keyword
MENU ▼
Read by QxMD icon Read
search

Genome annotation

keyword
https://www.readbyqxmd.com/read/28439836/prediction-of-mirna-mrna-interactions-using-mirgate
#1
Eduardo Andrés-León, Gonzalo Gómez-López, David G Pisano
miRGate ( http://mirgate.bioinfo.cnio.es /) is a freely available database that contains predicted and experimentally validated microRNA-messenger RNA (miRNA-mRNA) target pairs. This resource includes novel predictions from five well-established algorithms, but recalculated from a common and comprehensive sequence dataset. It includes all 3'-UTR sequences of all known genes of the three more widely employed genomes (human, mouse, and rat), and all annotated miRNA sequences from those genomes. Besides, it also contains predictions for all genes in human targeted by miRNA viruses such as Epstein-Barr and Kaposi sarcoma-associated herpes virus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439658/pan-genomic-approaches-in-lactobacillus-reuteri-as-a-porcine-probiotic-investigation-of-host-adaptation-and-antipathogenic-activity
#2
Jun-Yeong Lee, Geon Goo Han, Jaeyun Choi, Gwi-Deuk Jin, Sang-Kee Kang, Byung Jo Chae, Eun Bae Kim, Yun-Jaie Choi
After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of L. reuteri associated with host specificity and antipathogenic effect. We isolated 104 L. reuteri strains from porcine feces, and 16 strains, composed of eight strains exhibiting the higher antipathogenic effect (group HS) and eight strains exhibiting the lower effect (group LS), were selected for genomic comparison...
April 24, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28439475/transcriptomic-resources-for-an-endemic-neotropical-plant-lineage-gesneriaceae
#3
Martha L Serrano-Serrano, Anna Marcionetti, Mathieu Perret, Nicolas Salamin
PREMISE OF THE STUDY: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. METHODS AND RESULTS: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28439089/transcriptome-analysis-on-the-exoskeleton-formation-in-early-developmetal-stages-and-reconstruction-scenario-in-growth-moulting-in-litopenaeus-vannamei
#4
Yi Gao, Jiankai Wei, Jianbo Yuan, Xiaojun Zhang, Fuhua Li, Jianhai Xiang
Exoskeleton construction is an important issue in shrimp. To better understand the molecular mechanism of exoskeleton formation, development and reconstruction, the transcriptome of the entire developmental process in Litopenaeus vannamei, including nine early developmental stages and eight adult-moulting stages, was sequenced and analysed using Illumina RNA-seq technology. A total of 117,539 unigenes were obtained, with 41.2% unigenes predicting the full-length coding sequence. Gene Ontology, Clusters of Orthologous Group (COG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and functional annotation of all unigenes gave a better understanding of the exoskeleton developmental process in L...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28438136/normalized-long-read-rna-sequencing-in-chicken-reveals-transcriptome-complexity-similar-to-human
#5
Richard I Kuo, Elizabeth Tseng, Lel Eory, Ian R Paton, Alan L Archibald, David W Burt
BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28437448/expression-profiling-of-chrysanthemum-crassum-under-salinity-stress-and-the-initiation-of-morphological-changes
#6
Zhiyong Guan, Yitong Feng, Aiping Song, Xiaomeng Shi, Yachao Mao, Sumei Chen, Jiafu Jiang, Lian Ding, Fadi Chen
Chrysanthemum crassum is a decaploid species of Chrysanthemum with high stress tolerance that allows survival under salinity stress while maintaining a relatively ideal growth rate. We previously recorded morphological changes after salt treatment, such as the expansion of leaf cells. To explore the underlying salinity tolerance mechanisms, we used an Illumina platform and obtained three sequencing libraries from samples collected after 0 h, 12 h and 24 h of salt treatment. Following de novo assembly, 154,944 transcripts were generated, and 97,833 (63...
2017: PloS One
https://www.readbyqxmd.com/read/28433724/whole-genome-de-novo-sequencing-of-wood-rot-fungus-fomitopsis-palustris-atcc62978-with-both-a-cellulolytic-and-ligninolytic-enzyme-system
#7
Chang-Young Hong, Su-Yeon Lee, Sun-Hwa Ryu, Myungkil Kim
Fomitopsis palustris is a model brown rot fungus causing destructive wood decay based on the cellulase system. Endoglucanase secreted by F. palustris hydrolyzes cellulose in both the crystalline and amorphous form. In this study, whole-genome sequencing was conducted to identify genes related to F. palustris cellulose degradation and their functions. We determined the 43-Mb complete draft genome of F. palustris (ATCC 62978), comprising 14,592 predicted gene models. Gene annotation provided crucial information about the location and function of protein-encoding genes...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433722/high-precision-genome-sequencing-of-engineered-g-oxydans-621h-by-combining-long-nanopore-and-short-accurate-illumina-reads
#8
Angela Kranz, Alexander Vogel, Ursula Degner, Ines Kiefler, Michael Bott, Björn Usadel, Tino Polen
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28432803/sequencing-and-functional-validation-of-the-jgi-brachypodium-distachyon-t-dna-collection
#9
Mon Mandy Hsia, Ronan O'Malley, Amy Cartwright, Rita Nieu, Sean P Gordon, Sandra Kelly, Tina G Williams, Delilah F Wood, Yunjun Zhao, Jennifer Bragg, Mark Jordan, Markus Pauly, Joseph R Ecker, Yong Gu, John P Vogel
Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21,165 T-DNA lines, 15,569 of which were produced in this study. This increased the number of unique insertion sites in the T-DNA collection by 21,078 bringing the overall total to 26,112. Thirty seven percent (9,754) of these insertion sites are within genes (including UTRs and introns) and 28% (7,217) are within 500 bp of a gene...
April 22, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28432195/n-terminal-proteomics-assisted-profiling-of-the-unexplored-translation-initiation-landscape-in-arabidopsis-thaliana
#10
Patrick Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, Petra Van Damme
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N-termini encoded in the Arabidopsis thaliana genome...
April 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28431232/genome-wide-mapping-of-drosha-cleavage-sites-on-primary-micrornas-and-noncanonical-substrates
#11
Baekgyu Kim, Kyowon Jeong, V Narry Kim
MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gatekeeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. Here, we establish a protocol termed "formaldehyde crosslinking, immunoprecipitation, and sequencing (fCLIP-seq)," which allows identification of DROSHA cleavage sites at single-nucleotide resolution...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28431015/large-scale-collection-of-full-length-cdna-and-transcriptome-analysis-in-hevea-brasiliensis
#12
Yuko Makita, Kiaw Kiaw Ng, G Veera Singham, Mika Kawashima, Hideki Hirakawa, Shusei Sato, Ahmad Sofiman Othman, Minami Matsui
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28431014/the-draft-genome-of-ruellia-speciosa-beautiful-wild-petunia-acanthaceae
#13
Yongbin Zhuang, Erin A Tripp
The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28429027/a-metabolomic-study-on-high-risk-stroke-patients-determines-low-levels-of-serum-lysine-metabolites-a-retrospective-cohort-study
#14
Yeseung Lee, Adnan Khan, Seri Hong, Sun Ha Jee, Youngja H Park
Identifying changes in serum metabolites during cerebral ischemia is an important approach for early diagnosis of thrombotic stroke. Herein, we highlight novel biomarkers for early diagnosis of patients at high risk of thrombotic stroke using high resolution metabolomics (HRM). In this retrospective cohort study, serum samples obtained from patients at risk of thrombotic stroke (n  =  62) and non-risk individuals (n  =  348) were tested using HRM, coupled with LC-MS/MS, to discriminate between metabolic profiles of control and stroke risk patients...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28428989/generation-and-characterization-of-the-blood-transcriptome-of-macaca-thibetana-and-comparative-analysis-with-m-mulatta
#15
Peng Li, Lianming Du, Wujiao Li, Zhenxin Fan, Daiwen Zeng, Hui Chen, Liang Zhou, Yong Yi, Na Yang, Kefeng Dou, Bisong Yue, Jing Li
Transcriptome profiles provide a large transcript sequence data set for genomic study, particularly in organisms that have no accurate genome data published. The Tibetan macaque (Macaca thibetana) is commonly considered to be an endemic species to China and an important animal in biomedical research in the present day. In the present study, we report the de novo assembly and characterization of the blood transcriptome of the Tibetan macaque from three individuals, and we also sequenced the blood transcriptome of the rhesus macaque (Macaca mulatta) for comparison...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28428987/microarray-profiling-and-co-expression-network-analysis-of-the-lncrnas-and-mrnas-associated-with-acute-leukemia-in-adults
#16
Hui Cheng, Chong Mei Huang, Yang Wang, Xiao Xia Hu, Xiao Qian Xu, Xian Min Song, Gu Sheng Tang, Li Chen, Jian Min Yang
Acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) are common types of acute leukemia in adults and cause low survival rate and poor outcome after 5 years despite high rates of complete remission (CR) with modern chemotherapeutic regimens. To understand the distinct mechanisms in leukemogenesis for ALL and AML and to identify markers for diagnosis and treatment, lncRNA and mRNA expression profiles of AML and ALL patients and healthy controls were generated using microarray analysis. For comparison, the differentially expressed mRNA functions were annotated using gene ontology (GO) and pathway analysis...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28428834/genome-sequencing-and-analysis-of-ralstonia-solanacearum-phylotype-i-strains-fjat-91-fjat-452-and-fjat-462-isolated-from-tomato-eggplant-and-chili-pepper-in-china
#17
Yidan Sun, Keke Wang, Carlos Caceres-Moreno, Wei Jia, Aojun Chen, Heng Zhang, Renyi Liu, Alberto P Macho
Ralstonia solanacearum is an extremely destructive pathogen able to cause disease in a wide range of host plants. Here we report the draft genome sequences of the strains FJAT-91, FJAT-452 and FJAT-462, isolated from tomato, eggplant, and chili pepper, respectively, in China. In addition to the genome annotation, we performed a search for type-III secreted effectors in these strains, providing a detailed annotation of their presence and distinctive features compared to the effector repertoire of the reference phylotype I strain (GMI1000)...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28428832/a-meta-analysis-testing-eusocial-co-option-theories-in-termite-gut-physiology-and-symbiosis
#18
Michael E Scharf, Yunpeng Cai, Yijun Sun, Ruchira Sen, Rhitoban Raychoudhury, Drion G Boucias
The termite gut accomplishes key physiologic functions that underlie termite symbiosis and sociality. However, potential candidate functions of the host-symbiont holobiome have not yet been explored across seemingly divergent processes such as digestion, immunity, caste differentiation, and xenobiotic tolerance. This study took a meta-analysis approach for concurrently studying host and symbiont gut metatranscriptome responses of the lower termite Reticulitermes flavipes, which has ancestral characteristics and hosts a diverse mix of eukaryotic and bacterial symbionts...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28428828/bioinformatics-analysis-of-key-genes-and-latent-pathway-interactions-based-on-the-anaplastic-thyroid-carcinoma-gene-expression-profile
#19
Yun Huang, Yiming Tao, Xinying Li, Shi Chang, Bo Jiang, Feng Li, Zhi-Ming Wang
Anaplastic thyroid carcinoma (ATC) is an aggressive malignant disease in older adults with a high mortality rate. The present study aimed to examine several key genes and pathways, which are associated with ATC. The GSE33630 gene expression profile was downloaded from the Gene Expression Omnibus database, which included 11 ATC and 45 normal thyroid samples. The differentially expressed genes (DEGs) in ATC were identified using the Limma package in R. The Gene Ontology functions and Kyoto Encyclopedia of Genes and Genomes pathways of the selected DEGs were enriched using the Database for Annotation, Visualization and Integrated Discovery...
January 2017: Oncology Letters
https://www.readbyqxmd.com/read/28428793/transcriptomics-targeted-metabolomics-and-gene-expression-of-blackberry-leaves-and-fruits-indicate-flavonoid-metabolic-flux-from-leaf-to-red-fruit
#20
Enrique Gutierrez, Ana García-Villaraco, José A Lucas, Ana Gradillas, F Javier Gutierrez-Mañero, Beatriz Ramos-Solano
Blackberries (Rubus spp.) are among the high added value food products relevant for human health due to the increasing evidence of the beneficial effects of polyphenols, which are very abundant in these fruits. Interestingly, these compounds also play a role on plant physiology, being especially relevant their role in plant defense against biotic and abiotic stress. Hence, we hypothesize that since blackberry fruits have high amounts of flavonols and anthocyanins, leaves would also have high amounts of these compounds, and can be studied as a source of active molecules; furthermore, leaf synthesis would support their high contents in fruits...
2017: Frontiers in Plant Science
keyword
keyword
83321
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"