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Endogenous miRNA targets identified by sequencing of the Soybean degradome

ABSTRACT: To identify more targets in soybean, particularly specific targets of Cd-stress-responsive miRNAs, high-throughput degradome sequencing was used. In total, we obtained 8913111 raw reads from the library which was constructed from a mixture of four samples (HX3-CK, HX3-Cd-treatment, ZH24-CK and ZH24-Cd-treatment). After removing the reads without the CAGAG adaptor, 5430126 unique raw-reads were obtained. The unique sequences were aligned to the G. max genome database, and 6516276 reads were mapped to the genome. The mapped reads from the libraries represented 51481 annotated G. max genes.

ORGANISM(S): Glycine max

PROVIDER: GSE50063 | GEO | 2013/12/20

SECONDARY ACCESSION(S): PRJNA215930

REPOSITORIES: GEO

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Endogenous miRNA targets identified by sequencing of the Soybean degradome

Project description:To identify more targets in soybean, particularly specific targets of Cd-stress-responsive miRNAs, high-throughput degradome sequencing was used. In total, we obtained 8913111 raw reads from the library which was constructed from a mixture of four samples (HX3-CK, HX3-Cd-treatment, ZH24-CK and ZH24-Cd-treatment). After removing the reads without the CAGAG adaptor, 5430126 unique raw-reads were obtained. The unique sequences were aligned to the G. max genome database, and 6516276 reads were mapped to the genome. The mapped reads from the libraries represented 51481 annotated G. max genes. Identification of miRNA targerts in soybean roots

2013-12-20 | E-GEOD-50063 | biostudies-arrayexpress

degradome sequence data

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Project description:To gain insight into the functions of salt-regulated miRNAs, target genes were identified through degradome sequencing approach. Three cotton RNA libraries were constructed and sequenced under normal consideration, osmotic and ionic stress. A total of 73,988,644 reads represented by 3,254,054 unique reads from the 5â ends of uncapped and poly-adenylated RNAs were obtained. The PairFinder software was used to identify the sliced targets for the known miRNAs and novel miRNAs. These sequences were further compared with transcriptome sequencing data of G. arboretum and G. raimondii. We obtained the data from (Cotton Genome Project, http://cgp.genomics.org.cn/page/species/index.jsp).Based on degradome sequencing, 31 target genes were identified for 20 cotton miRNA families. The abundance of transcripts was plotted for each transcript. Conserved miRNAs target conserved homologous genes in diverse plant species. Three cDNA libraries were constructed using total RNA obtained from control samples (CK), the 4 h and 5 d salt-treated samples. A total of 74,351,180 sequence reads were obtained from three libraries. After removing the 3p and 5p adapter sequences and filtering out low quality âânââ sequences, 864,720, 1,217,757 and 1,171,577 clean reads remained in the CK, 4 h and 5 d samples, respectively.

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Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton [degradome]

2013-07-28 | GSE43389 | GEO

Identification and Comparative Analysis of Cotton miRNA Target Genes using Degradome Sequencing

Project description:To gain insight into the functions of salt-regulated miRNAs, target genes were identified through degradome sequencing approach. Three cotton RNA libraries were constructed and sequenced under normal consideration, osmotic and ionic stress. A total of 73,988,644 reads represented by 3,254,054 unique reads from the 5’ ends of uncapped and poly-adenylated RNAs were obtained. The PairFinder software was used to identify the sliced targets for the known miRNAs and novel miRNAs. These sequences were further compared with transcriptome sequencing data of G. arboretum and G. raimondii. We obtained the data from (Cotton Genome Project, http://cgp.genomics.org.cn/page/species/index.jsp).Based on degradome sequencing, 31 target genes were identified for 20 cotton miRNA families. The abundance of transcripts was plotted for each transcript. Conserved miRNAs target conserved homologous genes in diverse plant species.

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Project description:In this study, in order to identify miRNA targets, a degradome library derived from anthers of the WT and GMS (Genetic Male Sterility) mutant representing three stages of development was constructed and sequenced, resulting in the generation of 24.6 million raw reads. After removal of low quality sequences and adapter sequences, 24.4 million clean reads were obtained and 98% were 20 or 21 nt in length as expected in that normally length distribution peak of degradome fragment is between 20 and 21 nt [Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ: Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 2008, 18:758-762]. Identification of miRNA targets in the WT and GMS muant anthers. Anthers of the WT and GMS mutant representing three stages of development [the meiosis stage (WT: Mar-F-1; mutant: Mar-S-1) and tetrad stage (WT: Mar-F-2; mutant: Mar-S-2), together with the uninucleate microspore stage (WT: Mar-F-3; mutant: Mar-S-3) from the GMS M-bM-^@M-^XDong AM-bM-^@M-^Y mutant and its fertile wild type] were collected during early mornings.

2013-07-28 | E-GEOD-43389 | biostudies-arrayexpress

Utilization of transcriptome, small RNA, and degradome sequencing to provide insights into drought stress and re-watering treatment in Medicago ruthenica (Degradome-Seq)

Project description:Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, miRNAs, and key miRNA-target pairs in M. ruthenica under drought and re-watering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed between the re-watering (RW) vs. drought (DS) comparison and control (CK) groups. The degradome sequencing analysis revealed that 348 miRNAs (37 novel and 311 conserved miRNAs) were identified with 6,912 target transcripts, forming 11,390 miRNA-target pairs in the three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21,18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

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An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]

Project description:Cadmium (Cd) influence in rice is a growing global environmental concern. Although many miRNAs and target genes have been identified in rice exposure to Cd stress, no comprehensive study has been done comprising integrative analysis of small RNAs, degradome and trascriptome sequencing to identify Cd-regulated miRNAs and their targets under Cd stress. In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which were involved in signal transduction such as abscisic acid (ABA), Auxin, Gibberellin acid (GA) and MAPK (Mitogen-activated protein kinase). Functional analysis revealed that genes involved in photosynthesis pathway (osa00196, osa00195 and osa00710) and protein degradation pathway (osa04612) were identified to be participated in response to Cd in rice, including osa-miR156I-5p_R-1/SPLs, osa-miR171a_1ss12CT/DEGP10 and osa-miR169r-5p_R/NFYA6 circuits, respectively. We conclude that a combination of transcriptome, sRNAs and the degradome would confer a useful approach to investigate miRNA-mediated molecular mechanisms underlying plant response to Cd stress.

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RNA illumina sequencing of Panax notoginseng under CK and Cd stress treatment

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