobacter S2. Furthermore, using whole genome data, the taxonomic classification of R. sp. PBA and A. radiobacter S2 (both previously inferred from 16S rRNA gene) was re-investigated, providing new evidence to propose for their re-classification at the genus and species level, respectively.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"5 ","pages":"77-82"},"PeriodicalIF":0.0,"publicationDate":"2017-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.20216","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35244054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Complete Genome Sequence of Actinomadura Parvosata Subsp. Kistnae, A Rich Source of Novel Natural Product (Bio-)Chemistry. Actinomadura Parvosata Subsp. Kistnae 的完整基因组序列，新型天然产品（生物）化学的丰富来源。

Journal of Genomics Pub Date : 2017-07-02 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.19673

Kalina Kusserow, Tobias A M Gulder

引用次数: 0

Complete Genome Sequence and Comparative Genomics of a Streptococcus pyogenes emm3 Strain M3-b isolated from a Japanese Patient with Streptococcal Toxic Shock Syndrome. 日本链球菌中毒性休克综合征患者产化脓性链球菌emm3株M3-b的全基因组序列和比较基因组学分析

Journal of Genomics Pub Date : 2017-07-01 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.20915

Kohei Ogura, Shinya Watanabe, Teruo Kirikae, Tohru Miyoshi-Akiyama

引用次数: 2

Draft Genome Sequence of a Virulent Strain of Pasteurella Multocida Isolated From Alpaca. 从羊驼身上分离出的多杀性巴氏杆菌毒株的基因组序列草案。

Journal of Genomics Pub Date : 2017-06-28 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.19297

Raquel Enma Hurtado, Flavia Aburjaile, Diego Mariano, Marcus Vinicius Canário, Leandro Benevides, Daniel Antonio Fernandez, Nataly Olivia Allasi, Rocio Rimac, Julio Eduardo Juscamayta, Jorge Enrique Maximiliano, Raul Hector Rosadio, Vasco Azevedo, Lenin Maturrano

引用次数: 0

Draft Genome Sequence of the Symbiotic Frankia Sp. Strain KB5 Isolated from Root Nodules of Casuarina equisetifolia. 木麻黄根瘤共生菌株Frankia Sp. KB5基因组序列草图

Journal of Genomics Pub Date : 2017-06-09 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.20887

Céline Pesce, Erik Swanson, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Louis S Tisa, Anita Sellstedt

引用次数: 6

CNV Analysis of Host Responses to Porcine Reproductive and Respiratory Syndrome Virus Infection. 猪繁殖与呼吸综合征病毒感染对宿主反应的CNV分析

Journal of Genomics Pub Date : 2017-05-24 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.20358

El Hamidi A Hay, Igseo Choi, Lingyang Xu, Yang Zhou, Robert R R Rowland, Joan K Lunney, George E Liu

{"title":"CNV Analysis of Host Responses to Porcine Reproductive and Respiratory Syndrome Virus Infection.","authors":"El Hamidi A Hay, Igseo Choi, Lingyang Xu, Yang Zhou, Robert R R Rowland, Joan K Lunney, George E Liu","doi":"10.7150/jgen.20358","DOIUrl":"https://doi.org/10.7150/jgen.20358","url":null,"abstract":"Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease with a significant impact on the swine industry causing major economic losses. The objective of this study is to examine copy number variations (CNVs) associated with the group-specific host responses to PRRS virus infection. We performed a genome-wide CNV analysis using 660 animals genotyped with on the porcine SNP60 BeadChip and discovered 7097 CNVs and 271 CNV regions (CNVRs). For this study, we used two established traits related to host response to the virus, i.e. viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain (WG42 from 0 to 42 days post infection). To investigate the effects of CNVs on differential host responses to PRRS, we compared groups of animals with extreme high and low estimated breeding values (EBVs) for both traits using a case-control study design. For VL, we identified 163 CNVRs (84 Mb) from the high group and 159 CNVRs (76 Mb) from the low group. For WG42, we detected 126 (68 Mb) and 156 (79 Mb) CNVRs for high and low groups, respectively. Based on gene annotation within group-specific CNVRs, we performed network analyses and observed some potential candidate genes. Our results revealed these group-specific genes are involved in regulating innate and acquired immune response pathways. Specifically, molecules like interferons and interleukins are closely related to host responses to PRRS virus infection.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"5 ","pages":"58-63"},"PeriodicalIF":0.0,"publicationDate":"2017-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.20358","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35085938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7