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genomics,genome annotation,

Jelle Slager, Rieza Aprianto, Jan-Willem Veening
A precise understanding of the genomic organization into transcriptional units and their regulation is essential for our comprehension of opportunistic human pathogens and how they cause disease. Using single-molecule real-time (PacBio) sequencing we unambiguously determined the genome sequence of Streptococcus pneumoniae strain D39 and revealed several inversions previously undetected by short-read sequencing. Significantly, a chromosomal inversion results in antigenic variation of PhtD, an important surface-exposed virulence factor...
August 13, 2018: Nucleic Acids Research
Ashley F George, Teh-Yuan Ho, Nripesh Prasad, Brittney N Keel, Jeremy R Miles, Jeffrey L Vallet, Frank F Bartol, Carol A Bagnell
Reproductive performance of female pigs that do not receive sufficient colostrum from birth is permanently impaired. Whether lactocrine deficiency, reflected by low serum immunoglobulin immunocrit (iCrit), affects patterns of endometrial gene expression during the periattachment period of early pregnancy is unknown. Here, objectives were to determine effects of low iCrit at birth on the adult endometrial transcriptome on pregnancy day (PxD) 13. On the first day of postnatal life, gilts were assigned to high or low iCrit groups...
August 9, 2018: Biology of Reproduction
Matthew Jacobson, Adriana Estela Sedeño-Cortés, Paul Pavlidis
Background: The Gene Ontology (GO) is one of the most widely used resources in molecular and cellular biology, largely through the use of "enrichment analysis." To facilitate informed use of GO, we present GOtrack (, which provides access to historical records and trends in the Gene Ontology and GO annotations (GOA). Findings: GOtrack gives users access to gene- and term-level information on annotations for nine model organisms as well as an interactive tool that measures the stability of enrichment results over time for user-provided "hit lists" of genes...
August 9, 2018: GigaScience
Fei-Ran Han, Xuan-Min Guang, Qiu-Hong Wan, Sheng-Guo Fang
The giant panda (Ailuropoda melanoleuca) is popular around the world and is widely recognised as a symbol of nature conservation. A draft genome of the giant panda is now available, but its Y chromosome has not been sequenced. Y chromosome data is necessary for study of sex chromosome evolution, male development, and spermatogenesis. Thus, in the present study, we sequenced two parts of the giant panda Y chromosome utilizing a male giant panda fosmid library. The sequencing data was assembled into two contigs, each ∼100 kb in length with no gaps, providing high-quality resources for studying the giant panda Y chromosome...
August 13, 2018: Genome Biology and Evolution
Feng He, Xiong Zhang, Binxin Li, Asma Safdar, Gan Ai, Alex Machio Kange, Yancun Zhao, Haiqun Cao, Daolong Dou, Fengquan Liu
Valsa pyri, an ascomycete pathogen that is a member of the Valsaceae family (Sordariomycetes, Diaporthales), which causes pear or apple canker and leads to tree death and massive yield losses. Here, we selected two V. pyri isolates (Vp14 and Vp297) that exhibited different invasion abilities for transcriptomics analyses. Compared toVp297, Vp14 had stronger virulence and spread faster on host-like nutrients. Four samples, including mycelium or infectious mycelium, of the two isolates were sequenced. Clean reads were mapped to the V...
August 11, 2018: Microbial Pathogenesis
Hirofumi Ichinose, Takuya Kitaoka
A wide variety of sesquiterpenoids have been isolated from basidiomycetes, and their bioactive properties have attracted significant attention in an effort to understand biosynthetic machineries. As both sesquiterpene synthases and cytochrome P450 monooxygenases play key roles in the diversification of sesquiterpenoids, it is important to widely and mutually understand their biochemical properties. In this study, we performed genome-wide annotation and functional characterization of sesquiterpene synthases from the brown-rot basidiomycete Postia placenta...
August 13, 2018: Microbial Biotechnology
Khalid M Alharbi, Abdelhadi H Al-Mazroea, Atiyeh M Abdallah, Yousef Almohammadi, S Justin Carlus, Sulman Basit
Down syndrome (DS) is the most common autosomal chromosome anomaly. DS is frequently associated with congenital heart disease (CHD). Patients with DS have 40-60% chance of having CHD. It means that CHD in DS is not only due to trisomy 21 and there are some other genetic factors underlying CHD in DS children. In this study, a total of 240 DNA samples from patients were analyzed including 100 patients with CHD only, 110 patients having CHD along with DS and 30 patients with isolated DS. A cardiovascular gene panel consisting of probes for 406 genes was used to screen DNA samples of all 240 patients for mutation identification...
August 13, 2018: Pediatric Cardiology
Pier Francesco Palamara, Jonathan Terhorst, Yun S Song, Alkes L Price
Interest in reconstructing demographic histories has motivated the development of methods to estimate locus-specific pairwise coalescence times from whole-genome sequencing data. Here we introduce a powerful new method, ASMC, that can estimate coalescence times using only SNP array data, and is orders of magnitude faster than previous approaches. We applied ASMC to detect recent positive selection in 113,851 phased British samples from the UK Biobank, and detected 12 genome-wide significant signals, including 6 novel loci...
August 13, 2018: Nature Genetics
Elnaz Mirzaei Mehrabad, Reza Hassanzadeh, Changiz Eslahchi
The importance of protein subcellular localization problem is due to the importance of protein's functions in different cell parts. Moreover, prediction of subcellular locations helps to identify the potential molecular targets for drugs and has an important role in genome annotation. Most of the existing prediction methods assign only one location for each protein. But, since some proteins move between different subcellular locations, they can have multiple locations. In recent years, some multiple location predictors have been introduced...
August 13, 2018: Scientific Reports
Xuemei Ji, Yohan Bossé, Maria Teresa Landi, Jiang Gui, Xiangjun Xiao, David Qian, Philippe Joubert, Maxime Lamontagne, Yafang Li, Ivan Gorlov, Mariella de Biasi, Younghun Han, Olga Gorlova, Rayjean J Hung, Xifeng Wu, James McKay, Xuchen Zong, Robert Carreras-Torres, David C Christiani, Neil Caporaso, Mattias Johansson, Geoffrey Liu, Stig E Bojesen, Loic Le Marchand, Demetrios Albanes, Heike Bickeböller, Melinda C Aldrich, William S Bush, Adonina Tardon, Gad Rennert, Chu Chen, M Dawn Teare, John K Field, Lambertus A Kiemeney, Philip Lazarus, Aage Haugen, Stephen Lam, Matthew B Schabath, Angeline S Andrew, Hongbing Shen, Yun-Chul Hong, Jian-Min Yuan, Pier A Bertazzi, Angela C Pesatori, Yuanqing Ye, Nancy Diao, Li Su, Ruyang Zhang, Yonathan Brhane, Natasha Leighl, Jakob S Johansen, Anders Mellemgaard, Walid Saliba, Christopher Haiman, Lynne Wilkens, Ana Fernandez-Somoano, Guillermo Fernandez-Tardon, Erik H F M van der Heijden, Jin Hee Kim, Juncheng Dai, Zhibin Hu, Michael P A Davies, Michael W Marcus, Hans Brunnström, Jonas Manjer, Olle Melander, David C Muller, Kim Overvad, Antonia Trichopoulou, Rosario Tumino, Jennifer Doherty, Gary E Goodman, Angela Cox, Fiona Taylor, Penella Woll, Irene Brüske, Judith Manz, Thomas Muley, Angela Risch, Albert Rosenberger, Kjell Grankvist, Mikael Johansson, Frances Shepherd, Ming-Sound Tsao, Susanne M Arnold, Eric B Haura, Ciprian Bolca, Ivana Holcatova, Vladimir Janout, Milica Kontic, Jolanta Lissowska, Anush Mukeria, Simona Ognjanovic, Tadeusz M Orlowski, Ghislaine Scelo, Beata Swiatkowska, David Zaridze, Per Bakke, Vidar Skaug, Shanbeh Zienolddiny, Eric J Duell, Lesley M Butler, Woon-Puay Koh, Yu-Tang Gao, Richard Houlston, John McLaughlin, Victoria Stevens, David C Nickle, Ma'en Obeidat, Wim Timens, Bin Zhu, Lei Song, María Soler Artigas, Martin D Tobin, Louise V Wain, Fangyi Gu, Jinyoung Byun, Ahsan Kamal, Dakai Zhu, Rachel F Tyndale, Wei-Qi Wei, Stephen Chanock, Paul Brennan, Christopher I Amos
Genome-wide association studies (GWAS) identified the chromosome 15q25.1 locus as a leading susceptibility region for lung cancer. However, the pathogenic pathways, through which susceptibility SNPs within chromosome 15q25.1 affects lung cancer risk, have not been explored. We analyzed three cohorts with GWAS data consisting 42,901 individuals and lung expression quantitative trait loci (eQTL) data on 409 individuals to identify and validate the underlying pathways and to investigate the combined effect of genes from the identified susceptibility pathways...
August 13, 2018: Nature Communications
Young-Jin Park, Yong-Un Jeong, Won-Sik Kong
Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous...
August 13, 2018: International Journal of Molecular Sciences
Qingqing Wang, Donald C Rio
Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-sequencing data rely on preannotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated genomes and can further mask unknown AS patterns. To address this critical bioinformatics problem, we developed a method called the junction usage model (JUM) that uses a bottom-up approach to identify, analyze, and quantitate global AS profiles without any prior transcriptome annotations...
August 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
Martin Norling, Niclas Jareborg, Jacques Dainat
OBJECTIVE: The state-of-the-art genome annotation tools output GFF3 format files, while this format is not accepted as submission format by the International Nucleotide Sequence Database Collaboration (INSDC) databases. Converting the GFF3 format to a format accepted by one of the three INSDC databases is a key step in the achievement of genome annotation projects. However, the flexibility existing in the GFF3 format makes this conversion task difficult to perform. Until now, no converter is able to handle any GFF3 flavour regardless of source...
August 13, 2018: BMC Research Notes
Xiwu Qi, Hailing Fang, Xu Yu, Dongbei Xu, Li Li, Chengyuan Liang, Hongfei Lu, Weilin Li, Yin Chen, Zequn Chen
Mentha canadensis L. has important economic value for its abundance in essential oils. Menthol is the main component of M. canadensis essential oils, which is certainly the best-known monoterpene for its simple structure and wide applications. However, the regulation of menthol biosynthesis remains elusive in M. canadensis . In this study, transcriptome sequencing of M. canadensis with MeJA treatment was applied to illustrate the transcriptional regulation of plant secondary metabolites, especially menthol biosynthesis...
August 10, 2018: International Journal of Molecular Sciences
Long Sun, Juan Xu, Fang He
OBJECTIVES: Escherichia coli is the leading cause of urinary tract infections worldwide. Carbapenemase producing clinical isolates leave few therapeutic options. Here we report the draft genome sequence of a NDM-5, CTX-M-15, and OXA-1 co-producing E. coli ST167: a multidrug-resistant strain isolated from urine sample of a male hospitalized patient diagnosed with intracranial injury from a traffic accident. METHODS: The genome of E. coli ECWJ1 was sequenced using the Illumina HiSeq™ 4000 platform...
August 10, 2018: Journal of Global Antimicrobial Resistance
Zhaoxia Dong, Shaozhen Xing, Jin Liu, Xizhe Tang, Lifang Ruan, Ming Sun, Yigang Tong, Donghai Peng
Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a serious bacterial disease in rice-growing regions worldwide. Phage therapy has been proposed as a potential measure to treat bacterial infections. In this study, a novel phage, Xoo-sp2, which infects Xoo was isolated from soil. The characteristics of Xoo-sp2, including the morphology, one-step growth curve and host range, were analysed. The genome of phage Xoo-sp2 was sequenced and annotated. The results demonstrated that Xoo-sp2 is a siphovirus and has a broad lytic spectrum, infecting 9 out of 10 representative Xoo strains...
August 10, 2018: Journal of General Virology
Christopher Phillips, Laurence Devesse, David Ballard, Leanne van Weert, Maria de la Puente, Stefania Melis, Vanessa Álvarez Iglesias, Ana Freire-Aradas, Nicola Oldroyd, Cydne Holt, Denise Syndercombe Court, Ángel Carracedo, Maria Victoria Lareu
The 944 individuals of the HGDP-CEPH human genome diversity panel, a standard sample set of 51 globally distributed populations, were sequenced using the Illumina ForenSeq™ DNA Signature Prep Kit. The ForenSeq™ system is a single multiplex for the MiSeq/FGx™ massively parallel sequencing (MPS) instrument, comprising: amelogenin; 27 autosomal STRs; 24 Y-STRs; 7 X-STRs; and 94 SNPforID+Kiddlab autosomal ID-SNPs (plus optionally detected ancestry and phenotyping SNP sets). We report in detail the patterns of sequence variation observed in the repeat regions of the 58 forensic STR loci typed by the ForenSeq™ system...
August 13, 2018: Electrophoresis
Daniel Longhi Fernandes Pedro, Alan Péricles Rodrigues Lorenzetti, Douglas Silva Domingues, Alexandre Rossi Paschoal
Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although the relationship between ncRNAs and TEs is known, obtaining the organized data for sequenced genomes is not straightforward. In this study, we describe the PlaNC-TE (, a user-friendly portal harboring a knowledgebase created by integrating and analysing plant ncRNA-TE data...
August 2, 2018: Database: the Journal of Biological Databases and Curation
Richard J Edwards, Daniel Enosi Tuipulotu, Timothy G Amos, Denis O'Meally, Mark F Richardson, Tonia L Russell, Marcelo Vallinoto, Miguel Carneiro, Nuno Ferrand, Marc R Wilkins, Fernando Sequeira, Lee A Rollins, Edward C Holmes, Richard Shine, Peter A White
Background: The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research. Findings: We report a draft genome assembly for R...
August 7, 2018: GigaScience
Yuval Dor, Howard Cedar
DNA methylation represents an annotation system for marking the genetic text, thus providing instruction as to how and when to read the information and control transcription. Unlike sequence information, which is inherited, methylation patterns are established in a programmed process that continues throughout development, thus setting up stable gene expression profiles. This DNA methylation paradigm is a key player in medicine. Some changes in methylation closely correlate with age providing a marker for biological ageing, and these same sites could also play a part in cancer...
August 9, 2018: Lancet
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