Transcriptome Sequencing and Assembly of Canna indica Flower
Ontology highlight
ABSTRACT:
ORGANISM(S): Canna indica
PROVIDER: GSE72440 | GEO | 2016/09/01
SECONDARY ACCESSION(S): PRJNA294514
REPOSITORIES: GEO
Similar Datasets
Project description:Canna indica L. is an ornamental plant with petaloid staminodes and only a half fertile stamen in its flowers. The genetic basis for petaloid androecium remains unclear. In order to get comprehensive transcriptome data for further studies, RNA-Seq analysis were carried out. Two libraries from flower primordia and differentiated flowers of Canna indica were constructed and sequenced respectively, and totally 118,869 unigenes were assembled. The unigenes were aligned to the protein databases NR, NT, Swiss-Prot, KEGG, COG and GO (e-value<0.00001), and totally 67,299 unigenes were annotated. Our data constitute a preliminary basis for further studies on flower development of Canna indica. The two samples from flower primordium and differentiated flower were sequenced for transcriptome assembly, and gene expression information of the two stages was also obtained from these data.
2016-09-01 | E-GEOD-72440 | biostudies-arrayexpress
Project description:Stamen development is an important developmental process that directly affects the yield of Prunus sibirica. In this study, the male sterile flower buds and male fertile flower buds of Prunus sibirica were used as materials to performed RNA-Seq analyses to compare transcription differences. The results would provide a theoretical basis for further investigation of the formation mechanism of male sterile flower.
2021-08-30 | GSE167937 | GEO
Project description:Exceptionally andromonoecious individuals that flowers appeared to form that structure resembling a carpel attached to the reverse side of stamen cup were detected in strictly dioecious poplar. Andromonoecious poplarswere used to analyze transcript levels accurately. We used microarrays to detail the global programme of gene expression during flower development and identified distinct classes of different-regulated genes between sexes during this process.
2013-07-30 | E-GEOD-38432 | biostudies-arrayexpress
Project description:In Canna indica L, 3-4 (occasionally 5) petaloid staminodes and a one-theca stamen with a petaloid appendage constitute the androecium. In order to find out the genetic basis of petaloid development of androecium members, RNA-Seq analysis of petal (P), petaloid staminode (PS), anther (A) and petaloid appendage (PA) were carried out.
2016-09-01 | GSE72441 | GEO
Project description:In Canna indica L, 3-4 (occasionally 5) petaloid staminodes and a one-theca stamen with a petaloid appendage constitute the androecium. In order to find out the genetic basis of petaloid development of androecium members, RNA-Seq analysis of petal (P), petaloid staminode (PS), anther (A) and petaloid appendage (PA) were carried out. P-PS comparison was carried out to find the differences between the two kinds of petal-like organ, and A-PA comparison was conducted to reveal the mechanism for the differentiation of these two parts within stamen.
2016-09-01 | E-GEOD-72441 | biostudies-arrayexpress
Project description:The production of heather (Calluna vulgaris) in Germany is highly dependent on cultivars with mutated flower morphology, the so-called diplocalyx bud bloomers. So far, this unique flower type of C. vulgaris has not been reported in any other plant species. The flowers are characterised by an extremely extended flower attractiveness, since the flower buds remain closed throughout the complete flowering season. The flowers of C. vulgaris bud bloomers are male sterile, because the stamens are missing. Furthermore, petals are converted into sepals. Therefore the diplocalyx bud bloomer flowers consist of two whorls of sepals directly followed by the gynoecium. A broad comparison of wild type and bud bloomer’s flowers was undertaken to identify genes differentially expressed in the bud flowering phenotype and in the wild type of C. vulgaris. Transcriptome sequence reads were generated using next generation 454 sequencing of two flower type specific cDNA libraries. In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated. Transcript abundances in wild type and bud bloomer’s libraries were compared and 365 differentially expressed genes detected. Among these differentially genes, CvPI was identified which is the orthologue of the Arabidopsis B gene PISTILLATA (PI) and considered as the most promising candidate gene. Quantitative PCR was performed to analyse the gene expression levels of two C. vulgaris B genes CvPI and CvAP3 in both flower types. CvAP3 which is the orthologue of the Arabidopsis B gene APETALA (AP3) turned out to be ectopically expressed in sepals of wild type and bud bloomer flowers. CvPI expression was proven to be reduced in the flowers of bud blooming cultivars. Differential expression patterns of the B-class genes CvAP3 and CvPI were identified to cause characteristics of flower morphology in C. vulgaris wild type and bud blooming flowers leading to the following hypotheses: ectopic expression of CvAP3 is a convincing explanation for the formation of a completely petaloid perianth in the wild type and the “bud flowering” phenotype. In C. vulgaris, CvPI is essential for determination of petal and stamen identity. The characteristic transition of petals into sepals potentially depends on the observed deficiency of CvPI and CvAP3 expression in bud blooming flowers. However, the complete loss of stamens in bud blooming flowers remains to be explained.
2015-01-26 | GSE60105 | GEO
Project description:Flower maturation consists of several events that contribute to reproductive success as flowers open, including petal expansion, stamen filament elongation, pollen release, nectary maturation, stigma growth, and gynoecium maturation to support pollen tube growth. The Arabidopsis transcription factors ARF6 (Auxin Response Factor 6) and ARF8 regulate all of these processes, in part by activating jasmonate biosynthesis. Jasmonates in turn activate genes encoding the transcription factors MYB21 and MYB24, which mediate a subset of the processes controlled by ARF6 and ARF8. This experiment was designed to characterize gene expression in flowers before and after they open, and to determine how arf6 arf8 and myb21 myb24 mutation combinations affect these gene expression patterns.
2011-12-10 | GSE32193 | GEO
Project description:The production of heather (Calluna vulgaris) in Germany is highly dependent on cultivars with mutated flower morphology, the so-called diplocalyx bud bloomers. So far, this unique flower type of C. vulgaris has not been reported in any other plant species. The flowers are characterised by an extremely extended flower attractiveness, since the flower buds remain closed throughout the complete flowering season. The flowers of C. vulgaris bud bloomers are male sterile, because the stamens are missing. Furthermore, petals are converted into sepals. Therefore the diplocalyx bud bloomer flowers consist of two whorls of sepals directly followed by the gynoecium. A broad comparison of wild type and bud bloomer’s flowers was undertaken to identify genes differentially expressed in the bud flowering phenotype and in the wild type of C. vulgaris. Transcriptome sequence reads were generated using next generation 454 sequencing of two flower type specific cDNA libraries. In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated. Transcript abundances in wild type and bud bloomer’s libraries were compared and 365 differentially expressed genes detected. Among these differentially genes, CvPI was identified which is the orthologue of the Arabidopsis B gene PISTILLATA (PI) and considered as the most promising candidate gene. Quantitative PCR was performed to analyse the gene expression levels of two C. vulgaris B genes CvPI and CvAP3 in both flower types. CvAP3 which is the orthologue of the Arabidopsis B gene APETALA (AP3) turned out to be ectopically expressed in sepals of wild type and bud bloomer flowers. CvPI expression was proven to be reduced in the flowers of bud blooming cultivars. Differential expression patterns of the B-class genes CvAP3 and CvPI were identified to cause characteristics of flower morphology in C. vulgaris wild type and bud blooming flowers leading to the following hypotheses: ectopic expression of CvAP3 is a convincing explanation for the formation of a completely petaloid perianth in the wild type and the “bud flowering” phenotype. In C. vulgaris, CvPI is essential for determination of petal and stamen identity. The characteristic transition of petals into sepals potentially depends on the observed deficiency of CvPI and CvAP3 expression in bud blooming flowers. However, the complete loss of stamens in bud blooming flowers remains to be explained. two samples were analysed, each representing a flower type
2015-01-26 | E-GEOD-60105 | biostudies-arrayexpress
Project description:Purpose: this study provided a comprehensive sequence for a systemic view of the transcriptome between mango leaf and fruit, as well as fruit allergens, which will be useful for further genomic research studies and breeding of lower allergenic mango cultivars. Methods:Some allergens have previously been identified in mango (Mangifera indica Linn), including profilins, Bet v 1-like proteins and chitinase. In this paper, 66 potential allergen genes were identified and their relative expressions evaluated in mango fruit and leaf using Illumina RNA-Seq technology. Results:A total of 17.63Gb Clean Data was obtained.The number of %≥Q30 was above 94.58%.RNA-Seq generated 11,751,123 contigs that were assembled into 99,328 unigenes with 16,848 unigenes of >1000 bp. A total of 230,242 unigenes were annotated using public protein databases, with a cut-off E-value above 10−5, of which 27,295, 46,030, 24,227 and 14,023 unigenes were assigned to gene ontology terms, Nr, Swiss-Prot and clusters of orthologous groups, respectively. Allergens mainly belonged to pollen allergen, pathogenesis-related protein Bet v I family and NADPH-dependent FMN reductase.
2020-12-01 | GSE142427 | GEO
Project description:Flower maturation consists of several events that contribute to reproductive success as flowers open, including petal expansion, stamen filament elongation, pollen release, nectary maturation, stigma growth, and gynoecium maturation to support pollen tube growth. The Arabidopsis transcription factors ARF6 (Auxin Response Factor 6) and ARF8 regulate all of these processes, in part by activating jasmonate biosynthesis. Jasmonates in turn activate genes encoding the transcription factors MYB21 and MYB24, which mediate a subset of the processes controlled by ARF6 and ARF8. This experiment was designed to characterize gene expression in flowers before and after they open, and to determine how arf6 arf8 and myb21 myb24 mutation combinations affect these gene expression patterns. Three biological replicates were prepared at each of two developmental stages, stage 12 (oldest closed buds) and stage 13 (youngest open flowers), for three genotypes (Wild type, arf6-2 arf8-3, and myb21-5 myb24-5). For the mutant genotypes, stage 13 flowers do not actually open, so corresponding flowers of equivalent age were chosen based on the position of open flowers in wild-type inflorescences.
2011-12-10 | E-GEOD-32193 | biostudies-arrayexpress