ArticleBMC genomics2013
Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 47 citations in OpenAlex.
- Transcriptome Shock in Developing Embryos of aInternational journal of molecular sciences · 2023Article
- Transcriptional Interactions of Single B-Subgenome Chromosome with C-Subgenome inPlants (Basel, Switzerland) · 2023Article
- Character changes and Transcriptomic analysis of a cassava sexual Tetraploid.BMC plant biology · 2021Article
- Adaptation Strategies to Improve the Resistance of Oilseed Crops to Heat Stress Under a Changing Climate: An Overview.Frontiers in plant science · 2021Review
- Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus.BMC genomics · 2020Article
- Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus.BMC genomics · 2018Article
- Transcriptome Analysis of Male Drosophila melanogaster Exposed to Ethylparaben Using Digital Gene Expression Profiling.Journal of insect science (Online) · 2017Article
- Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima.Molecular ecology · 2017Article
- A comparative study of the seed structure between resynthesized allotetraploid and their diploid parents.Protoplasma · 2017Article
- Transcriptomic basis for drought-resistance in Brassica napus L.Scientific reports · 2017Article
- Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Genome-Wide Gene/Genome Dosage Imbalance Regulates Gene Expressions in SyntheticFrontiers in plant science · 2016Article
- Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.BMC plant biology · 2015Article
- Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq.Frontiers in plant science · 2015Article
- Integrative Analysis of mRNA and miRNA Expression Profiles of the Tuberous Root Development at Seedling Stages in Turnips.PloS one · 2015Article
- Transcriptome analysis of canola (Brassica napus) under salt stress at the germination stage.PloS one · 2015Article
- An RNA-seq transcriptome analysis of floral buds of an interspecific Brassica hybrid between B. carinata and B. napus.Plant reproduction · 2014Article
- The legacy of diploid progenitors in allopolyploid gene expression patterns.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2014Review
- Characterization and expression patterns of small RNAs in synthesized Brassica hexaploids.Plant molecular biology · 2014Article
- Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid.International journal of molecular sciences · 2014Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPolyploidy is an important evolutionary mechanism in flowering plants that often induces immediate extensive changes in gene expression through genomic merging and doubling. Brassica napus L. is one of the most economically important polyploid oil crops and has been broadly studied as an example of polyploid crop. RNA-seq is a recently developed technique for transcriptome study, which could be in choice for profiling gene expression pattern in polyploids.
resultsWe examined the global gene expression patterns of the first four generations of resynthesized B. napus (F1-F4), its diploid progenitors B. rapa and B. oleracea, and natural B. napus using digital gene expression analysis. Almost 42 million clean tags were generated using Illumina technology to produce the expression data for 25959 genes, which account for 63% of the annotated B. rapa genome. More than 56% of the genes were transcribed from both strands, which indicate the importance of RNA-mediated gene regulation in polyploidization. Tag mapping of the B. rapa genome generated 19023, 18547, 24383, 20659, 18881, 20692, and 19955 annotated genes for the B. rapa, B. oleracea, F1-F4 of synthesized B. napus, and natural B. napus libraries, respectively. The unambiguous tag-mapped genes in the libraries were functionally categorized via gene ontological analysis. Thousands of differentially expressed genes (DEGs) were identified and revealed the substantial changes in F1-F4. Among the 20 most DEGs are DNA binding/transcription factor, cyclin-dependent protein kinase, epoxycarotenoid dioxygenase, and glycine-rich protein. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs suggested approximately 120 biological pathways.
conclusionsThe systematic deep sequencing analysis provided a comprehensive understanding of the transcriptome complexity of early generations of synthesized B. napus. This information broadens our understanding of the mechanisms of B. napus polyploidization and contributes to molecular and genetic research by enriching the Brassica database.
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