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Transcriptomic changes accompanying allopolyploidization are commonly paralleled in Brassica napus.

ABSTRACT: Changes to gene expression and splicing are investigated between parental species (B. oleracea and B. rapa) and three resynthesized allopolyploids, as well as a natural B. napus

ORGANISM(S): synthetic construct Brassica napus Brassica rapa Brassica oleracea

PROVIDER: GSE84451 | GEO | 2019/07/13

REPOSITORIES: GEO

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Subgenome-dominant expression and alternative splicing in response to pathogen stress in polyploid Brassica napus and progenitors

Project description:Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both natural and resynthesized lines of polyploid Brassica napus, along with the progenitors B. rapa and B. oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-seq analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12,709 DAS events) and lower in resynthesized Brassica napus (8,863 DAS events). Natural B. napus had more up-regulated events and fewer down-regulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus specifically, this resulted a disproportionate C subgenome contribution to pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in natural and resynthesized B. napus, and indicate that abiotic stress can influence the evolution of homeologous genes in polyploids.

2023-02-04 | GSE201225 | GEO

Gene expression profilling of six species of Brassica and early four generation of resynthesized B. napus (F1-F4)

Project description:Analysis of the different gene expression profiles of natural and resynthesized Brassica polyploids with Illumina deep sequencing technology could help to improve our knowledge of polyploid genome evolution. We obtained approximately 6 million sequence tags per sample,and 6018254, 5930726, 6022170, 5950123, 5991210, 5798939, 5823113, 5772449,5858527 and 5657697 clean tags were obtained in libraries of B. rapa, B. oleracea, B. napus-F1, B. napus-F2, B. napus-F3, B. napus-F4, natural B. napus, B. nigra, B. juncea and B. carinata, respectively.16574, 15970, 22059, 18155, 16479, 18196, 17448, 13867, 19424 and 16645 genes of B. rapa genome were unambigously mapped by sequence tags of these ten DGE libraries, respectively. Differentially expressed genes during polyploidization were broadly discovered by comparing the tetraploids with their progenitors. mRNA obtained from young leaves of 28-days-old seedlings were compared during polyploidization.

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Project description:Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

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