title: Extending the sRNAome of apple by next-generation sequencing.
abstract: The global importance of apple as a fruit crop necessitates investigations into molecular aspects of the processes that influence fruit quality and yield, including plant development, fruit ripening and disease resistance. In order to study and understand biological processes it is essential to recognise the range of molecules, which influence these processes. Small non-coding RNAs are regulatory agents involved in diverse plant activities, ranging from development to stress response. The occurrence of these molecules in apple leaves was studied by means of next-generation sequencing. 85 novel microRNA (miRNA) gene loci were predicted and characterized along with known miRNA loci. Both cis- and trans-natural antisense transcript pairs were identified. Although the trans-overlapping regions were enriched in small RNA (sRNA) production, cis-overlaps did not seem to agree. More than 150 phased regions were also identified, and for a small subset of these, potential miRNAs that could initiate phasing, were revealed. Repeat-associated siRNAs, which are generated from repetitive genomic regions such as transposons, were also analysed. For this group almost all available repeat sequences, associated with the apple genome and present in Repbase, were found to produce siRNAs. Results from this study extend our current knowledge on apple sRNAs and their precursors significantly. A rich molecular resource has been created and is available to the research community to serve as a baseline for future studies.
authors.affiliation: Biotechnology Platform, Agricultural Research Council, Pretoria, Gauteng, South Africa; Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa.
authors.forename: Marike
authors.initials: M
authors.lastname: Visser
authors.affiliation: Central Analytical Facilities, Stellenbosch University, Stellenbosch, Western Cape, South Africa.
authors.forename: Anelda P
authors.initials: AP
authors.lastname: van der Walt
authors.affiliation: Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa; Infruitec-Nietvoorbij, Agricultural Research Council, Stellenbosch, Western Cape, South Africa.
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Maree
authors.affiliation: Biotechnology Platform, Agricultural Research Council, Pretoria, Gauteng, South Africa.
authors.forename: D Jasper G
authors.initials: DJ
authors.lastname: Rees
authors.affiliation: Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South Africa.
authors.forename: Johan T
authors.initials: JT
authors.lastname: Burger
mesh_terms: D018506:Gene Expression Regulation, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D027845:Malus / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
references.citation: Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1790-5
references.pmid: 22307647
references.citation: Bioinformatics. 2009 Jan 1;25(1):130-1
references.pmid: 19017659
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W132-8
references.pmid: 21515631
references.citation: Plant Cell. 2009 Apr;21(4):1053-69
references.pmid: 19376930
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W155-9
references.pmid: 21622958
references.citation: Bioinformatics. 2012 Oct 15;28(20):2561-8
references.pmid: 22914222
references.citation: Genes Dev. 2011 Dec 1;25(23):2540-53
references.pmid: 22156213
references.citation: PLoS One. 2013;8(2):e56842
references.pmid: 23418607
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
references.pmid: 21037258
references.citation: Nature. 2000 Mar 16;404(6775):293-6
references.pmid: 10749213
references.citation: Cell. 2005 Dec 29;123(7):1279-91
references.pmid: 16377568
references.citation: Genome Biol. 2005;6(4):R30
references.pmid: 15833117
references.citation: Plant Cell. 2008 Dec;20(12):3186-90
references.pmid: 19074682
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3318-23
references.pmid: 17360645
references.citation: RNA. 2009 Nov;15(11):1965-70
references.pmid: 19776157
references.citation: Genes Dev. 2010 May 15;24(10):1010-21
references.pmid: 20478994
references.citation: BMC Genomics. 2009 Dec 20;10:620
references.pmid: 20021695
references.citation: Genome Biol. 2006;7(10):R92
references.pmid: 17040561
references.citation: Nucleic Acids Res. 2008 Nov;36(19):6048-55
references.pmid: 18820301
references.citation: Plant Cell. 2013 May;25(5):1555-72
references.pmid: 23695981
references.citation: BMC Plant Biol. 2012 Aug 21;12:149
references.pmid: 22909020
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W68-76
references.pmid: 19433510
references.citation: Biosci Biotechnol Biochem. 2010;74(7):1435-40
references.pmid: 20622450
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: Nucleic Acids Res. 2012 Jul;40(13):6241-54
references.pmid: 22434877
references.citation: Science. 2001 Aug 10;293(5532):1146-50
references.pmid: 11498593
references.citation: BMC Genomics. 2012 Dec 22;13:721
references.pmid: 23259405
references.citation: Plant Cell. 2007 Mar;19(3):926-42
references.pmid: 17400893
references.citation: Plant Sci. 2013 Apr;203-204:17-24
references.pmid: 23415324
references.citation: Plant Mol Biol. 2013 Feb;81(3):211-20
references.pmid: 23306528
references.citation: Genome Res. 2008 Sep;18(9):1456-65
references.pmid: 18687877
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D1187-93
references.pmid: 22058132
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 24;107(34):15269-74
references.pmid: 20643946
references.citation: BMC Genomics. 2013 Apr 24;14:280
references.pmid: 23617936
references.citation: Dev Cell. 2003 Aug;5(2):337-50
references.pmid: 12919683
references.citation: Plant Physiol. 2005 Aug;138(4):2145-54
references.pmid: 16040653
references.citation: Chromosoma. 2011 Aug;120(4):409-22
references.pmid: 21594600
references.citation: Genes Dev. 2005 Sep 15;19(18):2164-75
references.pmid: 16131612
references.citation: Cell. 2006 Nov 3;127(3):565-77
references.pmid: 17081978
references.citation: Cell. 2005 Apr 22;121(2):207-21
references.pmid: 15851028
references.citation: Mol Cell. 2004 Oct 8;16(1):69-79
references.pmid: 15469823
references.citation: New Phytol. 2009;184(1):85-98
references.pmid: 19555436
references.citation: J Exp Bot. 2010;61(1):165-77
references.pmid: 19815687
references.citation: Nat Genet. 2010 Oct;42(10):833-9
references.pmid: 20802477
references.citation: Genes Dev. 2002 Jul 1;16(13):1616-26
references.pmid: 12101121
references.citation: Plant J. 2007 Dec;52(6):1131-9
references.pmid: 17944812
references.citation: Plant Physiol. 2009 Dec;151(4):2120-32
references.pmid: 19854858
references.citation: Annu Rev Plant Biol. 2013;64:137-59
references.pmid: 23330790
references.citation: Genome Res. 2009 Aug;19(8):1429-40
references.pmid: 19584097
references.citation: EMBO J. 2000 Oct 2;19(19):5194-201
references.pmid: 11013221
references.citation: Plant Physiol. 2013 Apr;161(4):2171-80
references.pmid: 23457227
references.citation: Gene. 2012 May 1;498(2):223-30
references.pmid: 22353365
references.citation: Cell. 2009 Feb 6;136(3):461-72
references.pmid: 19203581
references.citation: Science. 2004 Jan 30;303(5658):672-6
references.pmid: 14704433
references.citation: EMBO J. 2004 Oct 13;23(20):4051-60
references.pmid: 15372072
references.citation: Plant Physiol. 2007 Jul;144(3):1247-55
references.pmid: 17496106
references.citation: Nat Rev Genet. 2008 May;9(5):411-2; author reply 414
references.pmid: 18421312
references.citation: PLoS One. 2013;8(2):e57233
references.pmid: 23437348
references.citation: Mol Cell. 2010 May 14;38(3):465-75
references.pmid: 20381393
references.citation: Methods Mol Biol. 2008;453:3-31
references.pmid: 18712296
references.citation: Plant Physiol. 2013 Jun;162(2):741-54
references.pmid: 23580593
references.citation: Science. 1999 Oct 29;286(5441):950-2
references.pmid: 10542148
references.citation: Trends Plant Sci. 2013 Nov;18(11):601-10
references.pmid: 23993483
references.citation: EMBO J. 2002 Sep 2;21(17):4671-9
references.pmid: 12198169
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D1034-40
references.pmid: 17932055
references.citation: Genome Res. 2009 Jan;19(1):70-8
references.pmid: 18971307
references.citation: Plant Cell. 2012 Dec;24(12):4837-49
references.pmid: 23263766
references.citation: Plant Mol Biol. 2012 Nov;80(4-5):443-60
references.pmid: 22987114
references.citation: Genome Biol. 2012 Jun 15;13(6):R47
references.pmid: 22704043
references.citation: RNA. 2013 Jun;19(6):740-51
references.pmid: 23610128
references.citation: RNA. 2009 Jul;15(7):1233-40
references.pmid: 19474147
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):18002-7
references.pmid: 17071740
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12753-8
references.pmid: 15314213
references.citation: Chromosoma. 2001 Jul;110(3):203-13
references.pmid: 11513295
references.citation: Genomics Proteomics Bioinformatics. 2013 Jun;11(3):172-81
references.pmid: 23665476
references.citation: Plant Signal Behav. 2009 Feb;4(2):86-8
references.pmid: 19649178