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Genome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae inoculated cotton roots

ABSTRACT: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19â25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and on stress responses in plants.The objective of this study is to investigate the transcriptional profile of miRNAs and other small non-coding RNAs in Verticilliumâinoculated cotton roots. Four small RNA libraries were constructed from mocked and infected roots of two cotton cultured species which are with different Verticillium tolerance (âHai-7124â, Gossypium barbadense L., a Verticillium-tolerant cultivar, and âYi-11â, Gossypium hirsutum L. a Verticillium-sensitive cultivar). The length distribution of obtained small RNA pools was significantly different among libraries. A total of 215 conserved miRNA families were identified in the two cotton species, of them 14 are novel. There were >65 families with different expression between two libraries. We also identified two ta-siRNAs and thousands of endogenous siRNA candidates, and hundred of them exhibited altered expression after inoculation of Verticillium. The profiling of these miRNAs and other small non-coding RNAs lay the foundation for further understanding of small RNAs function in the regulation of Verticillium defence responses in cotton roots.

ORGANISM(S): Gossypium barbadense Gossypium hirsutum

PROVIDER: GSE28236 | GEO | 2011/04/30

SECONDARY ACCESSION(S): PRJNA139607

REPOSITORIES: GEO

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Genome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae inoculated cotton roots

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19â25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and on stress responses in plants.The objective of this study is to investigate the transcriptional profile of miRNAs and other small non-coding RNAs in Verticilliumâinoculated cotton roots. Four small RNA libraries were constructed from mocked and infected roots of two cotton cultured species which are with different Verticillium tolerance (âHai-7124â, Gossypium barbadense L., a Verticillium-tolerant cultivar, and âYi-11â, Gossypium hirsutum L. a Verticillium-sensitive cultivar). The length distribution of obtained small RNA pools was significantly different among libraries. A total of 215 conserved miRNA families were identified in the two cotton species, of them 14 are novel. There were >65 families with different expression between two libraries. We also identified two ta-siRNAs and thousands of endogenous siRNA candidates, and hundred of them exhibited altered expression after inoculation of Verticillium. The profiling of these miRNAs and other small non-coding RNAs lay the foundation for further understanding of small RNAs function in the regulation of Verticillium defence responses in cotton roots. Examination of 2 different traetments in 2 cotton types.

2011-04-29 | E-GEOD-28236 | biostudies-arrayexpress

Small RNA sequencing identifies miRNA roles in ovule and fiber development

Project description:To dissect the roles of miRNAs in fiber development, we sequenced small RNAs from ovules -1 to +1 day post anthesis (DPA) and young leaves. A series of conserved and novel miRNA were identified from cotton EST database and the genome of G.raimondii, many of which were shown to be expressed differentially between ovule and leaf, indicating their potential roles in fiber development or leaf development. Cotton (Gossypium Hirsutum L.) cultivar TM-1 were grown in the greenhouse. Cotton ovules -1 to +1 day post anthesis (DPA) and young leaves were harvested for five biological replicates and immediately frozen in liquid nitrogen. They were then stored at -80M-BM-0C following RNA extraction. Totals RNAs were extracted from each tissue sample using the mirVana miRNA isolation kit (Ambion, Austin, TX) according to the manufacturerM-bM-^@M-^Ys protocol. The small RNA samples extracted from the five biological replicates were pooled together for leaf and ovule, respectively. Finally, the construction of pooled small RNA libraries and sequenced were performed by LC Sciences (Houston, TX) using Illumina high-throughput sequencing platform.

2014-08-16 | E-GEOD-60380 | biostudies-arrayexpress

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

Project description:Genetic male sterility (GMS) in cotton (Gossypium hirsutum) plays an important role in the utilization of hybrid vigor. However, the molecular mechanism of the GMS is still unclear. While numerous studies have demonstrated that microRNAs (miRNA) regulate flower and anther development, whether different small RNA regulations exist in GMS and its wild type is unclear. To investigate the global expression and complexity of small RNAs during cotton anther development, three small RNA libraries were constructed from the anthers of three development stages each from fertile wild type (WT) and its GMS mutant cotton.

2013-07-28 | GSE43531 | GEO

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

2013-07-28 | E-GEOD-43531 | biostudies-arrayexpress

Transcriptome and metabolome profiling reveals key pathways and metabolites involved in defense response of upland cotton against Verticillium dahliae

Project description:Cotton is the main source of natural fiber in the textile industry, making it one of the most economically important fiber crops in the world. Verticillium wilt, caused by the pathogenic fungus Verticillium dahlia, is one of the most damaging biotic factors limiting cotton production. Mechanistic details of cotton defense responses to verticillium wilt remain unclear. In this study, GFP-labeled strain of V. dahlia was used to track colonization in cotton roots, and clear conidial germination could be observed at 48 hours post-inoculation (hpi), marking this as a crucial time point during infection. Transcriptome analysis identified 1,523 and 8,270 differentially expressed genes (DEGs) at 24 hpi and 48 hpi, respectively. Metabolomic screening found 78 differentially accumulated metabolites (DAMs) at 48 hpi. Conjoint analysis indicated that the phenylpropanoid biosynthesis pathway was activated in cotton infected with V. dahliae. The five metabolites in the phenylpropanoid biosynthesis pathway, including caffeic acid, coniferyl alcohol, coniferin, scopoletin and scopolin, could significantly inhibit V. dahlia growth in vitro, implicating their roles in cotton resistance to Verticillium wilt. The findings expand our understanding of molecular mechanisms underlying the pathogen defense response against V. dahlia infection in upland cotton, which may lead to future insights into controlling Verticillium wilt disease.

2023-12-26 | GSE221845 | GEO

Genome-wide profiling of miRNAs and their target genes during somatic embryogenesis in cotton by small RNA and degradome sequencing

Project description:MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target genes have been widely studied in model plants?and increasing studies have been performed on some crops?however, the number of identified miRNAs in cotton was limited, and global identification of related targets through degradome sequencing has not been developed previously. In this study, we globally identified small RNAs and their related target genes during cotton somatic embryogenesis by the high throughput small RNA and degradome sequencing technology using fresh hypocotyls and EC (embryogenic calli) of Gossypium hirsutum YZ1. A total of 36 differentially expressed conserved miRNA families of which 19 miRNA families represented by 29 precursors and 25 novel miRNAs were identified, with star sequences of 20 known miRNAs and 2 novel miRNAs discovered. 234 genes in EC and 322 genes in CK were identified as targets of 23 and 30 known miRNA families, and 16 genes were found as targets of 8 novel miRNAs. The expression profiles of several miRNAs and their targets were verified by qRT-PCR and 5’RACE were further used to validate the sliced sites of the targets. Interestingly, four TAS3 D6 and D7 were also found in both degradome libaries which can perfectly match their precursors. The profiling of the miRNAs and their target genes provides more information about the regulatory network of miRNAs during somatic embryogenesis in cotton. small RNA and degradome sequencing of CK(fresh hypocotyls) and EC (embryogenic calli) of Gossypium hirsutum YZ1

2013-03-08 | E-GEOD-41132 | biostudies-arrayexpress

Cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation

Project description:As an initial step to explore the cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation, conventional heirloom G. hirsutum (Gh) cultivars [susceptible Acala SJ-2 (SJ2), moderately resistant Upland Wild Mexico Jack Jones (WMJJ), and resistant Acala NemX] that have been shown to be useful as an informative genetic model for detecting and introgressing RKN resistance genes into commercial Upland cotton were used to enlighten the molecular mechanisms and gene expression of RKN resistance. Using the next generation sequencing (NGS) Illumina MiSeq and HiSeq, we performed RNA-seq profiling in roots with disease progression of 10 days and collected from 23 days old plants of SJ2, WMJJ, and NemX. With three biological replicates of each treatment from each cultivar, plants were subjected to RKN-infestation and non-infested control developing a total of 18 RNA-seq libraries

2022-04-01 | GSE190503 | GEO

Comparative analysis of cotton small RNAs in response to salt stress

Project description:Plants respond to stress by using multiple gene regulatory mechanisms including the post-transcriptional regulation of gene expression. The stresses suffered by plants under salinity include osmotic stress and ion stress. In this study, three cotton small RNA libraries were constructed and sequenced under normal consideration, osmotic and ionic stress. The length distribution of obtained small RNAs was significantly different between libraries. A total of 228 cotton miRNAs were identified. Of them 24 were novel miRNAs. There were 88 and 75 miRNAs with different expression in response to the influence of osmotic and ionic factors of saline stress, respectively. The identification of these small RNAs as well as elucidating their functional significance broadens our understanding of the post-transcriptional gene regulations in response to salt stress.

2016-06-08 | GSE69702 | GEO

High-throughput sequencing of eggplant small RNAs

Project description:MiRNAs are a class of non-coding, small RNAs that play important roles in the regulation of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including eggplant (Solanum melongena L.). To identify miRNAs in eggplant and their response to Verticillium dahliae infection, a fungal pathogen for which effective cure methods and a clear understanding of its mechanisms are currently lacking, we deep-sequenced two small RNA (sRNA) libraries prepared from mocked and infected seedlings of eggplants. Specifically, 30,830,792 reads produced 7,716,328 unique small RNAs have been identified.

2016-04-23 | GSE46330 | 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 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.

2016-06-11 | E-GEOD-69820 | biostudies-arrayexpress

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