Cactus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA812417 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18315900_1.fastq.gz | Fastqsanger.gz | |||
| SRR18315900_2.fastq.gz | Fastqsanger.gz | |||
| SRR18315901_1.fastq.gz | Fastqsanger.gz | |||
| SRR18315901_2.fastq.gz | Fastqsanger.gz | |||
| SRR18315902_1.fastq.gz | Fastqsanger.gz |
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Project description:Many Cactaceae species exhibit determinate growth of the primary root as a consequence of root apical meristem (RAM) exhaustion. The genetic regulation of this root growth pattern is unknown. We de novo assembled and annotated the root apex transcriptome of the Pachycereus pringlei primary root at three developmental stages with active or exhausted RAM. The assembled transcriptome was characterized and used to evaluate differential transcript expression, identify RT-qPCR reference genes, and infer a transcriptional regulatory network. We generated a robust and comprehensive transcriptome of the primary root apex of P. pringlei and identified putative orthologs of Arabidopsis regulators of RAM maintenance, as well as putative lineage-specific transcripts. Furthermore, the transcriptome contained putative orthologs of most proteins involved in housekeeping processes, hormone signaling, and metabolic pathways. Specific transcriptional programs operate in the root apex at specific developmental time points. The transcriptional state of the P. pringlei root apex as the RAM becomes exhausted is comparable to that of cells from the meristematic, elongation, and differentiation zones of Arabidopsis roots. We suggest that the genetic program underlying the drought stress response is induced during development of the Cactaceae root, and that lineage-specific transcripts could contribute to root apical meristem exhaustion in Cactaceae.
2018-05-25 | GSE104832 | GEO
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2012-04-01 | E-MTAB-959 | biostudies-arrayexpress
Project description:In the presence of environmental change, natural selection can shape the transcriptome. Under a scenario of environmental change, genotypes that are better able to modulate gene expression to maximize fitness will tend to be favored. Therefore, it is important to examine gene expression at the population level in order to distinguish random or neutral gene expression variation from the pattern produced by natural selection. This study investigates the natural variation in transcriptional response to a cactus host shift utilizing the mainland Sonora population of Drosophila mojavensis. Drosophila mojavensis is a cactophilic species composed of four cactus host populations endemic to the deserts of North America. Overall, the change in cactus host was associated with a significant reduction in larval viability, as well as the differential expression of 21% of the genome (3,109 genes). Among the genes identified were a set of genes previously known to be involved in xenobiotic metabolism, as well as genes involved in cellular energy production, oxidoreductase/carbohydrate metabolism, structural components and mRNA binding. Interestingly, of the 3,109 genes whose expression was affected by host use, there was a significant overrepresentation of genes that lacked an orthologous call to the D. melanogaster genome, suggesting the possibility of an accelerated rate of evolution in these genes. Of the genes with a significant cactus effect, the majority, 2,264 genes, did not exhibit a significant cactus-by-line interaction. This population level approach facilitated the identification of genes involved in past cactus host shifts. Dataset from Population transcriptomics of cactus host shifts in Drosophila mojavensis, Matzkin, LM. Molecular Ecology.
2012-06-18 | GSE35937 | GEO
Project description:In April 2018, a cyst nematode was discovered from soil samples collected from a cactus garden collection in Meridian, Ada County, Idaho, USA. The cactus garden collection field reported was observed with localized areas of heavily stunted plants. Roots from affected plants displayed moderate numbers of nematode cysts. Living nematode juveniles (J2) recovered from the cysts were examined morphologically and molecularly for species identification which indicated that the specimens were Cactodera cacti. This is the first report of the cactus cyst nematode, C. cacti in Idaho.In April 2018, a cyst nematode was discovered from soil samples collected from a cactus garden collection in Meridian, Ada County, Idaho, USA. The cactus garden collection field reported was observed with localized areas of heavily stunted plants. Roots from affected plants displayed moderate numbers of nematode cysts. Living nematode juveniles (J2) recovered from the cysts were examined morphologically and molecularly for species identification which indicated that the specimens were Cactodera cacti. This is the first report of the cactus cyst nematode, C. cacti in Idaho.
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Project description:We introduce a data structure, analysis, and visualization scheme called a cactus graph for comparing sets of related genomes. In common with multi-break point graphs and A-Bruijn graphs, cactus graphs can represent duplications and general genomic rearrangements, but additionally, they naturally decompose the common substructures in a set of related genomes into a hierarchy of chains that can be visualized as two-dimensional multiple alignments and nets that can be visualized in circular genome plots. Supplementary Material is available at www.liebertonline.com/cmb .
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