Abstract
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 Brassica 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 Brassica rapa , Brassica carinata , and Brassica allohexaploid, respectively. We compared 7,397 differentially expressed genes (DEGs) between Brassica hexaploid and its parents, as well as 2,545 nonadditive genes of Brassica 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 Brassica hexaploid and its paternal parent, B . rapa , were involved in the biosynthesis of secondary metabolites, plant–pathogen interactions, photosynthesis, and circadian rhythm. Among the 2,233 DEGs between Brassica hexaploid and its maternal parent, B . carinata , 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 Brassica 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 Brassica hexaploid and its parents. Our results demonstrate that the Brassica allohexaploid can generate extensive transcriptomic diversity compared with its parents. These changes may contribute to the normal growth and reproduction of allohexaploids.
Highlights
Polyploidization is an important evolutionary process in eukaryotes, and it is believed that all angiosperms underwent a whole genome duplication event during their evolution [1]
The trigenomic Brassica allohexaploid was generated by inter-specific hybridization followed with chromosome doubling, by using B. carinata as the maternal parent and B. rapa as the paternal parent in the year of 2004 [38]
70.35%, 46.20%, and 54.18% of reads uniquely matched to a genomic location in the B. rapa, B. carinata, and Brassica hexaploid libraries, while unmapped reads accounted for 23.39%, 46.37%, and 39.26%, respectively (Table 1)
Summary
Polyploidization is an important evolutionary process in eukaryotes, and it is believed that all angiosperms underwent a whole genome duplication event during their evolution [1]. The merging of genomes previously adapted to different environments allows allopolyploids to adapt to a wider range of environmental conditions [7]. Some important crops such as wheat, oat, cotton, coffee, and rapeseeds are allopolyploids [8]. Molecular studies have revealed dynamic and pervasive changes in the polyploid genome and transcriptome that vary among different allopolyploids; these include DNA sequence elimination [11,12], genome rearrangement [13,14], transposon activation [15,16], gene silencing [17], and alterations of gene expression [18,19]
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