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Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
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نویسنده
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janbon g. ,ormerod k.l. ,paulet d. ,byrnes iii e.j. ,yadav v. ,chatterjee g. ,mullapudi n. ,hon c.-c. ,billmyre r.b. ,brunel f. ,bahn y.-s. ,chen w. ,chen y. ,chow e.w.l. ,coppée j.-y. ,floyd-averette a. ,gaillardin c. ,gerik k.j. ,goldberg j. ,gonzalez-hilarion s. ,gujja s. ,hamlin j.l. ,hsueh y.-p. ,ianiri g. ,jones s. ,kodira c.d. ,kozubowski l. ,lam w. ,marra m. ,mesner l.d. ,mieczkowski p.a. ,moyrand f. ,nielsen k. ,proux c. ,rossignol t. ,schein j.e. ,sun s. ,wollschlaeger c. ,wood i.a. ,zeng q. ,neuvéglise c. ,newlon c.s. ,perfect j.r. ,lodge j.k. ,idnurm a. ,stajich j.e. ,kronstad j.w. ,sanyal k. ,heitman j. ,fraser j.a. ,cuomo c.a. ,dietrich f.s.
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منبع
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plos genetics - 2014 - دوره : 10 - شماره : 4
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چکیده
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Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. it occurs as two serotypes (a and d) representing two varieties (i.e. grubii and neoformans,respectively). here,we sequenced the genome and performed an rna-seq-based analysis of the c. neoformans var. grubii transcriptome structure. we determined the chromosomal locations,analyzed the sequence/structural features of the centromeres,and identified origins of replication. the genome was annotated based on automated and manual curation. more than 40,000 introns populating more than 99% of the expressed genes were identified. although most of these introns are located in the coding dna sequences (cds),over 2,000 introns in the untranslated regions (utrs) were also identified. poly(a)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. examination of the sequences around these sites revealed a new poly(a)-site-associated motif (aughah). in addition,1,197 miscrnas were identified. these miscrnas can be spliced and/or polyadenylated,but do not appear to have obvious coding capacities. finally,this genome sequence enabled a comparative analysis of strain h99 variants obtained after laboratory passage. the spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain,and identifies mutations involved in stress responses,mating efficiency,and virulence. © 2014 janbon et al.
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آدرس
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institut pasteur,unité biologie et pathogénicité fongiques,département génomes et génétique,paris,france,inra,usc2019,paris, France, university of queensland,school of chemistry and molecular biosciences,brisbane,qld, Australia, institut pasteur,plate-forme transcriptome et epigénome,département génomes et génétique,paris, France, duke university medical center,department of molecular genetics and microbiology,durham,nc,united states,office of the director,national institutes of health,bethesda,md, United States, jawaharlal nehru centre for advanced scientific research,molecular biology and genetics unit,bangalore, India, jawaharlal nehru centre for advanced scientific research,molecular biology and genetics unit,bangalore, India, genotypic technology private limited,bangalore, India, institut pasteur,unité biologie cellulaire du parasitisme,département biologie cellulaire et infection,paris, France, duke university medical center,department of molecular genetics and microbiology,durham,nc, United States, inra,umr 1319 micalis,jouy-en-josas, France, yonsei university,center for fungal pathogenesis,department of biotechnology,seoul, South Korea, rutgers new jersey medical school,department of microbiology and molecular genetics,newark,nj, United States, duke university medical center,department of molecular genetics and microbiology,durham,nc, United States, university of queensland,school of chemistry and molecular biosciences,brisbane,qld, Australia, institut pasteur,plate-forme transcriptome et epigénome,département génomes et génétique,paris, France, duke university medical center,department of molecular genetics and microbiology,durham,nc, United States, inra,umr 1319 micalis,jouy-en-josas, France, washington university school of medicine,department of molecular microbiology,st. louis,mo, United States, broad institute of mit and harvard,cambridge,ma, United States, institut pasteur,unité biologie et pathogénicité fongiques,département génomes et génétique,paris,france,inra,usc2019,paris, France, broad institute of mit and harvard,cambridge,ma, United States, university of virginia,department of biochemistry and molecular genetics,charlottesville,va, United States, duke university medical center,department of molecular genetics and microbiology,durham,nc,united states,california institute of technology,division of biology,pasadena,ca, United States, university of missouri-kansas city,school of biological sciences,division of cell biology and biophysics,kansas city,mo, United States, canada's michael smith genome sciences centre,bc cancer agency,vancouver,bc, Canada, broad institute of mit and harvard,cambridge,ma, United States, clemson university,department of genetics and biochemistry,clemson,sc, United States, washington university school of medicine,department of molecular microbiology,st. louis,mo, United States, canada's michael smith genome sciences centre,bc cancer agency,vancouver,bc, Canada, university of virginia,department of biochemistry and molecular genetics,charlottesville,va, United States, university of north carolina,department of genetics,chapel hill,nc, United States, institut pasteur,unité biologie et pathogénicité fongiques,département génomes et génétique,paris,france,inra,usc2019,paris, France, duke university medical center,department of molecular genetics and microbiology,durham,nc,united states,university of minnesota,microbiology department,minneapolis,mn, United States, institut pasteur,plate-forme transcriptome et epigénome,département génomes et génétique,paris, France, inra,umr 1319 micalis,jouy-en-josas, France, canada's michael smith genome sciences centre,bc cancer agency,vancouver,bc, Canada, duke university medical center,department of molecular genetics and microbiology,durham,nc, United States, institut pasteur,unité biologie et pathogénicité fongiques,département génomes et génétique,paris,france,inra,usc2019,paris, France, university of queensland,school of mathematics and physics,brisbane,qld, Australia, broad institute of mit and harvard,cambridge,ma, United States, inra,umr 1319 micalis,jouy-en-josas, France, rutgers new jersey medical school,department of microbiology and molecular genetics,newark,nj, United States, duke university medical center,duke department of medicine and molecular genetics and microbiology,durham,nc, United States, washington university school of medicine,department of molecular microbiology,st. louis,mo, United States, university of missouri-kansas city,school of biological sciences,division of cell biology and biophysics,kansas city,mo, United States, duke university medical center,department of molecular genetics and microbiology,durham,nc,united states,university of california,department of plant pathology and microbiology,riverside,ca, United States, michael smith laboratories,department of microbiology and immunology,vancouver,bc, Canada, jawaharlal nehru centre for advanced scientific research,molecular biology and genetics unit,bangalore, India, duke university medical center,department of molecular genetics and microbiology,durham,nc, United States, university of queensland,school of chemistry and molecular biosciences,brisbane,qld, Australia, broad institute of mit and harvard,cambridge,ma, United States, duke university medical center,department of molecular genetics and microbiology,durham,nc, United States
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Authors
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