Zamia vazquezii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA47419 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ancestral Angiosperm Genome Project
| PRJNA46857 | ENA
Project description:The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ dramatically among angiosperm lineages, but in general, sterile perianth organs surrounding stamens (male reproductive organs) and carpels (female reproductive organs) constitute the basic floral structure. However, the basal angiosperm lineages exhibit spectacular diversity in the number, arrangement, and structure, of floral organs, while the evolutionarily derived monocot and eudicot lineages share a far more uniform floral ground plan. As such, regulatory mechanisms underlying the archetypal floral plan, for instance that of the eudicot genetic model Arabidopsis thaliana, are unlikely to apply to the original flowers. Here we show that broadly overlapping transcriptional programs characterise the floral transcriptome of the basal angiosperm Persea americana (avocado), while floral gene expression domains are typically organ-specific in Arabidopsis. Our findings extend the “fading borders” model for basal angiosperms from organ identity genes to the downstream floral transcriptome, and suggest that the combinatorial mechanism for organ identity may not operate in basal angiosperms as it does in Arabidopsis. Furthermore, fading expression of components of the stamen transcriptome in central and peripheral regions of Persea flowers resembles the developmental program of the hypothesized gymnosperm “floral progenitor”. Accordingly, in contrast to the canalized organ-specific regulatory apparatus of Arabidopsis, floral development may have been originally regulated by overlapping transcriptional cascades with fading gradients of influence from focal to bordering organs.
2009-06-18 | GSE13737 | GEO
Project description:Fleshy fruits evolved independently multiple times during angiosperm history, including the use of ethylene for the initiation and maintenance of ripening. ENCODE data of 355 transcriptome, 66 accessible chromatin, 160 histone and 45 DNA methylation profiles from eleven fleshy fruit species revealed three types of transcriptional feedback loops controlling ripening. Eudicots peach, papaya and melon evolved their circuits using carpel senescence NAC genes, whereas tomato, apple and pear utilized floral identity MADS genes derived from recent whole-genome-duplications. The monocot banana used both, forming a unique dual-loop circuit. Genes in these circuits and their tissue-specific H3K27me3 mark could be traced back to both dry fruits and ethylene-independent fleshy fruits, suggesting that the ethylene-dependent ripening mechanisms evolved from pre-existing genetic and epigenetic pathways in the ancestral angiosperms. FruitENCODE provides a comprehensive annotation of functional elements for fleshy fruit crops and new insight into the origins of climacteric fruit ripening.
2018-07-04 | GSE116581 | GEO
Project description:Current understanding of floral developmental genetics comes primarily from the core-eudicot model Arabidopsis thaliana. Here we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. Several thousand Nuphar genes with significantly up-regulated floral expression are identified, including homologs of the well-known ABCE floral regulators. However, strong similarities in the expression profiles of different organ categories contradict the organ-specific spatial expression domains predicted by the ABCE model. The broadly overlapping transcriptional programs observed among floral organs in Nuphar are shared with the magnoliid Persea americana (avocado), supporting the inference that this is the ancestral condition in angiosperms. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived. The transcriptional landscapes in Arabidopsis correlate with a shift toward morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. In contrast to most eudicots, perianth organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Our findings suggest that genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology. Custom microarrays targeting 6,220 unique Nuphar floral transcripts were used to measure expression levels in eight tissues using an interwoven double-loop design for 16 arrays.
2011-07-19 | E-GEOD-23082 | biostudies-arrayexpress
Project description:The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ dramatically among angiosperm lineages, but in general, sterile perianth organs surrounding stamens (male reproductive organs) and carpels (female reproductive organs) constitute the basic floral structure. However, the basal angiosperm lineages exhibit spectacular diversity in the number, arrangement, and structure, of floral organs, while the evolutionarily derived monocot and eudicot lineages share a far more uniform floral ground plan. As such, regulatory mechanisms underlying the archetypal floral plan, for instance that of the eudicot genetic model Arabidopsis thaliana, are unlikely to apply to the original flowers. Here we show that broadly overlapping transcriptional programs characterise the floral transcriptome of the basal angiosperm Persea americana (avocado), while floral gene expression domains are typically organ-specific in Arabidopsis. Our findings extend the âfading bordersâ model for basal angiosperms from organ identity genes to the downstream floral transcriptome, and suggest that the combinatorial mechanism for organ identity may not operate in basal angiosperms as it does in Arabidopsis. Furthermore, fading expression of components of the stamen transcriptome in central and peripheral regions of Persea flowers resembles the developmental program of the hypothesized gymnosperm âfloral progenitorâ. Accordingly, in contrast to the canalized organ-specific regulatory apparatus of Arabidopsis, floral development may have been originally regulated by overlapping transcriptional cascades with fading gradients of influence from focal to bordering organs. Expression profiles of inflorescence buds, pre-meiotic floral buds, inner and outer tepals, stamens, carpels, initiating fruit, and leaves were assessed in an interwoven double loop design for eight samples with 16 arrays. Sample materials were collected from two individuals (biological replicates) cultivated on the University of Floridaâs Gainesville campus, and RNA was isolated twice for technical replication. Thus, four RNA extractions from each of the eight tissue types listed above were individually labeled with Cy3 (twice) or Cy5 (twice) and hybridized with four other Cy3 or Cy5 labeled samples as a dual channel array system.
2010-06-25 | E-GEOD-13737 | biostudies-arrayexpress
Project description:Cytosine methylation is a conserved base modification, but explanations for its interspecific variation remain elusive. Only through taxonomic sampling of disparate groups can unifying explanations for interspecific variation be thoroughly tested. Here we leverage phylogenetic resolution of cytosine DNA methyltransferases (DNA MTases) and genome evolution to better understand widespread interspecific variation across 40 diverse fungal species. DNA MTase genotypes have diversified from the ancestral DNMT1+DNMT5 genotype through numerous loss events, and duplications, whereas, DIM-2 and RID-1 are more recently derived in fungi. Methylation is typically enriched at intergenic regions, which includes repeats and transposons. Unlike certain Insecta and Angiosperm species, Fungi lack canonical gene body methylation. Some fungi species possess large clusters of contiguous methylation encompassing many genes, repetitive DNA and transposons, and are not ancient in origin. Broadly, methylation is partially explained by DNA MTase genotype and repetitive DNA content. Basidiomycota on average have the highest level of methylation, and repeat content, compared to other phyla. However, exceptions exist across Fungi. Other traits, including DNA repair mechanisms, might contribute to interspecific methylation variation within Fungi. Our results show mechanism and genome evolution are unifying explanations for interspecific methylation variation across Fungi.
2019-02-18 | GSE112636 | GEO
Project description:Current understanding of floral developmental genetics comes primarily from the core-eudicot model Arabidopsis thaliana. Here we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. Several thousand Nuphar genes with significantly up-regulated floral expression are identified, including homologs of the well-known ABCE floral regulators. However, strong similarities in the expression profiles of different organ categories contradict the organ-specific spatial expression domains predicted by the ABCE model. The broadly overlapping transcriptional programs observed among floral organs in Nuphar are shared with the magnoliid Persea americana (avocado), supporting the inference that this is the ancestral condition in angiosperms. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived. The transcriptional landscapes in Arabidopsis correlate with a shift toward morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. In contrast to most eudicots, perianth organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Our findings suggest that genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.
2011-07-20 | GSE23082 | GEO