Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.
Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.
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DOI：
10.1186/s12864-019-6080-8
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发表时间：
2019-10-24
期刊：
影响因子：
4.4
通讯作者：
Lu, Yun-Hai
中科院分区：
文献类型：
--
作者：
Alam, Intikhab;Liu, Cui-Cui;Lu, Yun-Hai
背景植物同源结构域指蛋白广泛存在于真核生物中，在染色质重塑和转录调控中发挥重要作用。PHD指可以特异性结合许多组蛋白修饰作为“表观基因组阅读器”，并介导潜在基因的激活或抑制。许多PHD指基因已在动物中被表征，但迄今为止对植物PHD指基因进行的研究很少。芜菁（Brassica rapa，AA，2n = 20）是一种重要的经济作物、油料作物和饲料作物，与拟南芥（Arabidopsis thaliana）亲缘关系近，是研究芸苔属植物重要基因家族功能和进化的理想模式作物。结果从当前版本的B中共鉴定出145个含有233个PHD结构域的PHD指蛋白。拉帕基因组数据库。基因本体分析表明，67.7%的基因定位于细胞核，91.3%的基因参与蛋白结合活性。系统发育，基因结构，和额外的域分析聚类成不同的组和亚组，反映了他们在植物生长和发育过程中的不同功能的角色。染色体定位分析表明，它们在10个B上分布不均匀。芜菁染色体从RNA-Seq数据的表达分析表明，其中55.7%的成员在所有测试的组织或器官中组成型表达，具有相对较高的表达水平，反映了它们在植物生长和发育中的重要管家作用，而其他几个成员被鉴定为在特定组织或器官中优先表达。18个B亚群的表达分析。在干旱和盐胁迫条件下，所有供试成员对这两种非生物胁迫都有响应。结论PHD指基因在植物生长发育过程中发挥着重要作用，可作为芸苔属作物抗逆基因工程和改良的候选基因。本研究为进一步研究芸苔属植物PHD指基因的功能奠定了基础。
Background Plant homeodomain (PHD) finger proteins are widely present in all eukaryotes and play important roles in chromatin remodeling and transcriptional regulation. The PHD finger can specifically bind a number of histone modifications as an "epigenome reader", and mediate the activation or repression of underlying genes. Many PHD finger genes have been characterized in animals, but only few studies were conducted on plant PHD finger genes to this day. Brassica rapa (AA, 2n = 20) is an economically important vegetal, oilseed and fodder crop, and also a good model crop for functional and evolutionary studies of important gene families among Brassica species due to its close relationship to Arabidopsis thaliana. Results We identified a total of 145 putative PHD finger proteins containing 233 PHD domains from the current version of B. rapa genome database. Gene ontology analysis showed that 67.7% of them were predicted to be located in nucleus, and 91.3% were predicted to be involved in protein binding activity. Phylogenetic, gene structure, and additional domain analyses clustered them into different groups and subgroups, reflecting their diverse functional roles during plant growth and development. Chromosomal location analysis showed that they were unevenly distributed on the 10 B. rapa chromosomes. Expression analysis from RNA-Seq data showed that 55.7% of them were constitutively expressed in all the tested tissues or organs with relatively higher expression levels reflecting their important housekeeping roles in plant growth and development, while several other members were identified as preferentially expressed in specific tissues or organs. Expression analysis of a subset of 18 B. rapa PHD finger genes under drought and salt stresses showed that all these tested members were responsive to the two abiotic stress treatments. Conclusions Our results reveal that the PHD finger genes play diverse roles in plant growth and development, and can serve as a source of candidate genes for genetic engineering and improvement of Brassica crops against abiotic stresses. This study provides valuable information and lays the foundation for further functional determination of PHD finger genes across the Brassica species.