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:Orchidaceae are renowned for their spectacular flowers as well as other reproductive and ecological adaptations. After the genome of the tropical epiphytic orchid Phalaenopsis equestris was sequenced, we combined Trinity data for de novo assembly and Illumina HiSeq1500 data for RNA-Seq analysis to characterize the transcriptomes of four different organs for a better understanding of the molecular mechanisms driving these characteristics. We present four de novo assembled transcripts reconstructed from RNA collected from the root, stem, leaf, and flower of Phalaenopsis equestris. These sets of transcripts greatly enrich the available data for Phalaenopsis equestris. Here, we present two databases, and each dataset allows for a different type of search for candidate homologues. The first dataset consists of the sets of assembled unigenes, which enable a sequence-based search. A comprehensive analysis of the assembled unigenes revealed the unigenes from root, stem, leaf, and flower with high e-values aligned versus the Nr, Swiss-Port, KEGG, COG, and GO database, respectively. This analysis enabled the production of a second database, which includes sequences correlated with annotated transcript names as well as the confidence of the best hit from BLAST.
2018-06-30 | GSE70411 | GEO
Project description:Gerbera delavayi Franch. endemic to southwest China, is a rare fiber plant. In this study, the leaves of G. delavayi were sequenced based on Illumina Hi-Seq2500. The results showed that 108694 unigenes were found. N50 was 593.90bp, and the mean length was 912bp. By comparing with Nr and Swiss-prot database, 40915 unigenes were annotated, and 67779 unigenes were unannotated. In addition, 30 unigenes had homology with Ces family, 20 unigenes had homology with Cls family, and 11 unigenes had homology with SuSy. 11369 unigenes were assigned to 25 categories with COG database, and 21378 unigenes were divided into 52 GO terms. Function annotation against KEGG database obtained 8087 unigenes and 118 pathways. 47 unigenes were found at “phenylpropanoid biosynthesis” pathway. Furthermore, 4908 unigenes contained 5179 SSRs, 1 SSR occurred every 12.46kb. The largest number of SSR type was mono-nucleotide repeat, and its frequency was 54.37%; the next was di-nucleotide repeat and tri-nucleotide repeat, with the frequencies of 22.90% and 21.70%, respectively. These results greatly enriched the genetic information of G. delavayi, and provided basic data for genetic breeding and exploitation of this unique plant resource.
2017-04-26 | GSE98179 | GEO
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of nervous system in locust Locusta migratoria manilensis. By obtaining over 57,000,000 bases of sequence from central nervous system, we generated 101836 contigs and 69440 scaffolds. We finally get 41179 unigene with an average length of 570bp. There are 5519 unigenes beyond the length of 1000bp. Using BLAST searches of the NR, NT, Swiss-Prot, KEGG and COG databases we are able to identify 13552 unigene (E<0.0001). Comprehensive assessment of all the unigenes by comparing with the studied genes of other insects nervous system reveals that our unigene are broadly representative of the transcriptome of insect nervous system. Our data provides the most large-scale EST-project for locust nervous system, which greatly benefits the exploring of this insect. In addition, we identify a large number of novel nervous genes which can be used in systematic studies of locust and other insects. Examination of 1 sample
2011-01-04 | E-GEOD-24498 | 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:We report the application of single-molecule-based sequencing technology for high-throughput profiling of nervous system in locust Locusta migratoria manilensis. By obtaining over 57,000,000 bases of sequence from central nervous system, we generated 101836 contigs and 69440 scaffolds. We finally get 41179 unigene with an average length of 570bp. There are 5519 unigenes beyond the length of 1000bp. Using BLAST searches of the NR, NT, Swiss-Prot, KEGG and COG databases we are able to identify 13552 unigene (E<0.0001). Comprehensive assessment of all the unigenes by comparing with the studied genes of other insects nervous system reveals that our unigene are broadly representative of the transcriptome of insect nervous system. Our data provides the most large-scale EST-project for locust nervous system, which greatly benefits the exploring of this insect. In addition, we identify a large number of novel nervous genes which can be used in systematic studies of locust and other insects.
2011-01-04 | GSE24498 | GEO
Project description:Transcriptomes analysis of the petals from a red-flowered white clover mutant (red flowers) and its shade-treated counterpart (white flowers) grown under shaded conditions was performed using high-throughput sequencing. We obtained 121,626,564 and 130,577,944 clean reads in red-flowered mutant and treated counterpart, respectively. Of these clean reads, we respectively gained 125,350 and 99,638 unigene sequencces in two groups. As a result, a total of 157,964 unigenes were obtained with an average length of 728 bp and a median length of 1346 bp. These findings provideed insights into the expression profiles in red-flowered white clover mutant, and deepened our understanding of flower pigmentation in white clower.
2018-12-04 | GSE101059 | GEO
Project description:RNA-Seq was conducted among sergeant bulks of four sex types of melon flowers, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aaGG), and andromonoecious (aagg), a total of about 105 million reads were generated from the melon transcriptome using Solexa sequencing.Totally 79,698 unigenes were generated and 75,537 unigenes were mapped to 11,805 annotated proteins in assembled melon genome (Garcia-Mas et al., 2012). Transcripts related to photomorphogenesis and flower development in plants were found, Most of the genes encoding plant hormone metabolism related protein, others related to flora development including Tasselseeds and male sterility genes which in phytohormones pathway were also detected. Comparison each two bulks (AAGG:AAgg, AAGG:aaGG, aagg:AAgg and aaGG:aagg ) exhibited different profiles of putative genes (include 745, 1342, 858 and 571 different expression genes, respectively). mRNA profiles of four sex types of melon flowers, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aaGG), and andromonoecious (aagg) were were generated by deep sequencing using Illumina Hiseq 2000.
2014-06-15 | E-GEOD-57580 | biostudies-arrayexpress
Project description:Here, the HPG axis transcriptomes of A. sinensis were sequenced using Illumina HiSeq 2000 and 4000 platforms. A total of 271.19 Gb filtered data from 45 samples belonging to 15 individuals (six individuals in stage I, six males and three females in stage II) were obtained, and 74.50% of 121,952 assembled unigenes were annotated to the non-redundant (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), InterPro, Gene Ontology (GO) and NT databases. Additionally, 78,770 unigenes contained complete open reading frames (ORFs). A total of 51,570 simple sequence repeats (SSRs) were detected, and the number of differentially expressed genes (DEGs) from 1,531 to 34,439 in 18 pairwise comparisons were identified for HPG samples of male and female A. sinensis in two stages. We reported the first integrated transcriptome data from HPG samples of male and female A. sinensis in stage I and II of gonadal development. These data offer valuable resources for research into reproductive regulation and the HPG axis interaction in A. sinensis and other sturgeons.
2019-05-15 | GSE126616 | GEO
Project description:Flower opening is important for successful pollination in many plant species, and some species repeat reversible flower opening and closing movements. This is thought to be due to the turgor pressure change caused by the water influx/efflux, which depends on osmotic oscillation in the cells. In some ornamental plants, it has been suggested that water channel aquaporin may play an important role in flower opening. However, the molecular mechanism(s) involved in flower movement are largely unknown. Using Gentiana flowers, which show reversible movement in response to temperature and light stimuli, as a model, we showed that reversible flower opening is regulated by aquaporin GsPIP2;2 and GsPIP2;7. In particular, phosphorylation of the C-terminal serine residue of GsPIP2;2 is important for the transport activity and correlates closely with the flower re-opening rate. Furthermore, GsPIP2;2 is phosphorylated and activated by GsCPK16, which is activated by elevated cytosolic Ca2+ levels in response to temperature and light stimuli. We propose that reversible flower opening is regulated by GsCPK16-dependent GsPIP2;2 phosphorylation and activation, with stimulus-induced calcium signals acting as triggers. CPK-dependent phosphorylation and activation of PIP2s may be one of the universal regulatory mechanisms for flower opening in plants.
2022-10-17 | PXD029169 | JPOST Repository