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Genome annotation

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https://www.readbyqxmd.com/read/29234695/an-improved-draft-of-the-pigeonpea-cajanus-cajan-l-millsp-genome
#1
Ajay Kumar Mahato, Ajay Kumar Sharma, Tilak Raj Sharma, Nagendra Kumar Singh
The first draft of the pigeonpea (Cajanus cajan (L.) Millsp. cv. Asha) genome with 511 Mbp of assembled sequence information has low genome coverage of about sixty percent. Here we present an improved version of this genome with 648.2 Mbp of assembled sequence of this popular pigeonpea variety, which is liked by the millers and has resistance to fusarium wilt and sterility mosaic diseases. With the addition of 137 Mb of assembled sequence information the present version has the highest available genome coverage of pigeonpea till date...
February 2018: Data in Brief
https://www.readbyqxmd.com/read/29234286/identification-of-biomarkers-correlated-with-the-tnm-staging-and-overall-survival-of-patients-with-bladder-cancer
#2
Sheng Li, Xiaoping Liu, Tongzu Liu, Xiangyu Meng, Xiaohong Yin, Cheng Fang, Di Huang, Yue Cao, Hong Weng, Xiantao Zeng, Xinghuan Wang
Objective: To identify candidate biomarkers correlated with clinical prognosis of patients with bladder cancer (BC). Methods: Weighted gene co-expression network analysis was applied to build a co-expression network to identify hub genes correlated with tumor node metastasis (TNM) staging of BC patients. Functional enrichment analysis was conducted to functionally annotate the hub genes. Protein-protein interaction network analysis of hub genes was performed to identify the interactions among the hub genes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29233922/deep-experimental-profiling-of-microrna-diversity-deployment-and-evolution-across-the-drosophila-genus
#3
Jaaved Mohammed, Alex S Flynt, Alexandra M Panzarino, Md Mosharrof Hussein Mondal, Matthew DeCruz, Adam Siepel, Eric C Lai
To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5' end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs...
December 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29233913/reference-quality-genome-assemblies-of-three-parastagonospora-nodorum%C3%A2-isolates-differing-in-virulence-on-wheat
#4
Jonathan K Richards, Nathan A Wyatt, Zhaohui Liu, Justin D Faris, Timothy L Friesen
Parastagonospora nodorum, the causal agent of Septoria nodorum blotch of wheat, has emerged as a model necrotrophic fungal organism for the study of host-microbe interactions. To date, three necrotrophic effectors have been identified and characterized from this pathogen, including SnToxA, SnTox1, and SnTox3. Necrotrophic effector identification was greatly aided by the development of a draft genome of Australian isolate SN15 via Sanger sequencing, yet remained largely fragmented. This research presents the development of near-finished genomes of P...
December 12, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29233850/ltr_retriever-a-highly-accurate-and-sensitive-program-for-identification-of-long-terminal-repeat-retrotransposons
#5
Shujun Ou, Ning Jiang
Long terminal-repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. Identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the well-conserved structure, multiple programs were developed for de novo identification of LTR-RTs; however, these programs are associated with low specificity and high false discovery rate (FDR). Here we report LTR_retriever, a multithreading empowered Perl program that identifies LTR-RTs and generates high-quality LTR libraries from genomic sequences...
December 12, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29233089/de-novo-transcriptome-assembly-from-flower-buds-of-dioecious-gynomonoecious-and-chemically-masculinized-female-coccinia-grandis-reveals-genes-associated-with-sex-expression-and-modification
#6
Ravi Suresh Devani, Sangram Sinha, Jayeeta Banerjee, Rabindra Kumar Sinha, Abdelhafid Bendahmane, Anjan Kumar Banerjee
BACKGROUND: Coccinia grandis (ivy gourd), is a dioecious member of Cucurbitaceae having heteromorphic sex chromosomes. Chromosome constitution of male and female plants of C. grandis is 22A + XY and 22A + XX respectively. Earlier we showed that a unique gynomonoecious form of C. grandis (22A + XX) also exists in nature bearing morphologically hermaphrodite flowers (GyM-H). Additionally, application of silver nitrate (AgNO3) on female plants induces stamen development leading to the formation of morphologically hermaphrodite flowers (Ag-H) despite the absence of Y-chromosome...
December 12, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29233025/ralstonia-eutropha-h16-in-progress-applications-beside-phas-and-establishment-as-production-platform-by-advanced-genetic-tools
#7
Matthias Raberg, Elena Volodina, Kaichien Lin, Alexander Steinbüchel
Ralstonia eutropha strain H16 is a Gram-negative non-pathogenic betaproteobacterium ubiquitously found in soils and has been the subject of intensive research for more than 50 years. Due to its remarkable metabolically versatility, it utilizes a broad range of renewable heterotrophic resources. The substrate utilization range can be further extended by metabolic engineering as genetic tools are available. It has become the best studied "Knallgas" bacterium capable of chemolithoautotrophic growth with hydrogen as the electron donor and carbon dioxide as the carbon source...
December 12, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29230584/mapping-of-a-major-quantitative-trait-locus-for-bakanae-disease-resistance-in-rice-by-genome-resequencing
#8
Hyeonso Ji, Tae-Ho Kim, Gang-Seob Lee, Hyun-Ju Kang, Seung-Bum Lee, Seok Cheol Suh, Song Lim Kim, Inchan Choi, Jeongho Baek, Kyung-Hwan Kim
Bakanae disease (BD) has emerged as a serious threat in almost all rice cultivation regions worldwide. Nampyeong is a Korean japonica rice variety known to be resistant to BD. In this study, quantitative trait locus (QTL) mapping was performed with F2 and F3 plants derived from a cross between the Nampyeong variety and a susceptible Korean japonica line, DongjinAD. First, resequencing of Nampyeong and DongjinAD was performed, which identified 171,035 single nucleotide polymorphisms (SNPs) between the two parental varieties...
December 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29229530/trichoderma-harzianum-mtcc-5179-impacts-the-population-and-functional-dynamics-of-microbial-community-in-the-rhizosphere-of-black-pepper-piper-nigrum-l
#9
Palaniyandi Umadevi, Muthuswamy Anandaraj, Vivek Srivastav, Sailas Benjamin
Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p=1...
November 29, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29228046/genome-wide-microarray-analysis-leads-to-identification-of-genes-in-response-to-herbicide-metribuzin-in-wheat-leaves
#10
Whitney Pilcher, Hana Zandkamiri, Kelly Arceneaux, Stephen Harrison, Niranjan Baisakh
Herbicides are an important component of weed management in wheat, particularly in the southeastern US where weeds actively compete with wheat throughout the winter for nutrients and reduce tillering and ultimately the yield of the crop. Some wheat varieties are sensitive to metribuzin, a low-cost non-selective herbicide, leading to leaf chlorosis, stand loss, and decreased yield. Knowledge of the genetics of herbicide tolerance in wheat is very limited and most new varieties have not been screened for metribuzin tolerance...
2017: PloS One
https://www.readbyqxmd.com/read/29226517/natural-selection-beyond-genes-identification-and-analyses-of-evolutionarily-conserved-elements-in-the-genome-of-the-collared-flycatcher-ficedula-albicollis
#11
Rory J Craig, Alexander Suh, Mi Wang, Hans Ellegren
It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence is particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts...
December 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29225727/the-genomic-study-of-an-environmental-isolate-of-scedosporium-apiospermum-shows-its-metabolic-potential-to-degrade-hydrocarbons
#12
Laura T Morales, Laura N González-García, María C Orozco, Silvia Restrepo, Martha J Vives
Crude oil contamination of soils and waters is a worldwide problem, which has been actively addressed in recent years. Sequencing genomes of microorganisms involved in the degradation of hydrocarbons have allowed the identification of several promoters, genes, and degradation pathways of these contaminants. This knowledge allows a better understanding of the functional dynamics of microbial degradation. Here, we report a first draft of the 44.2 Mbp genome assembly of an environmental strain of the fungus Scedosporium apiospermum...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29225705/using-bioinformatic-and-phylogenetic-approaches-to-classify-transposable-elements-and-understand-their-complex-evolutionary-histories
#13
REVIEW
Irina R Arkhipova
In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29225348/a-multi-dimensional-characterization-of-anxiety-in-monozygotic-twin-pairs-reveals-susceptibility-loci-in-humans
#14
Reid S Alisch, Carol Van Hulle, Pankaj Chopra, Anita Bhattacharyya, Su-Chun Zhang, Richard J Davidson, Ned H Kalin, H Hill Goldsmith
The etiology of individual differences in human anxiousness is complex and includes contributions from genetic, epigenetic (i.e., DNA methylation) and environmental factors. Past genomic approaches have been limited in their ability to detect human anxiety-related differences in these factors. To overcome these limitations, we employed both a multi-dimensional characterization method, to select monozygotic twin pairs discordant for anxiety, and whole genome DNA methylation sequencing. This approach revealed 230 anxiety-related differentially methylated loci that were annotated to 183 genes, including several known stress-related genes such as NAV1, IGF2, GNAS, and CRTC1...
December 11, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/29225048/de-novo-assembly-and-functional-annotations-of-the-transcriptome-of-metorchis-orientalis-trematoda-opisthorchiidae
#15
Jun-Feng Gao, Yuan Gao, Jian-Hua Qiu, Qiao-Cheng Chang, Yan Zhang, Ming Fang, Chun-Ren Wang
Metorchis orientalis is a neglected zoonotic parasite, living in the gallbladder and bile duct of poultry and some mammals as well as humans. In spite of its economic and medical importance, the information known about the transcriptome and genome of M. orientalis is limited. In this study, we performed de novo sequencing, transcriptome assembly and functional annotations of the adult M. orientalis, obtained about 77.4 million high-quality clean reads, among which the length of the transcript contigs ranged from 100 to 11,249 nt with mean length of 373 nt and N50 length of 919 nt...
December 7, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/29223802/proteogenomic-insights-into-uranium-tolerance-of-a-chernobyl-s-microbacterium-bacterial-isolate
#16
Gallois Nicolas, Alpha-Bazin Béatrice, Ortet Philippe, Barakat Mohamed, Piette Laurie, Long Justine, Berthomieu Catherine, Armengaud Jean, Chapon Virginie
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance...
December 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29223718/complete-genome-sequence-of-the-highly-mn-ii-tolerant-staphylococcus-sp-antimn-1-isolated-from-deep-sea-sediment-in-the-clarion-clipperton-zone
#17
Xing Wang, Danqiu Lin, Xiaohuan Jing, Sidong Zhu, Jifang Yang, Jigang Chen
Staphylococcus sp. AntiMn-1 is a deep-sea bacterium inhabiting seafloor sediment in the Clarion-Clipperton Zone (CCZ) that is highly tolerant to Mn(II) and displays efficient Mn(II) oxidation. Herein, we present the assembly and annotation of its genome.
December 6, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/29223164/the-mitochondrial-genome-of-the-moss-brachythecium-rivulare-hypnales-brachytheciaceae
#18
D V Goryunov, M D Logacheva, M S Ignatov, I A Milyutina, A V Fedorova, A V Troitsky
The mitochondrial genome of the pleurocarpous moss Brachythecium rivulare has been sequenced and annotated. The genome consists of 104,460 base pairs and has approximately the same gene set and organization as other bryophyte mitogenomes. Whole mitochondrial genome comparison between B. rivulare and Physcomitrella patens, Tetraphis pellucida, Anomodon rugelii, and Anomodon attenuatus was performed. The primary cause of bryophyte mitochondrial gene length variation was found to be numerous indels in the introns...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29222752/using-psamm-for-the-curation-and-analysis-of-genome-scale-metabolic-models
#19
Keith Dufault-Thompson, Jon Lund Steffensen, Ying Zhang
PSAMM is an open source software package that supports the iterative curation and analysis of genome-scale models (GEMs). It aims to integrate the annotation and consistency checking of metabolic models with the simulation of metabolic fluxes. The model representation in PSAMM is compatible with version tracking systems like Git, which allows for full documentation of model file changes and enables collaborative curations of large, complex models. This chapter provides a protocol for using PSAMM functions and a detailed description of the various aspects in setting up and using PSAMM for the simulation and analysis of metabolic models...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222751/reconstruction-and-analysis-of-central-metabolism-in-microbes
#20
Janaka N Edirisinghe, José P Faria, Nomi L Harris, Benjamin H Allen, Christopher S Henry
Genome-scale metabolic models (GEMs) generated from automated reconstruction pipelines often lack accuracy due to the need for extensive gapfilling and the inference of periphery metabolic pathways based on lower-confidence annotations. The central carbon pathways and electron transport chains are among the most well-understood regions of microbial metabolism, and these pathways contribute significantly toward defining cellular behavior and growth conditions. Thus, it is often useful to construct a simplified core metabolic model (CMM) that is comprised of only the high-confidence central pathways...
2018: Methods in Molecular Biology
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