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Series GSE119460 Query DataSets for GSE119460
Status Public on Jan 15, 2019
Title Genotype- and tissue-specific microRNA profiles and their targets in three alfalfa (Medicago sativa L) accessions
Organism Medicago sativa
Experiment type Non-coding RNA profiling by high throughput sequencing
Other
Summary Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially control almost all aspect of plant growth and development. Although miRNAs have been reported from alfalfa but their expression profiles in different tissues and novel miRNAs as well as their targets have not been confirmed in this plant species. Therefore, we sequenced small RNAs in whole plantlets, shoots and roots of three different alfalfa genotypes (Altet-4, NECS-141 and NF08ALF06) to identify tissue-specific profiles. After comprehensive analysis using bioinformatics methods, we have identified 100 miRNA families, of which 21 belongs to the highly conserved families whereas the remaining 79 families are conserved between M. truncatula and M. sativa. The profiles of the six highly expressed conserved miRNA families (miR156, 159, 166, 319, 396, 398,) were relatively similar between the plantlets, roots and shoots of three genotypes. Contrastingly, the differenecs were robust between shoots and roots for miR160 and miR408 levels, which were low in roots compared to shoots. The study also has identified 17 novel miRNAs that also differed in their abundanecs between tissues of the alfalfa genotypes. Additionally, we have generated and analyzed the degradome libraries from three alfalfa genotypes that has confirmed 69 genes as targets for 31 miRNA families in alfalfa. The identification of conserved and novel miRNAs as well as their targets in different tissues of three genotypes not only enhanced our understanding of miRNA-mediated gene regulation in alfalfa but could also be useful for practical applications in alfalfa as well as related legume species.
 
Overall design Identification and comprehensive analysis of conserved microRNAs and their targets in Alfalfa using Illumina HiSeq 2000 sequencer.
 
Contributor(s) Monteros M, Sunkar R, Zheng Y
Citation(s) 30598106
Submission date Sep 04, 2018
Last update date Jan 15, 2019
Contact name Yun Zheng
E-mail(s) zhengyun5488@gmail.com
Organization name Yunnan Agricultural University
Street address 452 Fengyuan Road
City Kunming
State/province Yunnan
ZIP/Postal code 650201
Country China
 
Platforms (2)
GPL17647 Illumina HiSeq 2000 (Medicago sativa)
GPL25536 Illumina HiSeq 2500 (Medicago sativa)
Samples (11)
GSM3374923 small RNA of Medicago sativa L. (Altet) plantlets
GSM3374924 small RNA of Medicago sativa L. (NECS) plantlets
GSM3374925 small RNA of Medicago sativa L. (NF08ALF06) plantlets
Relations
BioProject PRJNA489281
SRA SRP159567

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
GSE119460_RAW.tar 240.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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