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Genome sequencing

Joel A Boyd, Ben J Woodcroft, Gene W Tyson
Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees...
March 19, 2018: Nucleic Acids Research
Graham M Hughes, Emma M Boston, John A Finarelli, William J Murphy, Desmond G Higgins, Emma C Teeling
The olfactory receptor (OR) gene families, which govern mammalian olfaction, have undergone extensive expansion and contraction through duplication and pseudogenization. Previous studies have shown that broadly-defined environmental adaptations (e.g terrestrial vs aquatic) are correlated with the number of functional and non-functional OR genes retained. However, to date, no study has examined species-specific gene duplications in multiple phylogenetically divergent mammals to elucidate OR evolution and adaptation...
March 19, 2018: Molecular Biology and Evolution
Jamie McCann, Tae-Soo Jang, Jiri Macas, Gerald M Schneeweiss, Nicholas J Matzke, Petr Novák, Tod F Stuessy, José L Villaseñor, Hanna Weiss-Schneeweiss
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid...
March 19, 2018: Systematic Biology
A E Webb, I A Youngworth, M Kaya, C L Gitter, E A O'Hare, B May, H H Cheng, M E Delany
Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic lethal condition. Affected individuals exhibit a multisystem syndrome characterized by absent wings, truncated legs, and craniofacial, kidney, and feather malformations. Previously, work focused on phenotype description, establishing the autosomal recessive pattern of Mendelian inheritance and placing the mutation on an inbred genetic background to create the congenic line UCD Wingless-2.331. The research described in this paper employed the complementary tools of breeding, genetics, and genomics to map the chromosomal location of the mutation and successively narrow the size of the region for analysis of the causative element...
March 19, 2018: Poultry Science
Patrick J Short, Jeremy F McRae, Giuseppe Gallone, Alejandro Sifrim, Hyejung Won, Daniel H Geschwind, Caroline F Wright, Helen V Firth, David R FitzPatrick, Jeffrey C Barrett, Matthew E Hurles
We previously estimated that 42% of patients with severe developmental disorders carry pathogenic de novo mutations in coding sequences. The role of de novo mutations in regulatory elements affecting genes associated with developmental disorders, or other genes, has been essentially unexplored. We identified de novo mutations in three classes of putative regulatory elements in almost 8,000 patients with developmental disorders. Here we show that de novo mutations in highly evolutionarily conserved fetal brain-active elements are significantly and specifically enriched in neurodevelopmental disorders...
March 21, 2018: Nature
Mateja Hajdinjak, Qiaomei Fu, Alexander Hübner, Martin Petr, Fabrizio Mafessoni, Steffi Grote, Pontus Skoglund, Vagheesh Narasimham, Hélène Rougier, Isabelle Crevecoeur, Patrick Semal, Marie Soressi, Sahra Talamo, Jean-Jacques Hublin, Ivan Gušić, Željko Kućan, Pavao Rudan, Liubov V Golovanova, Vladimir B Doronichev, Cosimo Posth, Johannes Krause, Petra Korlević, Sarah Nagel, Birgit Nickel, Montgomery Slatkin, Nick Patterson, David Reich, Kay Prüfer, Matthias Meyer, Svante Pääbo, Janet Kelso
Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA...
March 21, 2018: Nature
Emily G Kaye, Matthew Booker, Jesse V Kurland, Alexander E Conicella, Nicolas L Fawzi, Martha L Bulyk, Michael Y Tolstorukov, Erica Larschan
Little is known about how variation in sequence composition alters transcription factor occupancy to precisely recruit large transcription complexes. A key model for understanding how transcription complexes are targeted is the Drosophila dosage compensation system in which the male-specific lethal (MSL) transcription complex specifically identifies and regulates the male X chromosome. The chromatin-linked adaptor for MSL proteins (CLAMP) zinc-finger protein targets MSL to the X chromosome but also binds to GA-rich sequence elements throughout the genome...
March 20, 2018: Cell Reports
Kwondo Kim, Jaehoon Jung, Kelsey Caetano-Anollés, Samsun Sung, DongAhn Yoo, Bong-Hwan Choi, Hyung-Chul Kim, Jin-Young Jeong, Yong-Min Cho, Eung-Woo Park, Tae-Jeong Choi, Byoungho Park, Dajeong Lim, Heebal Kim
Artificial selection has been demonstrated to have a rapid and significant effect on the phenotype and genome of an organism. However, most previous studies on artificial selection have focused solely on genomic sequences modified by artificial selection or genomic sequences associated with a specific trait. In this study, we generated whole genome sequencing data of 126 cattle under artificial selection, and 24,973,862 single nucleotide variants to investigate the relationship among artificial selection, genomic sequences and trait...
2018: PloS One
Zengrong Zhang, Huarui Du, Lijun Bai, Chaowu Yang, Qingyun Li, Xiaocheng Li, Mohan Qiu, Chunlin Yu, Zongrong Jiang, Xiaoyu Jiang, Lan Liu, Chenming Hu, Bo Xia, Xia Xiong, Xiaoyan Song, Xiaosong Jiang
BACKGROUND: Tibetan chickens living at high altitudes show specific adaptations to high-altitude conditions, but the epigenetic modifications associated with these adaptations have not been characterized. RESULTS: We investigated the genome-wide DNA methylation patterns in Tibetan chicken blood by using whole genome bisulfite sequencing. Generally, Tibetan chickens exhibited analogous methylation patterns to that of lowland chickens. A total of 3.92% of genomic cytosines were methylcytosines and 51...
2018: PloS One
Narmada Sambaturu, Sumanta Mukherjee, Martín López-García, Carmen Molina-París, Gautam I Menon, Nagasuma Chandra
Genetic differences contribute to variations in the immune response mounted by different individuals to a pathogen. Such differential response can influence the spread of infectious disease, indicating why such diseases impact some populations more than others. Here, we study the impact of population-level genetic heterogeneity on the epidemic spread of different strains of H1N1 influenza. For a population with known HLA class-I allele frequency and for a given H1N1 viral strain, we classify individuals into sub-populations according to their level of susceptibility to infection...
March 21, 2018: PLoS Computational Biology
Songzhen He, Xiaoling Tong, Minjin Han, Yanmin Bai, Fangyin Dai
The tyrosine kinases (TKs) are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable...
March 21, 2018: International Journal of Molecular Sciences
Josphat K Saina, Zhi-Zhong Li, Andrew W Gichira, Yi-Ying Liao
Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence...
March 21, 2018: International Journal of Molecular Sciences
Kathy H Y Shair, Akhil Reddy, Vaughn S Cooper
Latent membrane protein 1 (LMP1) is an Epstein-Barr virus (EBV) oncogenic protein that has no intrinsic enzymatic activity or sequence homology to cellular or viral proteins. The oncogenic potential of LMP1 has been ascribed to pleiotropic signaling properties initiated through protein-protein interactions in cytosolic membrane compartments, but the effects of LMP1 extend to nuclear and extracellular processes. Although LMP1 is one of the latent genes required for EBV-immortalization of B cells, the biology of LMP1 in the pathogenesis of the epithelial cancer nasopharyngeal carcinoma (NPC) is more complex...
March 21, 2018: Cancers
Christiana Leimena, Hongyu Qiu
Hypertension is a complex, multifactorial disease that involves the coexistence of multiple risk factors, environmental factors and physiological systems. The complexities extend to the treatment and management of hypertension, which are still the pursuit of many researchers. In the last two decades, various genes have emerged as possible biomarkers and have become the target for investigations of specialized drug design based on its risk factors and the primary cause. Owing to the growing technology of microarrays and next-generation sequencing, the non-protein-coding RNAs (ncRNAs) have increasingly gained attention, and their status of redundancy has flipped to importance in normal cellular processes, as well as in disease progression...
March 21, 2018: International Journal of Molecular Sciences
Lei Lei, Kesava Phaneendra Cherukuri, Uria Alcolombri, Diana Meltzer, Dan S Tawfik
Marine organisms release dimethylsulfide (DMS) via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known, yet these exhibit highly variable levels of activity. Most assigned bacterial DMSP lyases, including DddK, DddL, DddQ, DddW and DddY, appear to belong to one, cupin-like superfamily. Here, we attempted to define and map this superfamily dubbed Cupin-DLL: DMSP lyases and lyase-like. To this end, we have pursued the characterization of various recombinant DMSP lyases belonging to this superfamily of metallo-enzymes, and especially of DddY and DddL that seem to be the most active DMSP lyases in this superfamily...
March 21, 2018: Biochemistry
Dong-Min Kim, Dong Ho Kim, Woong Jung, Kye Young Lee, Dong-Eun Kim
Mutations in epidermal growth factor receptor (EGFR) are known as biomarkers that cause non-small cell lung cancer. Particularly, approximately 45% of non-small cell lung cancer patients possess a deletion in exon 19 of the EGFR gene. A less invasive method for detecting the EGFR mutation is required; thus, we developed a simple polymerase chain reaction (PCR)-based method for detecting EGFR exon 19 deletion by using a quencher-free fluorescent probe DNA and graphene oxide (GO). In the presence of the exon 19 deletion mutation, the fluorophore-labeled DNA probe was designed to be fully complementary to the mutant sequences...
March 21, 2018: Analyst
Liaoyuan Wang, Qing Wang, Yue Zhou, Qian Xue, Xiao Sun, Zhinong Wang, Guangyu Ji
RATIONALE: Carney complex (CNC) accounts for up to two-thirds of familial cardiac myxoma, which is a rare autosomal dominant syndrome characterized by multiple mucocutaneous lesions and endocrine tumors. Mutation in the cAMP-dependent protein kinase A (PKA) regulatory (R) subunit 1 (PRKAR1A) gene has been identified as a cause of CNC. In this article, we report 3 first-degree relatives with cardiac myxoma who were diagnosed with CNC and underwent surgical resection. PRESENTING CONCERNS: The recurrence of cardiac myxoma was detected in a 45-year-old male by echocardiography 5 years after the resection was carried out, without any additional symptoms...
March 2018: Medicine (Baltimore)
Hojun Sung, Hyun Sik Kim, June-Young Lee, Woorim Kang, Pil Soo Kim, Dong-Wook Hyun, Euon Jung Tak, Mi-Ja Jung, Ji-Hyun Yun, Min-Soo Kim, Na-Ri Shin, Tae Woong Whon, Jeong Rae Rho, Sun Duk Park, Hyung Eun Shim, Jin-Woo Bae
A Gram-stain-positive, facultatively aerobic, spore-forming, oxidase-positive, catalase- and DNase-negative, rod-shaped and motile bacterial strain, AR23208T , was isolated from the gut of a cinereous vulture (Aegypius monachus), collected at Seoul Grand Park Zoo (Republic of Korea). Strain AR23208T grew optimally at 25-30 °C, at pH 7 and in the absence of NaCl. Phylogenetic analysis revealed that strain AR23208T shared 98.2 and 97.1 % 16S rRNA gene sequence similarity with Tumebacillus algifaecis THMBR28T and Tumebacilluslipolyticus NIO-S10T , respectively...
March 21, 2018: International Journal of Systematic and Evolutionary Microbiology
Qing Liu, Yu-Hua Xin, Xiu-Ling Chen, Hong-Can Liu, Yu-Guang Zhou, Wen-Xin Chen
A Gram-stain-positive strain designated MDB1-42T was isolated from ice collected from Midui glacier in Tibet, PR China. Strain MDB1-42T was catalase-positive, oxidase-negative and grew optimally at 25-28 °C and pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that MDB1-42T represented a member of the genus Arthrobacter. The highest level of 16S rRNA gene sequence similarity (99.86 %) was found with Arthrobacter agilis NBRC 15319T . Multilocus sequence analysis revealed low similarity of 91...
March 21, 2018: International Journal of Systematic and Evolutionary Microbiology
Xia Liu, Yongdong Xu, Zhi Li, Shengwei Jiang, Shuo Yao, Rina Wu, Yingfeng An
A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16 s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities...
March 21, 2018: Preparative Biochemistry & Biotechnology
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