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Series GSE15443 Query DataSets for GSE15443
Status Public on Jul 31, 2009
Title Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids
Platform organisms Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica
Sample organisms Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica; Arabidopsis arenosa x Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Non-coding RNA profiling by array
Summary MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. arenosa), a natural allotetraploid (A. suecica), and two resynthesized allotetraploid lines (F1 and F7) derived from A. thaliana and A. arenosa. The siRNA populations present in A. thaliana were maintained in resynthesized allotetraploids and A. suecica. Although miRNA sequences were highly conserved, their expression patterns were highly variable between the allotetraploids and their progenitors. Significantly, many miRNAs were nonadditively expressed in the allotetraploids relative to the parents and preferentially degraded A. thaliana or A. arenosa targets. Stable inheritance of parental siRNAs in allopolyploids helps maintain genome stability in response to “genomic shock”, whereas expression diversity of miRNAs and their target preference lead to interspecies variation in gene expression, growth, and development.

NOTE: sff files unavailable for Samples AaL and F1L.
Overall design 10 samples examined: Arabidopsis thaliana leaf, flower, Arabidopsis arenosa leaf and flower, F1 synthetic allopolyploid leaf and flower, F7 synthetic allopolyploid leaf and flower, Arabidopsis suecica leaf and flower. To determine small RNA profiles in Arabidopsis allotetraploids and their progenitors, we made 10 small RNA libraries from rosette leaves (L) and flower buds (F) in five lines, A. thaliana, A. arenosa, Allo(F1), Allo733(F7), and A. suecica. To examine expression of small RNAs among related species and their hybrids, we employed miRNA microarrays and compared small RNA levels.
Contributor(s) Ha M, Lu J, Tian L, Ramachandran V, Kasschau K, Chapman E, Carrington J, Chen X, Wang X, Chen ZJ
Citation(s) 19805056
Submission date Mar 29, 2009
Last update date May 27, 2014
Contact name Misook Ha
Phone 7732795900
Organization name National Heart Lung Blood Institute
Lab Laboratory of Epigenome Biology
Street address NIH
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (5)
GPL8814 Arabidopsis thaliana microRNA 0.35K microarray
GPL9386 454 GS (Arabidopsis thaliana)
GPL9414 454 GS (Arabidopsis arenosa)
Samples (58)
GSM387513 Endogenous small RNAs from Arabidopsis thaliana ler, wild type, leaf (AtL)
GSM387514 Endogenous small RNAs from Arabidopsis thaliana ler, wild type, flower (AtF)
GSM387515 Endogenous small RNAs from Arabidopsis arenoa, wild type, leaf (AaL)
BioProject PRJNA115805

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE15443_454Reads_SID2368_AtL_AtF_AaF_AsF.fna.gz 7.8 Mb (ftp)(http) FNA
GSE15443_454Reads_SID2368_AtL_AtF_AaF_AsF.qual.gz 14.9 Mb (ftp)(http) QUAL
GSE15443_454Reads_SID2450_AsL_F1F_F7F_F7L.fna.gz 8.5 Mb (ftp)(http) FNA
GSE15443_454Reads_SID2450_AsL_F1F_F7F_F7L.qual.gz 16.1 Mb (ftp)(http) QUAL
GSE15443_C55G1reads_F1L.fna.gz 5.0 Mb (ftp)(http) FNA
GSE15443_C55G1reads_F1L.qual.gz 14.2 Mb (ftp)(http) QUAL
GSE15443_C55G2reads_AaL.fna.gz 6.1 Mb (ftp)(http) FNA
GSE15443_C55G2reads_AaL.qual.gz 16.0 Mb (ftp)(http) QUAL
GSE15443_RAW.tar 1.1 Mb (http)(custom) TAR (of TXT)
Raw data are available on Series record
Processed data included within Sample table
Raw data provided as supplementary file

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