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Asterids

ABSTRACT: A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads

PROVIDER: PRJDB1666 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR021687_1.fastq.gz	Fastqsanger.gz
	DRR021687_2.fastq.gz	Fastqsanger.gz
	DRR021688_1.fastq.gz	Fastqsanger.gz
	DRR021688_2.fastq.gz	Fastqsanger.gz
	DRR021689_1.fastq.gz	Fastqsanger.gz

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asterids

Project description:Asterid Phylogenomics/phylotranscriptomics Raw Sequence Reads

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Genetic variation in a plant-parasitic nematode is associated with host gene expression signals conserved across evolutionarily distant host plants

Project description:A hallmark of the interactions between endoparasites (parasites that live within plant tissue) and their hosts, is the parasites' ability to hijack host gene expression to support their own existence. While a number of studies have been performed to identify plant genes that are recruited in this manner, there is much that remains unknown. One mechanism by which this behavior can be explored is by using a traditional genetics approach: identifying connections between genetic variation and phenotype variation. To that end, we leverage experiments examining tissue from three host plant species, each infected with one of two genetically distinct strains of the endoparasite Meloidogyne hapla. Using RNA-Seq data, we identify plant gene expression patterns that differ according to the genetic background of the parasite they are infected with. We also show that parasite genotype-host expression phenotype associations are consistent across plant species. These results indicate that the plant genes recruited by the parasite are influenced by the parasite's genetic background, and that these differential choices are conserved across evolutionarily distant hosts. We also leverage public data to identify conserved host expression differences when comparing M. hapla-infected plants to uninfected plants. Finally, we demonstrate that parasite gene expression varies according to the parasites' genetic background, and show that these signals are also conserved under different host species.

2026-03-24 | GSE325830 | GEO

Profiling of alternative polyadenylation events in Arabidopsis thaliana

Project description:Use 3ʹ region extraction and deep sequencing (3'READS) and bioinformatics techniques to profile alternative polyadenylation and gene regulation in plant Arabidopsis thaliana exposed to light and darkness

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Project description:Stem cells rejuvinate the schistosome host-parasite interface

2019-05-14 | E-GEOD-75861 | ExpressionAtlas

asterids

Project description:Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation

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asterids

Project description:Tissue_Cultures_in_WildTobaccoCarrot

| PRJDB42369 | ENA

Identification and Differential Expression of MicroRNAs during Cold Acclimation of the Tea Plant (Camellia sinensis) by Deep Sequencing

Project description:In this study, we performed deep sequencing and bioinformatics analyses of tea plant leaves to identify and characterize known and novel miRNAs. A total of 26,876,261 raw reads were produced from 2 libraries. We detected 422 known miRNAs belonging to 125 families, and 68 putative novel miRNAs.

2018-08-01 | GSE63760 | GEO

Oryza sativa ssp. indica Illumina lwhole-genome bisulfite sequencing used for coverage comparison next to the method plant-RRBS

Project description:The contained data consist of Illumina HiSeq reads generated genomic DNA of Oryza sativa ssp. indica used for comparative coverage aspects with plant-RRBS methylome profiling by bioinformatics analyses. The inbred control line and a derived epiline LR2 of the 4th selfing were analysed using whole-genome bisulfite sequencing.

2017-12-14 | E-MTAB-5002 | biostudies-arrayexpress

Allium cepa, Ipheion uniflorum, Narcissus jonquilla, Muscari comosum

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Cryptosporidium secreted proteins form a complex layered interface with the host cell

Project description:Cryptosporidium parvum, one of the leading causes of diarrheal death in children, remodels its infection site through secreted effector proteins. Several of them accumulate at the host-parasite interface, forming a complex structure whose function and importance for infection remain poorly understood. Here, we localized and functionally characterized the putative dense granule protein DG8. We confirmed the protein to be in the dense granules, forming a ring structure once secreted at the host-parasite interface. Deletion of DG8 showed reduced infection in mice in vivo and early defect in vitro, revealing the importance of DG8 for parasite fitness. Five additional secreted proteins were identified as potential partners, among which SG4, a small granule protein, was shown to partially co-localize with DG8. Applying ultrastructure expansion microscopy on intestinal sections with newly generated antibodies against DG8 and SG4, we could precisely position the ring structure above the dense band, around the feeder organelle at the base of the parasitophorous vacuole membrane with an unprecedent resolution. Altogether, better visualization and understanding of the host-parasite interface through expanded intestinal tissue and effectors characterization reveal a complex and essential layered host-parasite interface.

2026-05-04 | PXD074689 | Pride

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