Rhizome metagenome
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ABSTRACT:
PROVIDER: PRJNA914541 | ENA |
REPOSITORIES: ENA
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Project description:Rhizome metagenome QHEI, Rhizome metagenome QJI, Rhizome metagenome QLU, Rhizome metagenome QPU, Rhizome metagenome XHEI, Rhizome metagenome XJI, Rhizome metagenome XLU, Rhizome metagenome XPU Raw sequence reads
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Project description:Our study provides the first comprehensive insight into the comparative transcriptome between shoot and rhizome in sorghum propinquum. Using the deep RNA sequencing technique, more than 70% of genes were identified to be expressed. Comparative analysis revealed that a strong difference in gene expression patterns between shoot and rhizome organs, especially a set of organ-specific TF genes and cis-elements were determined, implying a unique complicated molecular network controlling shoot or rhizome growth and development. Furthermore, this data set including a deep coverage of the subterranean rhizome transcriptome, provided essential information for future molecular genetic dissection of rhizome formation.
2013-12-31 | GSE43999 | GEO
Project description:The Oryza longistaminata is a perennial wild rice species with AA genome, which characterized by the presence of rhizomatous stem. The rhizomatousness trait in rice was previously identified quantitatively controlled by many genes, but the molecular mechanism related to the rhizome initiation and elongation is still unknown. In this study, the specific gene expression patterns across five tissues in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform, the rhizome-specific expressed genes and its corresponding regulatory were further analyzed. The different gene sets were determined exclusively expressed in five tissues; strikingly 58 genes with functions related to transcription regulation and cell proliferation were identified as prevalent sets in rhizome tip, of them, several genes were functionally involved in tiller initiation and elongation. And a set of genes were differentially regulated in the rhizome tip relative to shoot tip, the predominant repressed genes are involved in photosynthesis, while genes related to phytohormone and the gene families with redundancy function were obviously differentially regulated. Several cis-regulatory elements, including CGACG, GCCCORE, GAGAC and a Myb Core, were highly enriched in rhizome tip or internode, and two cis-elements such as RY repeat and TAAAG, which implicated in the ABA signaling pathway, were found overrepresented in the rhizome tip in comparison with shoot tip. A few rhizome-specific expressed genes were co-localized on the rhizome-related QTLs regions, indicating these genes may be good functional candidates for the rhizome related gene cloning. The whole genome profiling of oryza longistaminata indicated that a very complex gene regulatory network underlies rhizome development and growth, and there might be an overlapping regulatory mechanism in the establishment of rhizome and tiller. Phytohormone such as IAA and GA are involved in the signaling pathway in determining rhizome. Several cis-elements enriched in rhizome and the identified rhizome-specific genes co-localized on the rhizome-related QTL intervals provide a base for further dissection of the molecular mechanism of rhizomatousness
2010-10-31 | GSE24228 | GEO
Project description:Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to their well-developed rhizomes system. However, the post-transcriptional regulation mechanism has not been comprehensively studied for the development of rhizome system in bamboo. We therefore used single-molecule long-read sequencing technology to re-annotate the bamboo genome, and genome-wide identify alternative splicing (AS) and alternative polyadenylation (APA) in the rhizomes system. In total, 145,522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2,241 mis-annotated genes and identification of 8,091 previously unannotated loci. Markedly, more than 42,280 contiguous exon connectivity were derived from full-length splicing isoforms, including a large number of AS events that associated with rhizome systems. In addition, we characterized 25,069 polyadenylation sites from 11,450 genes, 6,311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements (TEs) within the intronic polyadenylation region. Furthermore, this study provided a quantitative altas of poly(A) usage and identified several hundreds of differential poly(A) sites in rhizome-root system using a combination of polyadenylation site sequencing (PAS-seq) and PacBio reads. Taken together, these results suggest that posttranscriptional regulation may potentially play vital role in the underground rhizome-root system.
2017-05-10 | GSE90517 | GEO
Project description:Black pepper rhizosphere microbiome Raw sequence reads
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