High-throughput sequencing technology identify the CGMMV responsive genes, lncRNAs and cirRNAs in watermelon
Ontology highlight
ABSTRACT:
ORGANISM(S): Citrullus lanatus
PROVIDER: GSE130223 | GEO | 2019/04/24
REPOSITORIES: GEO
Similar Datasets
Project description:High-throughput sequencing technology identify the CGMMV responsive genes, lncRNAs and cirRNAs in watermelon
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Project description:Purpose: The goals of this study are to compare differentially expressed transcripts in leaves of watermelon during drought stress using transcriptome profiling (RNA-seq)
2020-05-21 | GSE144814 | GEO
Project description:Male sterility is important mechanism in watermelon for production of hybrid seed. While some fruit development related studies were widely performed in watermelon, there are no reports of profiling gene expression in floral organs of watermelon. RNA-seq analysis was performed in order to identify male sterility related genes from two different groups of watermelon (genetic male-sterile (GMS) DAH3615-MS line and male-fertile DAH3615 line, respectively) to identify the differentially expressed genes (DEGs). This study employed tophat and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 2 tissues obtained from 2 different breeds of watermelon
2016-01-04 | E-GEOD-69073 | biostudies-arrayexpress
Project description:Male sterility is important mechanism in watermelon for production of hybrid seed. While some fruit development related studies were widely performed in watermelon, there are no reports of profiling gene expression in floral organs of watermelon. RNA-seq analysis was performed in order to identify male sterility related genes from two different groups of watermelon (genetic male-sterile (GMS) DAH3615-MS line and male-fertile DAH3615 line, respectively) to identify the differentially expressed genes (DEGs).
2016-01-04 | GSE69073 | GEO
Project description:In this study, Solexa sequencing technology has been used to discover small RNA populations of self-grafted watermelon and grafted watermelon (bottle gourd and squash were used as rootstocks). A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known and 15 novel miRNAs) and 51 (21 known miRNAs and 30 novel miRNAs) miRNAs were expressed significantly different with higher abundance or lower abundance in watermelon grafted on to bottle gourd and squash, respectively. The differentially expressed miRNA target various transcriptional factors and other genes which involved in a wide range of biological processes. This study was firstly conducted to identify and compare miRNAs on genome-wide scale in watermelon grafting system. The miRNAs expressed differentially when watermelon was grafted onto different rootstocks suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expression to regulate plant growth and response to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular basis of miRNA regulation of genes expressed in self-grafted and grafted watermelon.
2011-10-26 | GSE33209 | GEO
Project description:In this study, Solexa sequencing technology has been used to discover small RNA populations of self-grafted watermelon and grafted watermelon (bottle gourd and squash were used as rootstocks). A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known and 15 novel miRNAs) and 51 (21 known miRNAs and 30 novel miRNAs) miRNAs were expressed significantly different with higher abundance or lower abundance in watermelon grafted on to bottle gourd and squash, respectively. The differentially expressed miRNA target various transcriptional factors and other genes which involved in a wide range of biological processes. This study was firstly conducted to identify and compare miRNAs on genome-wide scale in watermelon grafting system. The miRNAs expressed differentially when watermelon was grafted onto different rootstocks suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expression to regulate plant growth and response to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular basis of miRNA regulation of genes expressed in self-grafted and grafted watermelon. Examination of 3 different small RNA expression profilings in self-grafted and grafted watermelon
2011-10-26 | E-GEOD-33209 | biostudies-arrayexpress
Project description:Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is an important cucurbit crop grown worldwide. Watermelon fruit quality, fertility, and the seed setting rate are closely related to male flower development. In this study, the different developmental stages of flower buds of the watermelon variety Xinteda Zhengkang 9 were distinguished by cytological observation, and transcriptome sequencing analysis was performed subsequently. Acetocarmine staining of anthers was performed and the longitudinal and transverse diameters of the unopened male flower buds were measured. Cytological observations of anthers at different developmental stages showed that the anther grew from the tetrad to the mature stage, and the longitudinal and transverse diameters of the flower buds increased. The length of the male flower buds also changed significantly during development. Transcriptome sequencing analysis at four periods, the tetrad (A group), mononuclear (B group), dikaryophase (C group), and mature stages (D group). Total 16288 differentially expressed genes (DEGs) were detected in the four stages, with the prolongation of developmental stages the number of DEGs increased gradually in the comparison groups, such as there was 2014, 3259, 4628, 1490, 3495 and 1132 DEGs were revealed in six comparison groups (A-VS-B, A-VS-C, A-VS-D, B-VS-C, B-VS-D, and C-VS-D), respectively. Gene ontology (GO) and KEGG enrichment analysis showed that the DEGs were mainly enriched in cellular component and starch and sucrose metabolism, phenylpropanoid biosynthesis and pentose sugar, etc. Finally, we totally screened 59 DEGs were in the six comparison groups, and most of them were up-regulated, interestingly, we find one pollen-specific protein (Cla001608) was significantly up-regulated (the value of log2Fold Change up to 17.32), which indicating that it may play important role in the development of male flowers. This work provides insight into the molecular basis of the developmental stages of male flowers in watermelon and may aid in dominant cross breeding.
2023-07-21 | GSE155092 | GEO
Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.
2018-05-23 | GSE102029 | GEO
Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.
2018-05-23 | GSE102028 | GEO
Project description:To determine the differential expression of proteins in leaf and fruit of diploid and tetraploid watermelon
2019-11-11 | PXD005179 | Pride