دورية أكاديمية
أعرض في EDS

Pan-genome analyses of model fungal species.

التفاصيل البيبلوغرافية
العنوان: Pan-genome analyses of model fungal species.
المؤلفون: McCarthy CGP; 1​Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.; 2​Human Health Research Institute, Maynooth University, Maynooth, Co. Kildare, Ireland., Fitzpatrick DA; 1​Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.; 2​Human Health Research Institute, Maynooth University, Maynooth, Co. Kildare, Ireland.
المصدر: Microbial genomics [Microb Genom] 2019 Feb; Vol. 5 (2). Date of Electronic Publication: 2019 Feb 04.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Microbiology Society Country of Publication: England NLM ID: 101671820 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2057-5858 (Electronic) Linking ISSN: 20575858 NLM ISO Abbreviation: Microb Genom Subsets: MEDLINE
أسماء مطبوعة: Publication: Oct. 2015- : [London] : Microbiology Society
Original Publication: [London] : Society for General Microbiology, [2015]-
مواضيع طبية MeSH: Genome, Fungal*, Fungi/*classification, Evolution, Molecular ; Fungi/genetics ; Genome-Wide Association Study ; Genomics ; Phylogeny
مستخلص: The concept of the species 'pan-genome', the union of 'core' conserved genes and all 'accessory' non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining 'accessory' gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.
References: Genome Biol Evol. 2010;2:646-55. (PMID: 20688752)
BMC Bioinformatics. 2011 May 24;12:193. (PMID: 21605461)
Bioinformatics. 2010 Aug 1;26(15):1910-2. (PMID: 20551134)
BMC Biol. 2018 Jan 11;16(1):5. (PMID: 29325559)
Fungal Genet Biol. 2010 Sep;47(9):736-41. (PMID: 20554054)
Bioinformatics. 2014 Dec 15;30(24):3476-83. (PMID: 25398610)
PLoS Genet. 2011 Jun;7(6):e1002111. (PMID: 21698134)
Genome Res. 2012 May;22(5):908-24. (PMID: 22369888)
Database (Oxford). 2013 Mar 13;2013:bat012. (PMID: 23487186)
Mol Biol Evol. 2013 Feb;30(2):369-83. (PMID: 23071100)
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5. (PMID: 27095192)
Nucleic Acids Res. 1995 May 11;23(9):1481-6. (PMID: 7784200)
Genome Biol. 2006;7(4):R34. (PMID: 16640791)
BMC Genomics. 2018 Jan 15;19(1):47. (PMID: 29334898)
Plant Biotechnol J. 2016 Apr;14(4):1099-105. (PMID: 26593040)
BMC Genomics. 2009 Aug 19;10:385. (PMID: 19691844)
Microbiol Mol Biol Rev. 2000 Dec;64(4):746-85. (PMID: 11104818)
Bioinformatics. 2009 Jun 1;25(11):1422-3. (PMID: 19304878)
Evol Appl. 2014 Nov;7(9):1026-42. (PMID: 25553065)
Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10136-41. (PMID: 20479238)
PLoS One. 2012;7(8):e42022. (PMID: 22916115)
Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12825-30. (PMID: 17652520)
Science. 2000 Nov 10;290(5494):1151-5. (PMID: 11073452)
Bioinformatics. 2015 Nov 15;31(22):3691-3. (PMID: 26198102)
PLoS Biol. 2017 Nov 17;15(11):e2003583. (PMID: 29149178)
Nat Rev Microbiol. 2005 Dec;3(12):937-47. (PMID: 16322742)
Genome Res. 2015 May;25(5):762-74. (PMID: 25840857)
Bioinformatics. 2014 May 1;30(9):1236-40. (PMID: 24451626)
Eukaryot Cell. 2005 Feb;4(2):401-6. (PMID: 15701802)
Genetics. 2002 Oct;162(2):737-45. (PMID: 12399384)
BMC Bioinformatics. 2005 Feb 15;6:31. (PMID: 15713233)
PLoS Pathog. 2008 Sep 12;4(9):e1000154. (PMID: 18787699)
PLoS Genet. 2008 Apr 11;4(4):e1000046. (PMID: 18404212)
mSphere. 2016 Sep 14;1(5):. (PMID: 27642638)
PLoS One. 2010 Aug 09;5(8):e12007. (PMID: 20711256)
mSphere. 2016 Oct 26;1(5):. (PMID: 27830189)
Sci Rep. 2016 Aug 31;6:32252. (PMID: 27577684)
Genetics. 2014 Jun;197(2):451-65. (PMID: 24939991)
J Bacteriol. 2008 Oct;190(20):6881-93. (PMID: 18676672)
Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16333-8. (PMID: 19805302)
Fungal Genet Biol. 2014 Sep;70:42-67. (PMID: 25011008)
BMC Bioinformatics. 2005 Jan 05;6:2. (PMID: 15634352)
Nat Biotechnol. 2014 Oct;32(10):1045-52. (PMID: 25218520)
Mol Biol Evol. 2014 Apr;31(4):872-88. (PMID: 24425782)
Bioinformatics. 2015 Oct 1;31(19):3210-2. (PMID: 26059717)
FEMS Yeast Res. 2004 Sep;4(8):821-32. (PMID: 15450189)
Nucleic Acids Res. 2017 Jan 4;45(D1):D592-D596. (PMID: 27738138)
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5. (PMID: 16172379)
IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92. (PMID: 26356912)
Sci Rep. 2016 Apr 13;6:24373. (PMID: 27071527)
Curr Biol. 2014 May 19;24(10):1153-9. (PMID: 24814147)
Nature. 2005 Dec 22;438(7071):1151-6. (PMID: 16372009)
Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15258-63. (PMID: 21878562)
EMBO Rep. 2004 Apr;5(4):392-8. (PMID: 15105830)
Nat Commun. 2017 Dec 19;8(1):2184. (PMID: 29259172)
BioData Min. 2013 Oct 16;6(1):18. (PMID: 24131735)
Adv Genet. 2017;100:211-266. (PMID: 29153401)
Sci Rep. 2018 Jul 18;8(1):10872. (PMID: 30022098)
Genetics. 2006 Sep;174(1):541-4. (PMID: 16816417)
Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):E99-107. (PMID: 23248299)
Genetics. 2007 Dec;177(4):2293-307. (PMID: 18073433)
BMC Genomics. 2011 Apr 13;12:187. (PMID: 21489287)
Nature. 2018 Apr;556(7701):339-344. (PMID: 29643504)
Evol Bioinform Online. 2012;8:623-44. (PMID: 23225993)
Nature. 2002 Jul 25;418(6896):387-91. (PMID: 12140549)
Trends Genet. 2010 Jan;26(1):5-8. (PMID: 19969385)
PLoS Genet. 2014 Apr 17;10(4):e1004261. (PMID: 24743168)
Proc Natl Acad Sci U S A. 2009 May 26;106(21):8605-10. (PMID: 19435847)
Genome Biol. 2007;8(10):R223. (PMID: 17949488)
Genome Res. 2008 Dec;18(12):1979-90. (PMID: 18757608)
Plant J. 2017 Jun;90(5):1007-1013. (PMID: 28231383)
BMC Genomics. 2017 Mar 27;18(1):261. (PMID: 28347275)
Mol Phylogenet Evol. 2010 Sep;56(3):1115-8. (PMID: 20416383)
Nat Rev Genet. 2008 Aug;9(8):605-18. (PMID: 18591983)
Nature. 2009 Mar 19;458(7236):337-41. (PMID: 19212322)
Science. 1996 Oct 25;274(5287):546, 563-7. (PMID: 8849441)
BMC Bioinformatics. 2004 Aug 19;5:113. (PMID: 15318951)
Trends Genet. 2009 Mar;25(3):107-10. (PMID: 19168257)
Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17252-5. (PMID: 20852068)
PLoS Genet. 2011 Jan 27;7(1):e1001284. (PMID: 21298028)
Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85. (PMID: 26673716)
Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):1092-7. (PMID: 15647350)
PLoS One. 2010 Mar 10;5(3):e9490. (PMID: 20224823)
Genetics. 2015 Nov;201(3):1213-28. (PMID: 26392286)
Plant Cell. 2014 Jan;26(1):121-35. (PMID: 24488960)
Bioinformatics. 2017 Sep 15;33(18):2938-2940. (PMID: 28645171)
Bioessays. 2017 Dec;39(12):. (PMID: 29068466)
PLoS One. 2015 Mar 17;10(3):e0120671. (PMID: 25781462)
Virulence. 2014 Feb 15;5(2):341-50. (PMID: 24504058)
New Microbes New Infect. 2015 Jun 26;7:72-85. (PMID: 26442149)
Nat Protoc. 2013 Aug;8(8):1494-512. (PMID: 23845962)
Nat Genet. 2017 Jun;49(6):913-924. (PMID: 28416820)
Genome Biol. 2007;8(6):R103. (PMID: 17550610)
PLoS Genet. 2014 Dec 04;10(12):e1004816. (PMID: 25474404)
Nucleic Acids Res. 2017 Jan 4;45(D1):D331-D338. (PMID: 27899567)
PLoS Biol. 2015 Aug 07;13(8):e1002221. (PMID: 26252643)
Nature. 2013 Jul 11;499(7457):209-13. (PMID: 23760476)
Proc Natl Acad Sci U S A. 2004 May 11;101(19):7329-34. (PMID: 15123810)
mSphere. 2018 Mar 14;3(2):. (PMID: 29564395)
Mol Biol Evol. 2008 Apr;25(4):787-94. (PMID: 18258610)
BMC Biol. 2016 Oct 17;14(1):89. (PMID: 27751184)
BMC Bioinformatics. 2009 Dec 15;10:421. (PMID: 20003500)
Nat Microbiol. 2017 Mar 28;2:17040. (PMID: 28350002)
Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. (PMID: 22096229)
Nucleic Acids Res. 2012 Dec;40(22):e172. (PMID: 22904089)
Nat Commun. 2016 Nov 11;7:13390. (PMID: 27834372)
فهرسة مساهمة: Keywords: Aspergillus; Cryptococcus; comparative genomics; fungal pangenomes; yeast
تواريخ الأحداث: Date Created: 20190205 Date Completed: 20190913 Latest Revision: 20210109
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC6421352
DOI: 10.1099/mgen.0.000243
PMID: 30714895
قاعدة البيانات: MEDLINE
الوصف
تدمد:2057-5858
DOI:10.1099/mgen.0.000243