Genome-wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN-in Physcomitrella patens and stress responses
Genome-wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN-in Physcomitrella patens and stress responses
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小立碗藓横向器官边界域的全基因组分析和应激反应
DOI：
10.1007/s13258-020-00931-x
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发表时间：
2020-04-11
期刊：
影响因子：
2.1
通讯作者：
Yi, Yin
中科院分区：
文献类型：
--
作者：
Huang, Xiaolong;Yan, Huiqing;Yi, Yin
背景：LBDs作为植物特有的基因家族，在侧生器官发育、植物再生以及非生物胁迫和病原体反应中发挥着重要作用。然而，Pyscomitrella patens的LBD基因数量和特征仍不清楚。目的：鉴定苔藓中的LBD家族基因，并确定LBD在非生物和病原体胁迫下的表达谱。方法：从Ensembl植物数据库下载Pyscomitrella patens的全基因组序列和转录组。保守 LOB 结构域的基于隐马尔可夫模型的配置文件作为查询提交，以使用 HMMER 软件识别所有潜在的 LOB 结构域序列。基于GEO公共数据库和qRT-PCR分析获得了PpLBDs的表达谱。结果：本研究在P. patens基因组中总共鉴定了31个LBDs，根据亮氨酸拉链样卷曲螺旋基序的存在将其分为两类。获得了来自 P. patens 的 31 个蛋白质和来自拟南芥基因组的 43 个蛋白质之间的系统发育关系，为了解它们的保守功能和潜在功能提供了见解。此外，还分析了每个 PpLBD 的外显子-内含子组织。所有 PpLBD 均含有保守的 DNA 结合基序（CX2CX6CX3C 锌指样基序），并预测位于细胞核中。根据物理位置，31 个 PpLBD 基因被不均匀地分配到 27 条染色体中的 18 条。在这些基因中，PpLBD27不仅在干燥条件下表达量最高，而且通过茉莉酸介导的信号通路成为病原体的易感基因。大多数 PpLBD 在甘露醇处理后上调。这些结果表明，它们在早期陆地殖民者的环境刺激中受到差异性诱导，并且具有潜在的功能。结论：尽管小叶松和开花植物的生命周期存在显着差异，但它们参与LBD调节的非生物和生物胁迫的功能已被鉴定，并且在两个谱系中似乎是保守的。这些结果提供了对 PpLBD 的全面分析，并为旨在更好地理解 PpLBD 的研究奠定了基础。
Background:LBDs, as the plant-specific gene family, play essential roles in lateral organ development, plant regeneration, as well as abiotic stress and pathogen response. However, the number and characteristic of LBD genes in Pyscomitrella patens were still obscure.Objective:This study was performed to identify the LBD family gene in moss and to determine the expression profiles of LBDs under the abiotic and pathogen stress.Methods:Complete genome sequences and transcriptomes of P. patens were downloaded from the Ensembl plant database. The hidden Markov model-based profile of the conserved LOB domain was submitted as a query to identify all potential LOB domain sequences with HMMER software. Expression profiles of PpLBDs were obtained based on the GEO public database and qRT-PCR analysis.Results:In this study, a total of 31 LBDs were identified in the P. patens genome, divided into two classes based on the presence of the leucine zipper-like coiled-coil motif. A phylogenetic relationship was obtained between 31 proteins from P. patens and 43 proteins from the Arabidopsis thaliana genome, providing insights into their conserved and potential functions. Furthermore, the exon-intron organization of each PpLBD were analyzed. All PpLBD contain the conserved DNA binding motif (CX2CX6CX3C zinc finger-like motif), and were predicted to be located in cell nuclear. The 31 PpLBD genes were unevenly assigned to 18 out of 27 chromosomes based on the physical positions. Among these genes, PpLBD27 was not only remarkably highest expressed in desiccation, but also a susceptible gene to pathogens through jasmonic acid-mediated signaling pathway. Most of PpLBDs were up-regulated with the treatment of mannitol. These results showed they were differentially induced and their potential functions in the environmental stimulus of the early terrestrial colonizers.Conclusion:Despite significant differences in the life cycle in P. patens and flowering plants, their functions involved in abiotic and biotic stress-regulated by LBDs have been identified and appear to be conserved in the two lineages. These results provided a comprehensive analysis of PpLBDs and paved insights into studies aimed at a better understanding of PpLBDs.