دورية أكاديمية
أعرض في EDS

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish ( Raphanus sativus L.) Line.

التفاصيل البيبلوغرافية
العنوان: Whole-Genome Sequencing and Analysis of Tumour-Forming Radish ( Raphanus sativus L.) Line.
المؤلفون: Kuznetsova X; Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia., Dodueva I; Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia., Afonin A; All-Russia Research Institute for Agricultural Microbiology, 190608 Saint Petersburg, Russia., Gribchenko E; All-Russia Research Institute for Agricultural Microbiology, 190608 Saint Petersburg, Russia., Danilov L; Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia., Gancheva M; Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia., Tvorogova V; Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia.; Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia., Galynin N; Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia., Lutova L; Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia.; Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia.
المصدر: International journal of molecular sciences [Int J Mol Sci] 2024 Jun 05; Vol. 25 (11). Date of Electronic Publication: 2024 Jun 05.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, [2000-
مواضيع طبية MeSH: Raphanus*/genetics , Whole Genome Sequencing*/methods , Genome, Plant*, Plant Tumors/genetics ; Polymorphism, Single Nucleotide ; Plant Proteins/genetics
مستخلص: Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish ( Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR ( CLE ) and WUSCHEL ( WOX ) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.
References: BMC Plant Biol. 2019 Jun 14;19(1):257. (PMID: 31200645)
Genetika. 2007 Oct;43(10):1411-23. (PMID: 18069346)
Plant Physiol. 2008 Sep;148(1):259-68. (PMID: 18599653)
Plant J. 2017 Apr;90(2):261-275. (PMID: 28107777)
Theor Appl Genet. 2016 Sep;129(9):1797-814. (PMID: 27377547)
Curr Opin Plant Biol. 2007 Dec;10(6):645-52. (PMID: 17884714)
Plant Signal Behav. 2013 Aug;8(8):. (PMID: 23759547)
PLoS Genet. 2014 Jan;10(1):e1003948. (PMID: 24465213)
Plant Physiol. 2019 Apr;179(4):1315-1329. (PMID: 30696746)
Plant Cell. 2011 Nov;23(11):4013-24. (PMID: 22045917)
J Plant Res. 2003 Apr;116(2):161-4. (PMID: 12736788)
Front Plant Sci. 2022 Mar 10;13:838421. (PMID: 35360299)
Mol Plant. 2021 Dec 6;14(12):2032-2055. (PMID: 34384905)
Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):2160-5. (PMID: 21245327)
Mol Plant. 2015 Jul;8(7):1011-23. (PMID: 25600279)
Curr Opin Plant Biol. 2016 Feb;29:95-103. (PMID: 26799131)
Plant Biol (Stuttg). 2020 Jul;22(4):709-721. (PMID: 32223006)
Genes Dev. 2018 Aug 1;32(15-16):1085-1100. (PMID: 30018102)
Plant Physiol. 2020 Nov;184(3):1573-1584. (PMID: 32907884)
Front Plant Sci. 2022 Mar 25;13:863892. (PMID: 35401607)
Plant J. 2007 May;50(4):735-50. (PMID: 17461780)
Plant J. 2007 Jan;49(2):265-75. (PMID: 17241449)
Plant J. 2013 May;74(3):486-97. (PMID: 23384085)
Plant Signal Behav. 2009 Sep;4(9):883-6. (PMID: 19847098)
Front Plant Sci. 2014 Jun 05;5:254. (PMID: 24926301)
PLoS One. 2016 Jan 11;11(1):e0146826. (PMID: 26752684)
Plant Physiol. 2012 Jul;159(3):884-901. (PMID: 22589469)
Plant J. 2013 Jun;74(5):767-80. (PMID: 23461773)
Front Plant Sci. 2012 Aug 24;3:191. (PMID: 22936940)
Biochim Biophys Acta. 2006 Jan-Feb;1759(1-2):69-79. (PMID: 16603259)
Curr Biol. 2003 May 13;13(10):837-42. (PMID: 12747832)
Plant Cell Physiol. 2014 Jul;55(7):1343-53. (PMID: 24793750)
Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404)
Plant Mol Biol. 2011 Jan;75(1-2):77-92. (PMID: 21052782)
New Phytol. 2020 Aug;227(4):1157-1173. (PMID: 32278327)
Plant Signal Behav. 2013 Nov;8(11):e27325. (PMID: 24309816)
DNA Res. 2020 Apr 01;27(2):. (PMID: 32426809)
Front Plant Sci. 2019 Jan 22;9:1955. (PMID: 30723487)
New Phytol. 2022 Sep;235(6):2300-2312. (PMID: 35642449)
J Plant Physiol. 2015 Jan 15;173:97-104. (PMID: 25462083)
Plant Physiol. 2019 May;180(1):634-653. (PMID: 30872424)
Plant Physiol. 2006 Aug;141(4):1363-75. (PMID: 16778018)
Vestn Leningr Univ Biol. 1967 Aug;3:144-9. (PMID: 5594721)
Plant J. 2007 Oct;52(1):94-104. (PMID: 17666024)
Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17588-93. (PMID: 24101471)
DNA Res. 2020 Feb 1;27(1):. (PMID: 32065621)
Front Genet. 2024 Jan 18;15:1328050. (PMID: 38304338)
Mol Biol Evol. 1987 Jul;4(4):406-25. (PMID: 3447015)
Plant Physiol. 2013 Mar;161(3):1127-40. (PMID: 23321422)
BMC Plant Biol. 2015 Jun 24;15:155. (PMID: 26099801)
Plant Physiol. 2022 Aug 1;189(4):2454-2466. (PMID: 35511168)
Plant Cell. 2019 Jan;31(1):52-67. (PMID: 30573473)
Genome Biol. 2002;3(4):RESEARCH0016. (PMID: 11983057)
Plant Biotechnol (Tokyo). 2016;33(4):245-253. (PMID: 31274988)
Epigenetics Chromatin. 2018 Nov 16;11(1):69. (PMID: 30446008)
Int J Mol Sci. 2021 Dec 04;22(23):. (PMID: 34884922)
Trends Plant Sci. 2014 Mar;19(3):146-57. (PMID: 24280109)
PLoS One. 2008 Jun 18;3(6):e2491. (PMID: 18560512)
Ann Bot. 2014 Nov;114(7):1507-15. (PMID: 25002525)
Genes (Basel). 2021 Feb 10;12(2):. (PMID: 33578704)
Plant Physiol. 2003 Jul;132(3):1315-21. (PMID: 12857813)
Plant Cell Physiol. 2012 Jun;53(6):953-64. (PMID: 22555815)
Front Plant Sci. 2020 Nov 24;11:601558. (PMID: 33329669)
Plant J. 1997 Sep;12(3):635-47. (PMID: 9351248)
J Exp Bot. 2014 Oct;65(18):5459-71. (PMID: 25053647)
Biophys J. 2020 Sep 1;119(5):1015-1024. (PMID: 32783879)
Nucleic Acids Res. 2014 Jan;42(1):485-98. (PMID: 24084084)
Plants (Basel). 2023 Oct 23;12(20):. (PMID: 37896124)
Plant Mol Biol. 2010 Jan;72(1-2):61-73. (PMID: 19795213)
Plant Biotechnol J. 2023 May;21(5):990-1004. (PMID: 36648398)
Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E5995-E6004. (PMID: 28673986)
EMBO J. 2021 Sep 1;40(17):e105043. (PMID: 34287990)
PLoS Genet. 2015 Oct 16;11(10):e1005598. (PMID: 26473486)
Plants (Basel). 2021 May 03;10(5):. (PMID: 34063717)
Mol Plant Pathol. 2020 Sep;21(9):1179-1193. (PMID: 32725756)
PLoS One. 2017 Dec 20;12(12):e0189672. (PMID: 29261741)
Plant Signal Behav. 2014;9(7):e29302. (PMID: 25763500)
Plant Mol Biol. 2002 Jun-Jul;49(3-4):373-85. (PMID: 12036261)
Plant Signal Behav. 2012 Oct 1;7(10):1251-4. (PMID: 22902690)
Planta. 2021 Nov 29;255(1):5. (PMID: 34841457)
J Biol Chem. 2004 May 21;279(21):22449-60. (PMID: 15004013)
Plant Physiol. 2017 Feb;173(2):1017-1030. (PMID: 27956490)
Theor Appl Genet. 2016 Jul;129(7):1357-1372. (PMID: 27038817)
Bioinformatics. 2016 Oct 1;32(19):3047-8. (PMID: 27312411)
Plant Physiol. 2010 Jun;153(2):485-513. (PMID: 20395450)
Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16319-24. (PMID: 12451175)
BMC Plant Biol. 2016 Jan 27;16 Suppl 1:7. (PMID: 26821718)
Nat Commun. 2022 Jan 11;13(1):235. (PMID: 35017541)
Biochim Biophys Acta. 2001 May 28;1539(1-2):1-6. (PMID: 11389963)
DNA Res. 2014 Oct;21(5):481-90. (PMID: 24848699)
Mol Cells. 2011 Apr;31(4):393-7. (PMID: 21359675)
J Exp Bot. 2011 Oct;62(14):4995-5002. (PMID: 21705390)
Plant J. 2005 Oct;44(2):223-36. (PMID: 16212602)
Front Plant Sci. 2020 Dec 10;11:596301. (PMID: 33362827)
Development. 2020 Aug 18;147(16):. (PMID: 32680933)
Genome Biol. 2007;8(11):R249. (PMID: 18034896)
Fly (Austin). 2012 Apr-Jun;6(2):80-92. (PMID: 22728672)
Plant Physiol. 2021 Jun 11;186(2):1220-1239. (PMID: 33693822)
Mol Plant Pathol. 2021 May;22(5):618-624. (PMID: 33650275)
Biol Open. 2019 Mar 12;8(3):. (PMID: 30787007)
Development. 2013 May;140(10):2224-34. (PMID: 23578929)
Curr Biol. 2021 Aug 9;31(15):3365-3373.e7. (PMID: 34129827)
PLoS One. 2011;6(9):e25154. (PMID: 21966441)
Plant Mol Biol. 2009 Dec;71(6):641-55. (PMID: 19826767)
Nat Rev Cancer. 2010 Nov;10(11):794-802. (PMID: 20966923)
Plant Cell. 2005 Mar;17(3):705-21. (PMID: 15722475)
J Biol Chem. 2006 Sep 1;281(35):25475-84. (PMID: 16803883)
Plant Physiol. 2016 Jan;170(1):499-514. (PMID: 26586833)
Planta. 2020 Mar 18;251(4):82. (PMID: 32189080)
Plant Physiol. 2008 Aug;147(4):1723-34. (PMID: 18583534)
Front Plant Sci. 2024 Feb 02;15:1329890. (PMID: 38371408)
New Phytol. 2021 Mar;229(6):3237-3252. (PMID: 33247457)
Plant J. 2020 Feb;101(3):590-603. (PMID: 31610057)
PLoS One. 2014 May 20;9(5):e97745. (PMID: 24844592)
Dev Cell. 2005 Jul;9(1):109-19. (PMID: 15992545)
Front Plant Sci. 2018 Mar 14;9:272. (PMID: 29593753)
Mol Biol (Mosk). 2021 May-Jun;55(3):362-391. (PMID: 34097673)
PLoS Genet. 2008 Nov;4(11):e1000274. (PMID: 19043546)
Biol Open. 2015 Sep 04;4(10):1229-36. (PMID: 26340943)
Evolution. 1985 Jul;39(4):783-791. (PMID: 28561359)
Int J Mol Sci. 2020 Jun 02;21(11):. (PMID: 32498390)
Biology (Basel). 2021 Nov 30;10(12):. (PMID: 34943165)
Front Plant Sci. 2015 Dec 01;6:1034. (PMID: 26648949)
Plant Mol Biol. 2016 Jul;91(4-5):471-84. (PMID: 27097903)
Genes Dev. 2004 Mar 15;18(6):700-14. (PMID: 15031265)
PLoS Biol. 2014 Sep 16;12(9):e1001950. (PMID: 25226037)
Mol Biol Evol. 2016 Jul;33(7):1870-4. (PMID: 27004904)
Plant Signal Behav. 2020 Sep 1;15(9):1782647. (PMID: 32552524)
Plant J. 2019 Nov;100(3):610-626. (PMID: 31350858)
Development. 2018 Feb 8;145(3):. (PMID: 29439132)
Nat Rev Mol Cell Biol. 2010 Feb;11(2):113-27. (PMID: 20094052)
Plant J. 2002 Dec;32(5):713-22. (PMID: 12472687)
Plant J. 2014 Apr;78(2):319-27. (PMID: 24517883)
PLoS Genet. 2011 Jun;7(6):e1002126. (PMID: 21698132)
Curr Biol. 2013 Nov 4;23(21):2090-9. (PMID: 24206843)
New Phytol. 2020 Dec;228(5):1611-1626. (PMID: 32634250)
BMC Plant Biol. 2021 Dec 6;21(1):576. (PMID: 34872513)
Plant Cell. 2007 Nov;19(11):3655-68. (PMID: 18055605)
Sci Rep. 2019 Jun 20;9(1):8869. (PMID: 31222090)
PLoS Genet. 2012;8(11):e1002997. (PMID: 23166504)
Plant Cell Rep. 2018 Nov;37(11):1499-1511. (PMID: 30014159)
Plant J. 2016 Nov;88(3):437-451. (PMID: 27402171)
معلومات مُعتمدة: № 075-15-2022-322 dated 22.04.2022 Ministry of Science and Higher Education of the Russian Federation in accordance with the agreement on providing a grant in the form of subsidies from the federal budget of the Russian Federation. The grant was provided for state support for the creation
فهرسة مساهمة: Keywords: CLE; Raphanus sativus; WOX; genomic sequence; inbred lines; single nucleotide variants; spontaneous tumours
المشرفين على المادة: 0 (Plant Proteins)
تواريخ الأحداث: Date Created: 20240619 Date Completed: 20240619 Latest Revision: 20240620
رمز التحديث: 20240620
مُعرف محوري في PubMed: PMC11172632
DOI: 10.3390/ijms25116236
PMID: 38892425
قاعدة البيانات: MEDLINE
الوصف
تدمد:1422-0067
DOI:10.3390/ijms25116236