Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8848600.fastq.gz | Fastqsanger.gz | |||
| SRR8848610.fastq.gz | Fastqsanger.gz | |||
| SRR8848620.fastq.gz | Fastqsanger.gz | |||
| SRR8848630.fastq.gz | Fastqsanger.gz | |||
| SRR8848601.fastq.gz | Fastqsanger.gz |
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Project description:Food resource access can mediate establishment success in invasive species, and generalist herbivorous insects are thought to rely on mechanisms of transcriptional plasticity to respond to dietary variation. While asexually reproducing invasives typically have low genetic variation, the twofold reproductive capacity of asexual organisms is a marked advantage for colonization. We studied host-related transcriptional acclimation in parthenogenetic, invasive, and polyphagous weevils: Naupactus cervinus and N. leucoloma. We analyzed patterns of gene expression in three gene categories that can mediate weevil-host plant interactions through identification of suitable host plants, short-term acclimation to host plant defenses, and long-term adaptation to host plant defenses and their pathogens. This approach employed comparative transcriptomic methods to investigate differentially expressed host detection, detoxification, immune defense genes, and pathway-level gene set enrichment. Our results show that weevil gene expression responses can be host plant-specific, and that elements of that response can be . Some host plant groups, such as legumes, appear to be more taxing as they elicit a complex gene expression response which is both strong in intensity and specific in identity. However, the weevil response to taxing host plants shares many differentially expressed genes with other stressful situations, such as host plant cultivation conditions and transition to novel host, suggesting that there is an evolutionarily favorable shared gene expression regime for responding to different types of stressful situations. Modulating gene expression in the absence of other avenues for phenotypic adaptation may be an important mechanism of successful colonization for these introduced insects.
2021-05-07 | GSE173980 | GEO
Project description:High-coverage whole genome sequencing of 11 Brazilian isolates of the root-knot nematode Meloidogyne incognita, presenting different host plant preferences and different geographical origins. Four M. incognita host races had been proposed in the past, based on host (in)compatibility on four different plant strains. The objective was to assess whether genomic variations (SNP) correlate with host range compatibility, geographical origin and host plant of origin.
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Project description:Dodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite, but the functional effects of these movements are not clear. Here we show that C. campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana hosts. Many of these miRNAs are 22 nts long, a usually rare size of plant miRNA associated with amplification of target silencing through secondary small interfering RNA (siRNA) production. Several A. thaliana mRNAs are targeted by C. campestris 22 nt miRNAs during parasitism, resulting in high levels of secondary siRNA production. The targeted mRNAs function in hormone perception, pathogen-defense signaling, phloem function, and stem-cell identity. Homologs of these target mRNAs from diverse plants also have high-confidence complementary sites to C. campestris miRNAs, suggesting that homologous mRNAs are targeted by C. campestris across its very broad host range. These data show that C. campestris miRNAs act as trans-species regulators of host gene expression, and suggest that they may act as virulence factors during parasitism.
2017-12-18 | GSE84955 | GEO
Project description:Small RNAs (sRNAs) are key regulators of plant defense and have been implicated in cross-kingdom interactions with pathogens. The hemibiotrophic fungus Colletotrichum higginsianum infects Arabidopsis thaliana through three stages: appressorial penetration, biotrophy, and necrotrophy. However, the dynamics of fungal and plant sRNA populations across these three stages has not been elucidated. Using high-throughput sequencing, we profiled sRNAs from A. thaliana and C. higginsianum during in planta appressorium (PA), biotrophic (BP), and necrotrophic (NP) phases, and compared them to fungal mycelia (MY) and in vitro appressoria (VA). Our analyses revealed stage-specific patterns in sRNA accumulation in both the plant and the pathogen. In C. higginsianum, sRNAs were dominated by 29 nt species in PA, BP, MY, and VA, but shifted to 18 nt in NP, consistent with RNA degradation during host cell death. In A. thaliana, sRNAs transitioned from 30-33-nt in PA/BP to a 21 nt dominant peak in NP. Also, TE-derived siRNAs and other regulatory sRNAs (miRNAs, ncRNA, snoRNAs and snRNAs) declined during NP. A total of 62 host miRNAs showed differential accumulation, including core plant developmental regulators active across infection stages, and stage-specific miRNAs such as miR396, miR170/171, miR472, and miR858b. tRFs displayed opposite trends in host and pathogen: fungal tRFs declined in NP, while host tRFs increased. These tRFs contrasting trends may reflect differences in RNA processing or degradation between host and pathogen. Our results provide new insights into RNA-mediated plant-fungal interactions.
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Project description:One fascinating aspect of plant pathogen co-evolution is that pathogens use effectors to alter a broad range of host responses. RNA splicing functions in many physiological processes including plant immunity. However, how plant pathogens manipulate host RNA splicing process remains unknown. Here we demonstrate that PsAvr3c, an avirulence effector from oomycete pathogen Phytophthora sojae, physically binds to and stabilizes soybean (Glycine max) serine/arginine/lysine rich proteins GmSRKPs in vivo. SRKP, novel proteins associating with spliceosome components, are plant susceptibility factors against Phytophthora. Furthermore, RNA-seq data uncovers that differential splicing over one thousand soybean mRNA transcripts, including defense related genes, are significantly changed in GmSRKP1 over-expressing lines. Representative splicing events are verified in either infection assay or soybean transient expression assay. Our results demonstrate that plant pathogen utilize effector to reprogram host RNA splicing, uncovering a new strategy evolved by pathogens to defeat host immune system
2019-10-20 | GSE88973 | GEO