|
| Status |
Public on Jan 24, 2017 |
| Title |
De novo Assembly and Comparative Analysis of Ten Petal Transcriptome (Brassicaceae) Revealed Phylogenetic Relationships and Genetic control of Flower Color Variation |
| Organisms |
Brassica oleracea; Matthiola incana; Raphanus sativus; Eruca vesicaria subsp. sativa; Erysimum cheiri; Orychophragmus violaceus; Iberis amara; Lobularia maritima; Malcolmia maritima; Aubrieta x cultorum |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Petal is not only the target of selection by horticulturalists to enhance the ornamental value of plants but also emerged as a unique model system for plant organogenesis studies. It is known that three major groups of pigments, betalains, carotenoids and anthocyanins, are responsible for the attractive natural display of flower colors. While carotenoids and betalains generally yield yellow or red colors, anthocyanins confer a diverse range of color from orange to red to violet and blue. In this study, we collected 11 species (Erysimum cheiri, Malcolmia maritime, Brassica oleracea, Raphanus sativus, Orychophragmus violaceus, Eruca sativa, Orychophragmus violaceus, Iberis amara, Aubrieta x cultorum, Lobularia maritime, Matthiola incana) belong to different tribe in Brassicaceae family with varied flower color and performed petal transcriptome analysis. de novo transcriptome assembly showed that average length of the contigs varied from 631bp in O. violaceus to 1212bp in Matthiola incana which indicated that the complexity of the genomes are different much. Protein homology between these species and those sequenced species in Brassicaceae family are consistent with the known phylogenetic relationships. However, O. violaceus has closer relationships with Sisymbrium irio than expected Brassica species. Clustering analysis of genes in anthocyanin and carotenoids synthesis pathway indicated that while silence or low expression of CCD4 (Carotenoid Cleavage Dioxygenase 4) leading to the yellow color formation in different species, purple or red color variation might result from different genes expression variation. These results not only provide transcriptome data for petal development study but also provide useful information for Brassica flower improvement for ornamental purpose.
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| |
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| Overall design |
22 samples were used here, each with two biological replicates. Gene expression value was calculated using the Arabidopsis as reference.
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| Contributor(s) |
Chen D, Pan Q, Li Z, Ge X |
| Citation missing |
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| |
| Submission date |
Jan 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chen Daozong |
| E-mail(s) |
chendaozong1030@126.com
|
| Organization name |
Huazhong agricultural university
|
| Street address |
Shizishan Street ยท Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
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| Platforms (10)
|
| GPL16360 |
Illumina HiSeq 2000 (Brassica oleracea) |
| GPL22620 |
Illumina HiSeq 2000 (Raphanus sativus) |
| GPL22878 |
Illumina HiSeq 2000 (Orychophragmus violaceus) |
| GPL22956 |
Illumina HiSeq 2000 (Erysimum cheiri) |
| GPL22957 |
Illumina HiSeq 2000 (Eruca vesicaria subsp. sativa) |
| GPL22958 |
Illumina HiSeq 2000 (Iberis amara) |
| GPL22959 |
Illumina HiSeq 2000 (Lobularia maritima) |
| GPL22960 |
Illumina HiSeq 2000 (Malcolmia maritima) |
| GPL22961 |
Illumina HiSeq 2000 (Matthiola incana) |
| GPL22976 |
Illumina HiSeq 2000 (Aubrieta x cultorum) |
|
| Samples (44)
|
|
| Relations |
| BioProject |
PRJNA362874 |
| SRA |
SRP097616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE93879_Aubrieta_cultorum.genes.fpkm_tracking.xls.gz |
129.4 Kb |
(ftp)(http) |
XLS |
| GSE93879_Brassica_oleracea.genes.fpkm_tracking.xls.gz |
147.1 Kb |
(ftp)(http) |
XLS |
| GSE93879_Eruca_sativa.genes.fpkm_tracking.xls.gz |
150.9 Kb |
(ftp)(http) |
XLS |
| GSE93879_Erysimum_cheiri.genes.fpkm_table.xls.gz |
508.3 Kb |
(ftp)(http) |
XLS |
| GSE93879_Iberis_amara.genes.fpkm_table.xls.gz |
220.4 Kb |
(ftp)(http) |
XLS |
| GSE93879_Lobularia_maritima.genes.fpkm_table.xls.gz |
192.7 Kb |
(ftp)(http) |
XLS |
| GSE93879_Malcolmia_maritima.genes.fpkm_table.xls.gz |
323.0 Kb |
(ftp)(http) |
XLS |
| GSE93879_Matthiola_incana.genes.fpkm_table.xls.gz |
374.1 Kb |
(ftp)(http) |
XLS |
| GSE93879_Orychophragmus_violaceus.genes.fpkm_table.xls.gz |
254.6 Kb |
(ftp)(http) |
XLS |
| GSE93879_Raphanus_sativus.genes.fpkm_table.xls.gz |
260.6 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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