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高钙胁迫下拟南芥钙代谢相关基因家族的全基因组鉴定、特征分析及其调控

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in and Their Regulation by Under High Calcium Stress.

作者信息

Gong Jiyi, Shi Tianlong, Li Yuke, Wang Hancheng, Li Fei

机构信息

The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China.

Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China.

出版信息

Front Plant Sci. 2021 Aug 11;12:707496. doi: 10.3389/fpls.2021.707496. eCollection 2021.

DOI:10.3389/fpls.2021.707496
PMID:34456948
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8387222/
Abstract

Several gene families involved in calcium signaling have been detected in plants, including calmodulin (CaM), calcium dependent protein kinases (CDPK), calcineurin B-like (CBL) and cyclic nucleotide-gated channels (CNGCs). In our previous study, we demonstrated that LZ04 ( LZ04) regulate genes involved in calcium stress in (). Here, we aimed to explore the potential involvement of calcium-related gene families in the response of to calcium stress and the potential regulatory effects of LZ04 on these genes. The structure, duplication, synteny, and expression profiles of 102 genes in calcium-related gene families in were investigated. Hidden Markov Models (HMMs) and BLASTP were used to predict candidate genes and conserved domains of the candidate genes were confirmed in SMART and NCBI CDD databases. Gene duplications and synteny were uncovered by BLASTP and phylogenetic analysis. The transcriptome expression profiles of candidate genes were investigated by strand-specific sequencing. Cluster analysis was used to find the expression profiles of calcium-related genes families under different treatment conditions. A total of 102 genes in calcium-related gene families were detected in genome, including 34 CDPK genes, 20 CNGC genes, 18 CIPK genes, 22 IQD genes, and 10 CBP genes. Additionally, of the 102 genes, 33 duplications (32.35%) and 26 gene pairs including 48 genes (47.06%) were detected. Treatment with LZ04 enhanced the resistance of under high calcium stress by regulating some of the genes in the calcium-related gene families. Functional enrichment analysis revealed that the genes clustered in the 42nd expression profile which may be -responsive genes under calcium stress were enriched in protein phosphorylation and protein modification process. Transcriptome data was validated by RT-PCR and the results generally corroborated the transcriptome sequencing results. These results may be useful for agricultural improvement in high calcium stress regions.

摘要

在植物中已检测到几个参与钙信号传导的基因家族，包括钙调蛋白（CaM）、钙依赖蛋白激酶（CDPK）、类钙调神经磷酸酶B（CBL）和环核苷酸门控通道（CNGC）。在我们之前的研究中，我们证明了LZ04调控参与钙胁迫的基因。在此，我们旨在探讨钙相关基因家族在[具体植物名称]对钙胁迫的响应中的潜在作用以及LZ04对这些基因的潜在调控作用。研究了[具体植物名称]中钙相关基因家族102个基因的结构、复制、共线性和表达谱。利用隐马尔可夫模型（HMM）和BLASTP预测候选基因，并在SMART和NCBI CDD数据库中确认候选基因的保守结构域。通过BLASTP和系统发育分析揭示基因复制和共线性。通过链特异性测序研究候选基因的转录组表达谱。聚类分析用于发现不同处理条件下钙相关基因家族的表达谱。在[具体植物名称]基因组中总共检测到102个钙相关基因家族的基因，包括34个CDPK基因、20个CNGC基因、18个CIPK基因、22个IQD基因和10个CBP基因。此外，在这102个基因中，检测到33个重复基因（32.35%）和26个基因对，包括48个基因（47.06%）。用LZ04处理通过调控钙相关基因家族中的一些基因增强了[具体植物名称]在高钙胁迫下的抗性。功能富集分析表明，聚集在第42个表达谱中的基因可能是钙胁迫下的[具体植物名称]响应基因，这些基因在蛋白质磷酸化和蛋白质修饰过程中富集。通过RT-PCR验证转录组数据，结果总体上证实了转录组测序结果。这些结果可能有助于高钙胁迫地区的农业改良。

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