Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR894776_1.fastq.gz | Fastqsanger.gz | |||
| ERR894776_2.fastq.gz | Fastqsanger.gz | |||
| ERR894777_1.fastq.gz | Fastqsanger.gz | |||
| ERR894777_2.fastq.gz | Fastqsanger.gz | |||
| ERR894778_1.fastq.gz | Fastqsanger.gz |
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Project description:The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ greatly in morphology, physiology, and development, yet we have a poor understanding of the underlying genetic basis of this divergence. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. In this study, we compared gene expression at different developmental time points between two locally adapted populations derived from the coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. We conducted gene co-expression network analyses to identify putative genetic and molecular mechanisms driving ecotypic divergence and evaluated gene ontology enrichment. Overall, we found significant global expression differences between the ecotypes and among developmental stages. We also found evidence to support the hypothesis that interacting hormone pathways, especially the gibberellin and jasmonic acid pathways, may play a key role in annual versus perennial ecotype divergence. Further, genes within known chromosomal inversions were more likely to be differentially expressed than genes in colinear regions, but only in leaves and not for floral buds. Collectively, our results reinforce our existing hypotheses about how ecotype formation has occurred in this system through shifts in hormone biosynthesis/signaling and help advance our understanding of the evolution of annuality versus perenniality in plants.
2024-11-10 | GSE280929 | GEO
Project description:Seasonal cycles of light, temperature and precipitation provide signals that set the timing of gene expression and growth for trees. Conifers possess evergreen needles to sense and respond to year-round external signals. We monitored gene activity in Douglas-fir needles for one year and found that gene expression is dependent on light at daily and annual scales. The majority of rhythmic genes achieve maximum activity +/- 2 hours from sunrise and sunset, and +/- 20 days from the winter and summer solstices. Remarkably, the dormant period is characterized by significant gene activation, with thousands of genes achieving peak activity. This study identifies annual gene rhythms in conifers needles, and provides a framework for identifying genes that respond to other environmental cues. Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x10^9 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
2017-01-04 | GSE93066 | GEO
Project description:Seasonal cycles of light, temperature and precipitation provide signals that set the timing of gene expression and growth for trees. Conifers possess evergreen needles to sense and respond to year-round external signals. We monitored gene activity in Douglas-fir needles for one year and found that gene expression is dependent on light at daily and annual scales. The majority of rhythmic genes achieve maximum activity +/- 2 hours from sunrise and sunset, and +/- 20 days from the winter and summer solstices. Remarkably, the dormant period is characterized by significant gene activation, with thousands of genes achieving peak activity. This study identifies annual gene rhythms in conifers needles, and provides a framework for identifying genes that respond to other environmental cues. Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x10^9 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
2017-01-04 | GSE93067 | GEO
Project description:Perennial plants maintain their life span through several growth seasons. Arabis alpina serves as model Brassicaceae species to study perennial traits. A. alpina lateral stems have a proximal vegetative zone with a dormant bud zone, and a distal senescing seed-producing inflorescence zone. We addressed the questions of how this zonation is distinguished at the anatomical level, whether it is related to nutrient storage, and which signals affect the zonation. We found that the vegetative zone ehxibits secondary growth, which we termed the perennial growth zone (PZ). High-molecular weight carbon compounds accumulate there in cambium and cambium derivatives. Neither vernalization nor flowering were requirements for secondary growth and sequestration of storage compounds. The inflorescence zone with only primary growth, termed annual growth zone (AZ), or roots exhibited different storage characteristics. Following cytokinin application, cambium activity was enhanced and secondary phloem parenchyma was formed in the PZ and also in the AZ. In transcriptome analysis cytokinin-related genes represented enriched gene ontology terms and were expressed at higher level in PZ than AZ. Thus, A. alpina uses primarily the vegetative PZ for nutrient storage, coupled to cytokinin-promoted secondary growth. This finding lays a foundation for future studies addressing signals for perennial growth.
2020-06-14 | GSE152417 | GEO
Project description:Towards understanding gene expression variation among related rice lineages on a genome-wide scale, we sought to assess global gene expression in the heading-stage panicle using a whole genome oligonucleotide microarray designed to represent 36,926 annotated indica genes. Using a loop-design, we interrogated gene expression patterns in six related rice lineages, including O. sativa (two Asian cultivars indica and japonica), O. nivara (Asian annual wild rice), O. rufipogon (Asian perennial wild rice) and O. glaberrima (African cultivated rice). Series_sample_order: Sample 1-12 Slide A; Sample 13-24 Slide B
2008-06-10 | E-GEOD-11712 | biostudies-arrayexpress
Project description:Venoms have convergently evolved in all major animal lineages and are ideal candidates to unravel the underlying genomic processes of convergent trait evolution. However, few animal groups have been studied in detail, and large-scale comparative genomic analyses to address toxin gene evolution are rare. Hyper-diverse hymenopterans are the most speciose group of venomous animals, but the origin of their toxin genes have been largely overlooked. We combined proteo-transcriptomics with comparative genomics compiling an up-to-date list of core bee venom proteins to investigate the origin of 11 venom genes in 30 hymenopteran genomes including two new stingless bees.
2023-09-28 | PXD029934 | Pride
Project description:Venoms have convergently evolved in all major animal lineages and are ideal candidates to unravel the underlying genomic processes of convergent trait evolution. However, few animal groups have been studied in detail, and large-scale comparative genomic analyses to address toxin gene evolution are rare. Hyper-diverse hymenopterans are the most speciose group of venomous animals, but the origin of their toxin genes have been largely overlooked. We combined proteo-transcriptomics with comparative genomics compiling an up-to-date list of core bee venom proteins to investigate the origin of 11 venom genes in 30 hymenopteran genomes including two new stingless bees.
2022-04-04 | PXD029823 | Pride
Project description:Endophytic bacterial communities of perennial wheatgrass and annual wheat
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