Differentially expressed genes detected between <i>Brassica</i> hexaploid and its parents.

<p>The number of up-regulated and down-regulated genes between <i>Brassica</i> hexaploid (C) and <i>B</i><i>. rapa</i> (A), <i>Brassica</i> hexaploid (C) and <i>B</i><i>. carinata</i> (B) are revealed.</p

Venn diagram showing genes expressed in <i>Brassica</i> hexaploid and its parents.

<p>A, <i>B</i><i>. rapa</i>; B, <i>B</i><i>. carinata</i>; C, <i>Brassica</i> hexaploid.</p

Hierarchical clustering analysis of 7397 DEGs based on log ratio RPKM data.

<p>A, <i>B</i><i>. rapa</i>; B, <i>B</i><i>. carinata</i>; C, <i>Brassica</i> hexaploid. The column represents individual experiment, and row represents individual gene. Genes up-regulated is represented by red, and genes down-regulated is represented by green.</p

Tracing the Transcriptomic Changes in Synthetic Trigenomic allohexaploids of <i>Brassica</i> Using an RNA-Seq Approach

<div><p>Polyploidization has played an important role in plant evolution and speciation, and newly formed allopolyploids have experienced rapid transcriptomic changes. Here, we compared the transcriptomic differences between a synthetic <i>Brassica</i> allohexaploid and its parents using a high-throughput RNA-Seq method. A total of 35,644,409 sequence reads were generated, and 32,642 genes were aligned from the data. Totals of 29,260, 29,060, and 29,697 genes were identified in <i>Brassica</i><i>rapa</i>, <i>Brassica</i><i>carinata</i>, and <i>Brassica</i> allohexaploid, respectively. We compared 7,397 differentially expressed genes (DEGs) between <i>Brassica</i> hexaploid and its parents, as well as 2,545 nonadditive genes of <i>Brassica</i> hexaploid. We hypothesized that the higher ploidy level as well as secondary polyploidy might have influenced these changes. The majority of the 3,184 DEGs between <i>Brassica</i> hexaploid and its paternal parent, <i>B</i><i>. rapa</i>, were involved in the biosynthesis of secondary metabolites, plant–pathogen interactions, photosynthesis, and circadian rhythm. Among the 2,233 DEGs between <i>Brassica</i> hexaploid and its maternal parent, <i>B</i><i>. carinata</i>, several played roles in plant–pathogen interactions, plant hormone signal transduction, ribosomes, limonene and pinene degradation, photosynthesis, and biosynthesis of secondary metabolites. There were more significant differences in gene expression between the allohexaploid and its paternal parent than between it and its maternal parent, possibly partly because of cytoplasmic and maternal effects. Specific functional categories were enriched among the 2,545 nonadditive genes of <i>Brassica</i> hexaploid compared with the additive genes; the categories included response to stimulus, immune system process, cellular process, metabolic process, rhythmic process, and pigmentation. Many transcription factor genes, methyltransferases, and methylation genes showed differential expression between <i>Brassica</i> hexaploid and its parents. Our results demonstrate that the <i>Brassica</i> allohexaploid can generate extensive transcriptomic diversity compared with its parents. These changes may contribute to the normal growth and reproduction of allohexaploids.</p> </div

Functional annotation of DEGs between <i>Brassica</i> hexaploid and its parents based on GO terms.

<p>DEGs between <i>Brassica</i> hexaploid (C)-<i>B</i><i>. rapa</i> (A) and <i>Brassica</i> hexaploid (C)-<i>B</i><i>. carinata</i> (B) are grouped to the secondary classification of GO terms. There are 8, 9, and 20 functional groups in the three main categories (molecular function, cellular component, and biological process) of GO classification, respectively.</p

Functional annotation of nonadditive genes and additive genes in <i>Brassica</i> hexaploid based on GO terms.

<p>Nonadditive genes and additive genes are grouped to the secondary classification of GO terms. There are 12, 9, and 23 functional groups in the three main categories (molecular function, cellular component, and biological process) of GO classification, respectively.</p

The different read coverage of genes in three libraries.

<p>The genes with different read coverage were indicated by different colours. The capital letters A, B, and C in brackets refer to libraries of <i>B</i><i>. rapa</i>, <i>B</i><i>. carinata</i>, and <i>Brassica</i> hexaploid respectively.</p

Gene ontology (GO) annotations of all detected genes.

<p>The histogram shows the result of classifying 24658 genes to the secondary classification of GO terms. The y-axis indicates the number of genes in a functional term.</p

The saturation analysis of genes detected by sequencing reads.

<p>The gene saturation analysis are taken in the libraries of <i>B</i><i>. rapa</i> (A), <i>B</i><i>. carinata</i> (B), and <i>Brassica</i> hexaploid (C) respectively. The curve indicated that the number of detected genes almost ceases to increase when the number of reads reaches 2 million.</p

Four clusters of gene expression pattern.

<p>A, <i>B</i><i>. rapa</i>; B, <i>B</i><i>. carinata</i>; C, <i>Brassica</i> hexaploid. The four clusters of gene expression pattern were grouped by up or down regulation in <i>Brassica</i> hexaploid compared to its parents.</p