Transcriptome profiling for floral bud development in reblooming cultivar 'High Noon' of Paeonia suffruticosa
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ABSTRACT:
ORGANISM(S): Paeonia lutea x Paeonia suffruticosa
PROVIDER: GSE133476 | GEO | 2019/06/29
REPOSITORIES: GEO
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Project description:Tree peony (Paeonia suffruticosa Andrew) is a popular ornamental plant due to its large, fragrant and colorful flowers. The floral development is the most important event in its lifecycle. To explore the mechanism that regulate flower development, we sequenced the flower bud transcriptomes of 'High Noon', a reblooming cultivar of P. suffruticosa × P. lutea, using both full-length isoform-sequencing (ISO-seq) and RNA-seq were sequenced. A total of 15.94 Gb raw data were generated in full-length transcriptome sequencing of the 3 floral developmental stages, resulting 0.11 M protein-coding transcripts. Over 457.0 million reads were obtained by RNA-seq in the 3 floral buds. Here, we openly released the full-length transcriptome database of 'High Noon' and RNA-seq database of floral development. These databases can provide a fundamental genetic information of tree peony to investigate its transcript structure, variants and evolution. Data will facilitate to deep analyses of the transcriptome for flower development.
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2016-09-01 | GSE77672 | GEO
Project description:Poplar GeneChip was employed to detect genes expressed during the whole floral developmental process, in order to improve understanding of poplar flower development, since current knowledge on flower development was mainly from model plant Arabidopsis.
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Project description:Paeonia × lemoinei 'High Noon' is one of the most important cultivars in tree peony (Paeonia sect. Moutan), a traditional horticultural plant in China, with a re-blooming characteristic which was quite different from other cultivars. So, the genetic resources in 'High Noon' were incredibly valuable in flowering-time-modified molecular breeding in tree peony. However, the molecular mechanism underlying the floral bud formation of 'High Noon' was not clear yet. To explore the molecular mechanism in this process, the transcriptomes of three stages during floral bud development were deeply analyzed in this study. As a result, a total of 5816 differentially expressed genes (DEGs) were identified between the three developmental stages, and pathways including ''DNA replication'', ''metabolic pathways'', ''circadian rhythm'', and ''plant hormone signal transduction'' were mostly enriched in the functional enrichment and expression pattern analysis. Furthermore, a total of 584 genes related to the photoperiod pathway were further identified and a novel CO homolog gene PlCO was identified to be a stable hydrophilic protein, which contained both CCT domain and B-box domain. Over-expression of PlCO in Arabidopsis resulted in early flowering, which suggested a promotion role of flowering. The PlCO protein localized in nucleus and possessed a transcription activity ability, which implied that PlCO might function as a transcription factor. The transcriptome analysis revealed pathways involved in floral bud development in tree peony and provided new insight into the regulatory network underlying the floral bud development. The gene identification in 'High Noon' provided new valuable candidate genes for flowering-time-modified molecular breeding in tree peony.
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Project description:Temperate perennial plants have to adapt their growth in order to survive over winter conditions and protect their tissues by entering into dormancy. The dormancy phenomenon is a complex process regulated by many factors, externals (photoperiod and temperature) or internals through the transport towards the buds. In order to better understand the molecular mechanisms involved in the regulation of dormancy, we conducted a transcriptomic analysis of flower buds from the late flowering sweet cherry cultivar 'Fertard' during dormancy, from October 2017 to March 2018.
2023-04-15 | GSE229429 | GEO
Project description:Poplar GeneChip was employed to detect genes expressed during the whole floral developmental process, in order to improve understanding of poplar flower development, since current knowledge on flower development was mainly from model plant Arabidopsis. Male and female floral buds of Populus tomentosa were selected at successive stages of the whole development process for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain genes contributed to floral development, but not the dynamic expression changes. To that end, equal amount of floral buds RNA per gender from different stages were mixed for the detection of expressed genes.
2011-07-01 | E-GEOD-30320 | biostudies-arrayexpress
Project description:Flower-lotus with many attractive floral characteristics has been studied and discussed the most. These characteristics are used as the standards of the classification in most cases, and always attracted the attention of lotus breeders on improvement program because of associating with ornamental and economic values of lotus. However, molecular mechanisms underlying the formation of these attractive floral features still remain largely unknown. Transcriptome sequencing technique has been established as an efficient approach for gene discovery and expression pattern identification. For some plants, a lot of important genes involved in plant critical metabolisms have been successfully identified by this technique. In the study, mass sequence data obtained from the deep sequencing of a mixed flower-bud cDNA pool from three individuals of N. nucifera provide a platform to comprehensively understand the processes of flower formation and development at the molecular level, and will greatly facilitate the genetic improvement of ornamental characteristics and the directive molecular breeding for lotus in the future. A mixed cDNA pool from young flower-buds (35-40mm in length) of three accessions of N. nucifera were used for deep sequencing using 454 GS-FLX Titanium.
2014-12-08 | E-GEOD-57601 | biostudies-arrayexpress
Project description:To facilitate the functional annotation of the pepper genome, we generated 90.84 Gb of RNA-Seq data from 33 libraries representing all major tissue types and developmental stages of Zunla 1, as well as fruits from other accessions with significant phenotypic differences. Pepper ‘Zunla 1’ and other inbred lines were grown in a greenhouse as described in Table S1, with their different developmental stages Plants at full-bloom stage were harvested for roots, stems, and leaves as the same as the samples for phased small RNAs (see text S3.4.2 for details). Mature plants were harvested for unopened flower buds (buds) and fully open flowers (flowers). Additional flowers were allowed to self-pollinate and fruit was harvested at four pre-breaker stages (1-3cm, 3-4cm, 4-5cm fruit length, and mature green), the breaker stage (when the fruit was turning red) and three post-breaker stages (3, 5, and 7 days after breaker). These samples will respectively be referred to as Root, Stem, Leaf, Bud, Flower, F-Dev-1, F-Dev-2, F-Dev-3, F-Dev-4, F-Dev-5, F-Dev-6, F-Dev-7, F-Dev-8, and F-Dev-9. Similar roots, stems, leaves, immature fruit and red fruit were harvested from other inbred lines from domesticated Capsicum species. Meanwhile, chiltepin plants were grown under long days at controlled temperature and RNA was extracted from a mix of leaves from four stages (seedling, early blooming, full bloom, and fruit breaker phases), a mix of flowers from unopened flower buds (buds) and fully open flowers (flowers), and fruit at breaker and breaker plus five days respectively. All tissues were frozen in liquid nitrogen and then stored at -80℃. Total RNA was isolated from different samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions. Strand-specific RNA-Seq library preparations were performed as previously described (39) with 12 independently bar-coded samples sequenced on one lane of an Illumina HiSeq2000 system. The 200 bp paired-end libraries were sequenced using Illumina HiSeq 2000 (90 bp PE).
2014-03-14 | E-GEOD-45037 | biostudies-arrayexpress