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orphan genes, de novo genes

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https://www.readbyqxmd.com/read/28396521/evaluation-of-grch38-and-de-novo-haploid-genome-assemblies-demonstrates-the-enduring-quality-of-the-reference-assembly
#1
Valerie A Schneider, Tina Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul A Kitts, Terence D Murphy, Kim D Pruitt, Françoise Thibaud-Nissen, Derek Albracht, Robert S Fulton, Milinn Kremitzki, Vincent Magrini, Chris Markovic, Sean McGrath, Karyn Meltz Steinberg, Kate Auger, William Chow, Joanna Collins, Glenn Harden, Timothy Hubbard, Sarah Pelan, Jared T Simpson, Glen Threadgold, James Torrance, Jonathan M Wood, Laura Clarke, Sergey Koren, Matthew Boitano, Paul Peluso, Heng Li, Chen-Shan Chin, Adam M Phillippy, Richard Durbin, Richard K Wilson, Paul Flicek, Evan E Eichler, Deanna M Church
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues...
May 2017: Genome Research
https://www.readbyqxmd.com/read/28379977/comparative-transcriptomics-of-entelegyne-spiders-araneae-entelegynae-with-emphasis-on-molecular-evolution-of-orphan-genes
#2
David E Carlson, Marshal Hedin
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C...
2017: PloS One
https://www.readbyqxmd.com/read/28355220/high-gc-content-causes-orphan-proteins-to-be-intrinsically-disordered
#3
Walter Basile, Oxana Sachenkova, Sara Light, Arne Elofsson
De novo creation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population. These orphan proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not aggregate. Therefore, although the creation of short ORFs could be truly random, the fixation should be subjected to some selective pressure. The selective forces acting on orphan proteins have been elusive, and contradictory results have been reported...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/27783449/essential-role-of-bordetella-nadc-in-a-quinolinate-salvage-pathway-for-nad-biosynthesis
#4
Timothy J Brickman, Ryan J Suhadolc, Pamela J McKelvey, Sandra K Armstrong
Nicotinamide adenine dinucleotide (NAD) is produced via de novo biosynthesis pathways and by salvage or recycling routes. The classical Bordetella bacterial species are known to be auxotrophic for nicotinamide or nicotinic acid. This study confirmed that Bordetella bronchiseptica, Bordetella pertussis and Bordetella parapertussis have the recycling/salvage pathway genes pncA and pncB, for use of nicotinamide or nicotinic acid, respectively, for NAD synthesis. Although these Bordetellae lack the nadA and nadB genes needed for de novo NAD biosynthesis, remarkably, they have one de novo pathway gene, nadC, encoding quinolinate phosphoribosyltransferase...
October 26, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27709374/exploring-drought-stress-regulated-genes-in-senna-cassia-angustifolia-vahl-a-transcriptomic-approach
#5
Rucha Harishbhai Mehta, Manivel Ponnuchamy, Jitendra Kumar, Nagaraja Reddy Rama Reddy
De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress...
January 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27381092/estrogen-related-receptor-gamma-implicated-in-a-phenotype-including-hearing-loss-and-mild-developmental-delay
#6
Samantha Lp Schilit, Benjamin B Currall, Ruen Yao, Carrie Hanscom, Ryan L Collins, Vamsee Pillalamarri, Dong-Young Lee, Tammy Kammin, Cinthya J Zepeda-Mendoza, Tarja Mononen, Lisa S Nolan, James F Gusella, Michael E Talkowski, Jun Shen, Cynthia C Morton
Analysis of chromosomal rearrangements has been highly successful in identifying genes involved in many congenital abnormalities including hearing loss. Herein, we report a subject, designated DGAP242, with congenital hearing loss (HL) and a de novo balanced translocation 46,XX,t(1;5)(q32;q15)dn. Using multiple next-generation sequencing techniques, we obtained high resolution of the breakpoints. This revealed disruption of the orphan receptor ESRRG on chromosome 1, which is differentially expressed in inner ear hair cells and has previously been implicated in HL, and disruption of KIAA0825 on chromosome 5...
November 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27356763/transcriptome-sequencing-and-marker-development-in-winged-bean-psophocarpus-tetragonolobus-leguminosae
#7
Mohammad Vatanparast, Prateek Shetty, Ratan Chopra, Jeff J Doyle, N Sathyanarayana, Ashley N Egan
Winged bean, Psophocarpus tetragonolobus (L.) DC., is similar to soybean in yield and nutritional value but more viable in tropical conditions. Here, we strengthen genetic resources for this orphan crop by producing a de novo transcriptome assembly and annotation of two Sri Lankan accessions (denoted herein as CPP34 [PI 491423] and CPP37 [PI 639033]), developing simple sequence repeat (SSR) markers, and identifying single nucleotide polymorphisms (SNPs) between geographically separated genotypes. A combined assembly based on 804,757 reads from two accessions produced 16,115 contigs with an N50 of 889 bp, over 90% of which has significant sequence similarity to other legumes...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27352968/loss-of-function-of-the-retinoid-related-nuclear-receptor-rorb-gene-and-epilepsy
#8
Gabrielle Rudolf, Gaetan Lesca, Mana M Mehrjouy, Audrey Labalme, Manal Salmi, Iben Bache, Nadine Bruneau, Manuela Pendziwiat, Joel Fluss, Julitta de Bellescize, Julia Scholly, Rikke S Møller, Dana Craiu, Niels Tommerup, Maria Paola Valenti-Hirsch, Caroline Schluth-Bolard, Frédérique Sloan-Béna, Katherine L Helbig, Sarah Weckhuysen, Patrick Edery, Safia Coulbaut, Mohamed Abbas, Ingrid E Scheffer, Sha Tang, Candace T Myers, Hannah Stamberger, Gemma L Carvill, Deepali N Shinde, Heather C Mefford, Elena Neagu, Robert Huether, Hsiao-Mei Lu, Alice Dica, Julie S Cohen, Catrinel Iliescu, Cristina Pomeran, James Rubenstein, Ingo Helbig, Damien Sanlaville, Edouard Hirsch, Pierre Szepetowski
Genetic generalized epilepsy (GGE), formerly known as idiopathic generalized epilepsy, is the most common form of epilepsy and is thought to have predominant genetic etiology. GGE are clinically characterized by absence, myoclonic, or generalized tonic-clonic seizures with electroencephalographic pattern of bilateral, synchronous, and symmetrical spike-and-wave discharges. Despite their strong heritability, the genetic basis of generalized epilepsies remains largely elusive. Nevertheless, recent advances in genetic technology have led to the identification of numerous genes and genomic defects in various types of epilepsies in the past few years...
December 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27174936/an-updated-human-snornaome
#9
Hadi Jorjani, Stephanie Kehr, Dominik J Jedlinski, Rafal Gumienny, Jana Hertel, Peter F Stadler, Mihaela Zavolan, Andreas R Gruber
Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the post-transcriptional processing of other non-coding RNAs (mostly ribosomal RNAs), but have also been implicated in processes ranging from microRNA-dependent gene silencing to alternative splicing. In order to construct an up-to-date catalog of human snoRNAs we have combined data from various databases, de novo prediction and extensive literature review. In total, we list more than 750 curated genomic loci that give rise to snoRNA and snoRNA-like genes...
June 20, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26911138/translatomics-combined-with-transcriptomics-and-proteomics-reveals-novel-functional-recently-evolved-orphan-genes-in-escherichia-coli-o157-h7-ehec
#10
Klaus Neuhaus, Richard Landstorfer, Lea Fellner, Svenja Simon, Andrea Schafferhans, Tatyana Goldberg, Harald Marx, Olga N Ozoline, Burkhard Rost, Bernhard Kuster, Daniel A Keim, Siegfried Scherer
BACKGROUND: Genomes of E. coli, including that of the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. To find such genes, global gene expression of EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) and mass spectrometry (proteome). RESULTS: Using the above methods, 72 short, non-annotated protein-coding genes were detected...
February 24, 2016: BMC Genomics
https://www.readbyqxmd.com/read/26833063/identification-and-characterization-of-abundant-repetitive-sequences-in-eragrostis-tef-cv-enatite-genome
#11
Yohannes Gedamu Gebre, Edoardo Bertolini, Mario Enrico Pè, Andrea Zuccolo
BACKGROUND: Eragrostis tef is an allotetraploid (2n = 4 × = 40) annual, C4 grass with an estimated nuclear genome size of 730 Mbp. It is widely grown in Ethiopia, where it provides basic nutrition for more than half of the population. Although a draft assembly of the E. tef genome was made available in 2014, characterization of the repetitive portion of the E. tef genome has not been a subject of a detailed analysis. Repetitive sequences constitute most of the DNA in eukaryotic genomes...
2016: BMC Plant Biology
https://www.readbyqxmd.com/read/26798323/orphan-crops-browser-a-bridge-between-model-and-orphan-crops
#12
Claire Lessa Alvim Kamei, Edouard I Severing, Annemarie Dechesne, Heleen Furrer, Oene Dolstra, Luisa M Trindade
Many important crops have received little attention by the scientific community, either because they are not considered economically important or due to their large and complex genomes. De novo transcriptome assembly, using next-generation sequencing data, is an attractive option for the study of these orphan crops. In spite of the large amount of sequencing data that can be generated, there is currently a lack of tools which can effectively help molecular breeders and biologists to mine this type of information...
2016: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/26677845/evidence-for-the-recent-origin-of-a-bacterial-protein-coding-overlapping-orphan-gene-by-evolutionary-overprinting
#13
Lea Fellner, Svenja Simon, Christian Scherling, Michael Witting, Steffen Schober, Christine Polte, Philippe Schmitt-Kopplin, Daniel A Keim, Siegfried Scherer, Klaus Neuhaus
BACKGROUND: Gene duplication is believed to be the classical way to form novel genes, but overprinting may be an important alternative. Overprinting allows entirely novel proteins to evolve de novo, i.e., formerly non-coding open reading frames within functional genes become expressed. Only three cases have been described for Escherichia coli. Here, a fourth example is presented. RESULTS: RNA sequencing revealed an open reading frame weakly transcribed in cow dung, coding for 101 residues and embedded completely in the -2 reading frame of citC in enterohemorrhagic E...
2015: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/26568894/adaptive-evolution-coupled-with-retrotransposon-exaptation-allowed-for-the-generation-of-a-human-protein-specific-coding-gene-that-promotes-cancer-cell-proliferation-and-metastasis-in-both-haematological-malignancies-and-solid-tumours-the-extraordinary-case
#14
Spyros I Papamichos, Dimitrios Margaritis, Ioannis Kotsianidis
The incidence of cancer in human is high as compared to chimpanzee. However previous analysis has documented that numerous human cancer-related genes are highly conserved in chimpanzee. Till date whether human genome includes species-specific cancer-related genes that could potentially contribute to a higher cancer susceptibility remains obscure. This study focuses on MYEOV, an oncogene encoding for two protein isoforms, reported as causally involved in promoting cancer cell proliferation and metastasis in both haematological malignancies and solid tumours...
2015: Scientifica
https://www.readbyqxmd.com/read/26296317/identification-and-evolution-of-the-orphan-genes-in-the-domestic-silkworm-bombyx-mori
#15
Wei Sun, Xin-Wei Zhao, Ze Zhang
Orphan genes (OGs) which have no recognizable homology to any sequences in other species could contribute to the species specific adaptations. In this study, we identified 738 OGs in the silkworm genome. About 31% of the silkworm OGs is derived from transposable elements, and 5.1% of the silkworm OGs emerged from gene duplication followed by divergence of paralogs. Five de novo silkworm OGs originated from non-coding regions. Microarray data suggested that most of the silkworm OGs were expressed in limited tissues...
September 14, 2015: FEBS Letters
https://www.readbyqxmd.com/read/26096451/stimulus-selective-induction-of-the-orphan-nuclear-receptor-ngfib-underlies-different-influences-of-angiotensin-ii-and-potassium-on-the-human-adrenal-gland-zona-glomerulosa-specific-3%C3%AE-hsd-isoform-gene-expression-in-adrenocortical-h295r-cells
#16
Daisuke Yarimizu, Masao Doi, Takumi Ota, Hitoshi Okamura
In the adrenal, the type I 3β-hydroxysteroid dehydrogenase (HSD3B1) is expressed exclusively in the zona glomerulosa (ZG), where aldosterone is produced. Angiotensin II (AngII) and potassium (K(+)) are the major physiological regulators of aldosterone synthesis. However, their respective roles in regulation of aldosterone synthesis are not fully defined, particularly in terms of transcriptional regulation of steroidogenic enzyme genes. We previously showed that AngII can stimulate expression of HSD3B1. But, K(+) responsiveness of this gene has remained unexplored...
2015: Endocrine Journal
https://www.readbyqxmd.com/read/25960047/exploring-the-possible-link-between-mecp2-and-oxidative-stress-in-rett-syndrome
#17
REVIEW
Stefania Filosa, Alessandra Pecorelli, Maurizio D'Esposito, Giuseppe Valacchi, Joussef Hajek
Rett syndrome (RTT, MIM 312750) is a rare and orphan progressive neurodevelopmental disorder affecting girls almost exclusively, with a frequency of 1/15,000 live births of girls. The disease is characterized by a period of 6 to 18 months of apparently normal neurodevelopment, followed by early neurological regression, with a progressive loss of acquired cognitive, social, and motor skills. RTT is known to be caused in 95% of the cases by sporadic de novo loss-of-function mutations in the X-linked methyl-CpG-binding protein 2 (MECP2) gene encoding methyl-CpG binding protein 2 (MeCP2), a nuclear protein able to regulate gene expression...
November 2015: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/25917918/rna-seq-based-gene-annotation-and-comparative-genomics-of-four-fungal-grass-pathogens-in-the-genus-zymoseptoria-identify-novel-orphan-genes-and-species-specific-invasions-of-transposable-elements
#18
Jonathan Grandaubert, Amitava Bhattacharyya, Eva H Stukenbrock
The fungal pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a prominent pathogen of wheat. The reference genome of the isolate IPO323 is one of the best-assembled eukaryotic genomes and encodes more than 10,000 predicted genes. However, a large proportion of the previously annotated gene models are incomplete, with either no start or no stop codons. The availability of RNA-seq data allows better predictions of gene structure. We here used two different RNA-seq datasets, de novo transcriptome assemblies, homology-based comparisons, and trained ab initio gene callers to generate a new gene annotation of Z...
July 2015: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/25880035/inferring-bona-fide-transfrags-in-rna-seq-derived-transcriptome-assemblies-of-non-model-organisms
#19
Stanley Kimbung Mbandi, Uljana Hesse, Peter van Heusden, Alan Christoffels
BACKGROUND: De novo transcriptome assembly of short transcribed fragments (transfrags) produced from sequencing-by-synthesis technologies often results in redundant datasets with differing levels of unassembled, partially assembled or mis-assembled transcripts. Post-assembly processing intended to reduce redundancy typically involves reassembly or clustering of assembled sequences. However, these approaches are mostly based on common word heuristics and often create clusters of biologically unrelated sequences, resulting in loss of unique transfrags annotations and propagation of mis-assemblies...
2015: BMC Bioinformatics
https://www.readbyqxmd.com/read/25799347/de-novo-origin-of-vcy2-from-autosome-to-y-transposed-amplicon
#20
Peng-Rong Cao, Lei Wang, Yu-Chao Jiang, Yin-Sha Yi, Fang Qu, Tao-Cheng Liu, Yuan Lv
The formation of new genes is a primary driving force of evolution in all organisms. The de novo evolution of new genes from non-protein-coding genomic regions is emerging as an important additional mechanism for novel gene creation. Y chromosomes underlie sex determination in mammals and contain genes that are required for male-specific functions. In this study, a search was undertaken for Y chromosome de novo genes derived from non-protein-coding sequences. The Y chromosome orphan gene variable charge, Y-linked (VCY)2, is an autosome-derived gene that has sequence similarity to large autosomal fragments but lacks an autosomal protein-coding homolog...
2015: PloS One
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