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| 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
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| 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.
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| 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.
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| 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 |
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| Submission date |
Mar 29, 2009 |
| Last update date |
May 27, 2014 |
| Contact name |
Misook Ha |
| E-mail(s) |
misook.ha@gmail.com
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| Phone |
7732795900
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| Organization name |
National Heart Lung Blood Institute
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| Lab |
Laboratory of Epigenome Biology
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| Street address |
NIH
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (5)
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| GPL8814 |
Arabidopsis thaliana microRNA 0.35K microarray |
| GPL9386 |
454 GS (Arabidopsis thaliana) |
| GPL9414 |
454 GS (Arabidopsis arenosa) |
| GPL9415 |
454 GS (Arabidopsis suecica) |
| GPL18731 |
454 GS (Arabidopsis arenosa; Arabidopsis thaliana) |
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| Samples (58)
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| 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) |
| GSM387516 |
Endogenous small RNAs from Arabidopsis arenoa, wild type, flower (AaF) |
| GSM387517 |
Endogenous small RNAs from synthetic allopolyploid, F1 generation, wild type, leaf (F1L) |
| GSM387518 |
Endogenous small RNAs from synthetic allopolyploid, F1 generation, wild type, flower (F1F) |
| GSM387519 |
Endogenous small RNAs from synthetic allopolyploid, F7 generation, wild type, leaf (F7L) |
| GSM387520 |
Endogenous small RNAs from synthetic allopolyploid, F7 generation, wild type, flower (F7F) |
| GSM387521 |
Endogenous small RNAs from Arabidopsis suecica, wild type, leaf (AsL) |
| GSM387522 |
Endogenous small RNAs from Arabidopsis suecica, wild type, flower (AsF) |
| GSM554239 |
small RNA_chip_A_thaliana_leaf1 |
| GSM554240 |
small RNA_chip_A_thaliana_leaf2 |
| GSM554241 |
small RNA_chip_A_thaliana_leaf3 |
| GSM554242 |
small RNA_chip_A_thaliana_leaf4 |
| GSM554243 |
small RNA_chip_A_thaliana_leaf5 |
| GSM554244 |
small RNA_chip_A_thaliana_leaf6 |
| GSM554245 |
small RNA_chip_A_thaliana_leaf7 |
| GSM554246 |
small RNA_chip_A_thaliana_leaf8 |
| GSM554247 |
small RNA_chip_A_thaliana_leaf9 |
| GSM554248 |
small RNA_chip_A_arenosa_leaf1 |
| GSM554249 |
small RNA_chip_A_arenosa_leaf2 |
| GSM554250 |
small RNA_chip_A_arenosa_leaf3 |
| GSM554251 |
small RNA_chip_A_arenosa_leaf4 |
| GSM554252 |
small RNA_chip_A_arenosa_leaf5 |
| GSM554253 |
small RNA_chip_A_arenosa_leaf6 |
| GSM554254 |
small RNA_chip_A_arenosa_leaf7 |
| GSM554255 |
small RNA_chip_A_arenosa_leaf8 |
| GSM554256 |
small RNA_chip_A_arenosa_leaf9 |
| GSM554257 |
small RNA_chip_F7_leaf1 |
| GSM554258 |
small RNA_chip_F7_leaf2 |
| GSM554259 |
small RNA_chip_F7_leaf3 |
| GSM554260 |
small RNA_chip_F7_leaf4 |
| GSM554261 |
small RNA_chip_F7_leaf5 |
| GSM554262 |
small RNA_chip_F7_leaf6 |
| GSM554263 |
small RNA_chip_F7_leaf7 |
| GSM554264 |
small RNA_chip_F7_leaf8 |
| GSM554265 |
small RNA_chip_F7_leaf9 |
| GSM554266 |
small RNA_chip_A_suecica_leaf1 |
| GSM554267 |
small RNA_chip_A_suecica_leaf2 |
| GSM554268 |
small RNA_chip_A_suecica_leaf3 |
| GSM554269 |
small RNA_chip_A_suecica_leaf4 |
| GSM554270 |
small RNA_chip_A_suecica_leaf5 |
| GSM554271 |
small RNA_chip_A_suecica_leaf6 |
| GSM554272 |
small RNA_chip_A_suecica_leaf7 |
| GSM554273 |
small RNA_chip_A_suecica_leaf8 |
| GSM554274 |
small RNA_chip_A_suecica_leaf9 |
| GSM554275 |
small RNA_chip_A_thaliana_flower1 |
| GSM554276 |
small RNA_chip_A_thaliana_flower2 |
| GSM554277 |
small RNA_chip_A_thaliana_flower3 |
| GSM554278 |
small RNA_chip_A_arenoa_flower1 |
| GSM554279 |
small RNA_chip_A_arenoa_flower2 |
| GSM554280 |
small RNA_chip_A_arenoa_flower3 |
| GSM554281 |
small RNA_chip_F7_flower1 |
| GSM554282 |
small RNA_chip_F7_flower2 |
| GSM554283 |
small RNA_chip_F7_flower3 |
| GSM554284 |
small RNA_chip_A_suecica_flower1 |
| GSM554285 |
small RNA_chip_A_suecica_flower2 |
| GSM554286 |
small RNA_chip_A_suecica_flower3 |
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| Relations |
| BioProject |
PRJNA115805 |
| 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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