Tracing the transcriptomic changes in synthetic Trigenomic allohexaploids of Brassica using an RNA-Seq approach.
Tracing the transcriptomic changes in synthetic Trigenomic allohexaploids of Brassica using an RNA-Seq approach.
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使用 RNA-Seq 方法追踪芸苔属合成三基因组异源六倍体的转录组变化
DOI：
10.1371/journal.pone.0068883
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Wang J
中科院分区：
文献类型：
--
作者：
Zhao Q;Zou J;Meng J;Mei S;Wang J
多倍体在植物进化和物种形成过程中起着重要的作用，新形成的异源多倍体在转录组学上发生了快速的变化。在这里，我们使用高通量RNA-Seq方法比较了合成的芸苔异源六倍体与其亲本之间的转录组差异。共生成35,644,409个序列reads，并从数据中对齐了32,642个基因。在rapa、carinata和allo六倍体芸苔中分别鉴定出29,260、29,060和29,697个基因。本研究比较了芸苔六倍体与亲本之间的7397个差异表达基因和2545个非加性基因。我们推测较高的倍性水平和继发性多倍体可能影响了这些变化。六倍体芸芥与其父本B。Rapa，参与了次生代谢物的生物合成，植物与病原体的相互作用，光合作用和昼夜节律。在芸苔六倍体与母本之间的2233个基因序列中，B。在植物与病原体的相互作用、植物激素信号转导、核糖体、柠檬烯和蒎烯降解、光合作用和次生代谢产物的生物合成等方面发挥着重要作用。异源六倍体与父本之间的基因表达差异比与母本之间的差异更显著，可能部分是由于细胞质和母本的影响。与加性基因相比，芸苔六倍体的2545个非加性基因具有丰富的特定功能类别；分类包括对刺激的反应、免疫系统过程、细胞过程、代谢过程、节律过程和色素沉着。许多转录因子基因、甲基转移酶和甲基化基因在芸苔六倍体和亲本之间存在差异表达。我们的研究结果表明，与亲本相比，芸苔同种六倍体可以产生广泛的转录组多样性。这些变化可能有助于同种六倍体的正常生长和繁殖。
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.
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