دورية أكاديمية
Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes).
العنوان: | Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes). |
---|---|
المؤلفون: | Merényi Z; Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary., Virágh M; Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary., Gluck-Thaler E; Department of Biology, University of Pennsylvania, Philadelphia, United States., Slot JC; College of Food, Agricultural, and Environmental Sciences, Department of Plant Pathology, Ohio State University, Columbus, United States., Kiss B; Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary., Varga T; Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary., Geösel A; Institute of Horticultural Science, Department of Vegetable and Mushroom Growing, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary., Hegedüs B; Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary., Bálint B; Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary., Nagy LG; Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary.; Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary. |
المصدر: | ELife [Elife] 2022 Feb 14; Vol. 11. Date of Electronic Publication: 2022 Feb 14. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: eLife Sciences Publications, Ltd Country of Publication: England NLM ID: 101579614 Publication Model: Electronic Cited Medium: Internet ISSN: 2050-084X (Electronic) Linking ISSN: 2050084X NLM ISO Abbreviation: Elife Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: Cambridge, UK : eLife Sciences Publications, Ltd., 2012- |
مواضيع طبية MeSH: | Agaricales*/genetics , Agaricales*/metabolism , Ascomycota*/metabolism , Basidiomycota*, Fruiting Bodies, Fungal/genetics ; Fruiting Bodies, Fungal/metabolism ; Fungal Proteins/metabolism ; Gene Expression Regulation, Fungal |
مستخلص: | Multicellularity has been one of the most important innovations in the history of life. The role of gene regulatory changes in driving transitions to multicellularity is being increasingly recognized; however, factors influencing gene expression patterns are poorly known in many clades. Here, we compared the developmental transcriptomes of complex multicellular fruiting bodies of eight Agaricomycetes and Cryptococcus neoformans , a closely related human pathogen with a simple morphology. In-depth analysis in Pleurotus ostreatus revealed that allele-specific expression, natural antisense transcripts, and developmental gene expression, but not RNA editing or a 'developmental hourglass,' act in concert to shape its transcriptome during fruiting body development. We found that transcriptional patterns of genes strongly depend on their evolutionary ages. Young genes showed more developmental and allele-specific expression variation, possibly because of weaker evolutionary constraint, suggestive of nonadaptive expression variance in fruiting bodies. These results prompted us to define a set of conserved genes specifically regulated only during complex morphogenesis by excluding young genes and accounting for deeply conserved ones shared with species showing simple sexual development. Analysis of the resulting gene set revealed evolutionary and functional associations with complex multicellularity, which allowed us to speculate they are involved in complex multicellular morphogenesis of mushroom fruiting bodies. Competing Interests: ZM, MV, EG, JS, BK, TV, AG, BH, BB, LN No competing interests declared (© 2022, Merényi et al.) |
References: | Nucleic Acids Res. 2014 Jan;42(Database issue):D26-31. (PMID: 24225321) Nat Biotechnol. 2015 Mar;33(3):290-5. (PMID: 25690850) BMC Genomics. 2021 May 4;22(1):324. (PMID: 33947322) Nat Ecol Evol. 2017 Dec;1(12):1931-1941. (PMID: 29085064) Genome Res. 2005 Mar;15(3):364-8. (PMID: 15710751) Nature. 2010 Dec 9;468(7325):815-8. (PMID: 21150997) PeerJ. 2020 Jun 12;8:e9336. (PMID: 32566411) Genome Res. 2010 Jun;20(6):816-25. (PMID: 20354124) Genome Biol. 2014 Jul 31;15(7):411. (PMID: 25091826) Nucleic Acids Res. 2014 Jan;42(Database issue):D705-10. (PMID: 24194595) Genetics. 2014 Apr;196(4):1047-57. (PMID: 24496007) Genomics. 2018 May;110(3):201-209. (PMID: 28970048) PLoS Comput Biol. 2013;9(8):e1003118. (PMID: 23950696) PLoS One. 2015 Oct 28;10(10):e0141586. (PMID: 26510163) Bioinformatics. 2014 Apr 1;30(7):923-30. (PMID: 24227677) Cell Mol Life Sci. 2019 Jan;76(2):329-340. (PMID: 30302531) mBio. 2018 Aug 14;9(4):. (PMID: 30108170) Methods Mol Biol. 2014;1079:155-70. (PMID: 24170401) Genome Biol Evol. 2017 May 1;9(5):1266-1279. (PMID: 28453623) Appl Microbiol Biotechnol. 2013 Jan;97(2):705-17. (PMID: 22395908) Nat Biotechnol. 2017 Nov;35(11):1026-1028. (PMID: 29035372) Mol Microbiol. 2013 Jul;89(1):29-51. (PMID: 23650872) Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690) Mol Biol Evol. 2015 Jun;32(6):1556-66. (PMID: 25725429) G3 (Bethesda). 2021 Feb 9;11(2):. (PMID: 33585864) Curr Opin Genet Dev. 2017 Aug;45:69-75. (PMID: 28347942) Bioinformatics. 2014 May 1;30(9):1236-40. (PMID: 24451626) Nucleic Acids Res. 2021 Jan 8;49(D1):D192-D200. (PMID: 33211869) Elife. 2021 Aug 09;10:. (PMID: 34369376) New Phytol. 2019 Oct;224(2):902-915. (PMID: 31257601) Bioinformatics. 2014 May 1;30(9):1312-3. (PMID: 24451623) Appl Microbiol Biotechnol. 2018 Sep;102(18):7795-7803. (PMID: 30027491) PLoS Pathog. 2018 Sep 6;14(9):e1007184. (PMID: 30188951) Mol Syst Biol. 2012;8:602. (PMID: 22893000) Nat Rev Mol Cell Biol. 2009 Sep;10(9):637-43. (PMID: 19638999) Science. 2003 Jul 18;301(5631):361-3. (PMID: 12869759) Bioinformatics. 2009 Jul 15;25(14):1841-2. (PMID: 19468054) PLoS Genet. 2013 Apr;9(4):e1003476. (PMID: 23637639) Nat Commun. 2016 Apr 18;7:11101. (PMID: 27089393) Fungal Genet Biol. 2008 Jun;45(6):818-28. (PMID: 18448367) Biosci Biotechnol Biochem. 2003 Nov;67(11):2431-7. (PMID: 14646204) Environ Microbiol. 2016 Dec;18(12):4710-4726. (PMID: 27117896) Mol Biol Evol. 2007 Aug;24(8):1586-91. (PMID: 17483113) Nat Genet. 2002 Nov;32(3):432-7. (PMID: 12410233) RNA. 2017 Nov;23(11):1648-1659. (PMID: 28802259) Microbiol Mol Biol Rev. 2021 Nov 24;:e0001921. (PMID: 34817241) Mol Gen Genet. 1993 May;239(1-2):196-204. (PMID: 8389977) Sci Rep. 2017 Jul 18;7(1):5711. (PMID: 28720793) Mol Biol Evol. 2020 Aug 1;37(8):2228-2240. (PMID: 32191325) Appl Microbiol Biotechnol. 2020 Jul;104(13):5689-5695. (PMID: 32382933) Biol Rev Camb Philos Soc. 2018 Nov;93(4):1778-1794. (PMID: 29675836) Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):707-12. (PMID: 15647348) Mol Microbiol. 2012 Aug;85(3):405-17. (PMID: 22703386) Int J Mol Sci. 2019 Dec 14;20(24):. (PMID: 31847351) Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9451-9457. (PMID: 32300014) Trends Genet. 2007 Nov;23(11):533-9. (PMID: 18029048) Genome Biol. 2002;3(2):RESEARCH0008. (PMID: 11864370) BMC Genomics. 2017 May 2;18(1):340. (PMID: 28464849) Nucleic Acids Res. 2012 Jan;40(Database issue):D695-9. (PMID: 22039153) J Biol Chem. 2010 Apr 2;285(14):10715-23. (PMID: 20061575) Proc Natl Acad Sci U S A. 2019 Apr 9;116(15):7409-7418. (PMID: 30902897) Sci Rep. 2021 Apr 14;11(1):8178. (PMID: 33854169) Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9923-8. (PMID: 24958869) Sci Adv. 2016 Mar 04;2(3):e1501363. (PMID: 26973873) Fungal Genet Biol. 2010 Nov;47(11):917-21. (PMID: 20471485) Appl Microbiol Biotechnol. 2019 Jul;103(14):5567-5581. (PMID: 31147756) Environ Microbiol. 2010 Apr;12(4):833-44. (PMID: 20050873) Bioinformatics. 2010 Jan 1;26(1):139-40. (PMID: 19910308) Nucleic Acids Res. 2011 Jul;39(Web Server issue):W339-46. (PMID: 21672958) Nucleic Acids Res. 2014 Jan;42(Database issue):D699-704. (PMID: 24297253) Nat Commun. 2014 Jul 18;5:4471. (PMID: 25034666) Bioinformatics. 2016 Jan 1;32(1):43-9. (PMID: 26519505) Mol Microbiol. 2011 Sep;81(6):1433-45. (PMID: 21815946) Genome Res. 2016 Apr;26(4):499-509. (PMID: 26934920) Nat Commun. 2017 Feb 08;8:14444. (PMID: 28176784) Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4429-4434. (PMID: 29643074) PLoS One. 2018 Sep 19;13(9):e0198234. (PMID: 30231028) Mol Biol Evol. 2020 May 1;37(5):1530-1534. (PMID: 32011700) PLoS Pathog. 2012;8(5):e1002700. (PMID: 22693445) Nat Commun. 2019 Sep 9;10(1):4080. (PMID: 31501435) Nat Rev Microbiol. 2019 Mar;17(3):167-180. (PMID: 30531948) F1000Res. 2020 Apr 28;9:304. (PMID: 32489650) Science. 2008 Feb 15;319(5865):946-8. (PMID: 18276888) G3 (Bethesda). 2014 Mar 20;4(3):389-98. (PMID: 24374639) Front Microbiol. 2019 Oct 09;10:2336. (PMID: 31649657) Heredity (Edinb). 2008 Feb;100(2):191-9. (PMID: 17519966) Nat Biotechnol. 2010 Sep;28(9):957-63. (PMID: 20622885) Elife. 2018 May 31;7:. (PMID: 29848444) Bioinformatics. 2009 Aug 1;25(15):1972-3. (PMID: 19505945) Fungal Genet Biol. 2020 Sep;142:103416. (PMID: 32522620) Nat Ecol Evol. 2019 Apr;3(4):668-678. (PMID: 30886374) Cell. 2018 May 31;173(6):1520-1534.e20. (PMID: 29856957) Appl Environ Microbiol. 2017 Feb 15;83(5):. (PMID: 28039134) Elife. 2018 Oct 03;7:. (PMID: 30281018) Science. 2011 May 20;332(6032):930-6. (PMID: 21511999) Trends Genet. 2014 Oct;30(10):439-52. (PMID: 25218058) Proc Natl Acad Sci U S A. 2020 Dec 8;117(49):31267-31277. (PMID: 33229585) Nucleic Acids Res. 2011 Feb;39(3):837-47. (PMID: 20935054) Nat Rev Genet. 2017 Aug;18(8):498-512. (PMID: 28479598) Elife. 2022 Feb 14;11:. (PMID: 35156613) Bioinformatics. 2011 Feb 15;27(4):592-3. (PMID: 21169378) PLoS Genet. 2019 May 23;15(5):e1008160. (PMID: 31120894) Genome Biol Evol. 2017 Apr 1;9(4):855-868. (PMID: 28338982) Nucleic Acids Res. 2017 Jul 3;45(W1):W12-W16. (PMID: 28521017) J Appl Genet. 2013 Aug;54(3):271-83. (PMID: 23609142) Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7756-E7765. (PMID: 28847945) Bioinformatics. 2018 Sep 15;34(18):3094-3100. (PMID: 29750242) Int J Genomics. 2019 May 2;2019:9702342. (PMID: 31192251) Science. 2018 Jul 13;361(6398):125-126. (PMID: 30002238) Bioinformatics. 2017 Mar 1;33(5):640-649. (PMID: 27998934) Sci Rep. 2016 Sep 27;6:33964. (PMID: 27670777) Nature. 2003 Apr 24;422(6934):859-68. (PMID: 12712197) Mol Biol Evol. 2017 Apr 1;34(4):843-856. (PMID: 28087778) Science. 2002 Jul 19;297(5580):395-400. (PMID: 12089449) Bioinformatics. 2013 Nov 15;29(22):2933-5. (PMID: 24008419) Science. 2002 Feb 22;295(5559):1482-5. (PMID: 11859185) J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712) |
معلومات مُعتمدة: | 758161 International ERC_ European Research Council |
فهرسة مساهمة: | Keywords: Coprinopsis cinerea; Cryptococcus neoformans; Pleurotus ostreatus; allelic imbalance; developmental biology; developmental hourglass; evolutionary biology; mushroom-forming fungi |
سلسلة جزيئية: | Dryad 10.5061/dryad.5qfttdz5m GEO GSE176181; GSE125198; GSE125184; GSE125199; GSE111975; GSE132826; GSE100213 |
المشرفين على المادة: | 0 (Fungal Proteins) |
تواريخ الأحداث: | Date Created: 20220214 Date Completed: 20220429 Latest Revision: 20220727 |
رمز التحديث: | 20221213 |
مُعرف محوري في PubMed: | PMC8893723 |
DOI: | 10.7554/eLife.71348 |
PMID: | 35156613 |
قاعدة البيانات: | MEDLINE |
تدمد: | 2050-084X |
---|---|
DOI: | 10.7554/eLife.71348 |