Persea americana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA391003 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5738276_1.fastq.gz | Fastqsanger.gz | |||
| SRR5738276_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
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: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:Phytophthora cinnamomi Rands (Pc) is a hemibiotrophic oomycete and the causal agent of Phytophthora root rot (PRR) of the commercially important fruit crop avocado (Persea americana Mill.). Plant defense against pathogens is modulated by phytohormone signaling pathways such as salicylic acid (SA), jasmonic acid (JA), ethylene (ET), auxin and abscisic acid. The role of specific signaling pathways induced and regulated during hemibiotroph-plant interactions has been widely debated. Some studies report SA mediated defense while others hypothesize that JA responses restrict the spread of pathogens. This study aimed to identify the role of SA- and JA- associated genes in the defense strategy of a resistant avocado rootstock, Dusa® in response to Pc infection. Transcripts associated with SA-mediated defense pathways and lignin biosynthesis were upregulated at 6 hours post-inoculation (hpi). Results suggest that auxin, reactive oxygen species (ROS) and Ca2+ signaling was also important during this early time point, while JA signaling was absent. Both SA and JA defense responses were shown to play a role during defense at 18 hpi. Induction of genes associated with ROS detoxification and cell wall digestion (β-1-3-glucanase) was also observed. Most genes induced at 24 hpi were linked to JA responses. Other processes at play in avocado at 24 hpi include cell wall strengthening, the formation of phenolics and induction of arabinogalactan, a gene linked to Pc zoospore immobility. This study represents the first transcriptome wide analysis of a resistant avocado rootstock treated with SA and JA compared to Pc infection. The results provide evidence of a biphasic defense response against the hemibiotroph, which initially involves SA-mediated gene expression followed by the enrichment of JA-mediated defense from 18 to 24 hpi. Genes and molecular pathways linked to Pc resistance are highlighted and may serve as future targets for manipulation in the development of PRR resistant avocado rootstocks.
2018-11-14 | GSE119635 | GEO
Project description:Transcriptome response of avocado roots subjected to flooding and infection by the oomycete Phytophthora cinnamomi
| PRJNA321206 | ENA
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Persea americana tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
2011-05-10 | GSE28981 | GEO
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Persea americana tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, flowers and fruit of Persea americana. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Doug Soltis for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-05-09 | E-GEOD-28981 | biostudies-arrayexpress
Project description:Avocodo is an oil-rich, highly nutritious fruit native to Mexico
| PRJNA73885 | ENA
Project description:Pollination is limiting for avocado production. We examined whether adding bumblebees (BBs; ca. 10 hives/ha) to conventional honeybees (HB; 5 hives/ha) would improve 'Hass' avocado pollination and yields. A preliminary trial (2017/18) in an avocado orchard with four consecutive rows of 'Hass' followed by one row of 'Ettinger' serving as a pollenizer (20% 'Ettinger') showed a considerable increase in 'Hass' yield in rows adjacent to (up to 80 m from) the BB hives vs. distant rows (=controls). In 2018/19, the trials were extended to three additional orchards. A significant yield increase was obtained in the BB hive-adjacent trees compared to BB hive-distant ones. Similar results were obtained in 2019/20, in experiments conducted throughout the country. The SNP analysis, to determine the parents of 'Hass' fruit at varying distances from the BB hives, showed no differences in the cross-pollination rate ('Hass' × 'Ettinger'). However, pollination rates and the number of germinating pollen grains per stigma decreased with distance from the hives, and correlated to the negative gradient in yield. Taken together, our data suggest that adding BB hives to 'Hass' avocado orchards, at ca. 10 hives/ha resulting in 0.5-1.0 BB visits/tree per min, increases pollination and, accordingly, total yield.
| S-EPMC8309347 | biostudies-literature
Project description:High-throughput sequencing of small RNAs in Persea americana
| PRJNA142837 | ENA