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.
Highlights
Polyploidy is an important evolutionary mechanism in flowering plants that often induces immediate extensive changes in gene expression through genomic merging and doubling
A total of 6178564 raw tags were obtained from B. rapa (Br), 6059222 from B. oleracea (Bo), 6155227 from B. napus-F1 (Bn-F1), 6092805 from B. napus-F2 (Bn-F2), 6142098 from B. napus-F3 (Bn-F3), 5938583 from B. napus-F4 (Bn-F4), and 5964594 from natural B. napus (Bn-N)
Differences in gene expression between synthesized B. napus-F1 and its progenitors Based on analysis of the leaf transcriptome data for synthesized B. napus-F1 and its progenitors, as well as the natural B. napus generated in this study, we found that the majority of the B. napus-F1 transcripts were conserved with the parental sequences
Summary
Polyploidy is an important evolutionary mechanism in flowering plants that often induces immediate extensive changes in gene expression through genomic merging and doubling. RNA-seq is a recently developed technique for transcriptome study, which could be in choice for profiling gene expression pattern in polyploids. Polyploidization is an ancient and ongoing evolutionary process that promotes plant evolution by reshaping genomes [1,2]. The majority of flowering plants have undergone polyploidization (complete or partial) and chromosome rearrangement [3]. Many studies have revealed that methylation status, gene expression profile, chromosomal rearrangements, deletions, insertions, and sequence substitutions in many allopolyploids differ to their progenitor [9,10]. Angiosperm genome plasticity in polyploids is always related to changes in gene expression, which are largely controlled by epigenetic profiles [12,13].
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