Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes.
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes. Four-condition experiment, comparison of transcription profiles of the genomes. Four biological replicates were used, independently grown and harvested. One replicate per array.
Project description:We present an atlas of global gene expression covering embryo and seed coat development in B. rapa, B. nigra, B. oleracea, B. juncea, B. napus and B. carinata, providing insights into the evolution of gene expression in embryogenesis and seed development of brassica species.
Project description:we deep-sequenced two small RNA libraries made from V. longisporum infected/non-infected roots and employed Brassica rapa and Brassica oleracea genomes as reference for miRNA prediction and characterization as well. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to AA and CC genomes, respectively. Among them, 62 miRNAs were responsive to the V. longisporum infection.
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.
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.
Project description:we deep-sequenced two small RNA libraries made from V. longisporum infected/non-infected roots and employed Brassica rapa and Brassica oleracea genomes as reference for miRNA prediction and characterization as well. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to AA and CC genomes, respectively. Among them, 62 miRNAs were responsive to the V. longisporum infection. two small RNA libraries constructed from V. longsiporum infected and non-infected roots after 6 days were sequenced by Illumina’s Solexa sequencing technology (BGI, China)
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.
Project description: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
