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Genome-wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN-in Physcomitrella patens and stress responses

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Abstract

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.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (Grant nos. 31660554 and 31660046). The talent platform of Qiankehe ([2017] 5726-49 and [2017] 5726-50).

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Author notes

  1. Huiqing Yan

    Present address: School of Life Sciences, Guizhou Normal University, Huaxi District, Guiyang, 550001, Guizhou, China

  2. Xiaolong Huang and Huiqing Yan are equally contributed to this work and should be considered co-first authors.

Authors and Affiliations

  1. Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China

    Xiaolong Huang, Yanjing Liu & Yin Yi

  2. Key Laboratory of State Forestry Administration on Biodiversity Conservation in Mountainous Karst Area of Southwestern China, Guizhou Normal University, Guiyang, 550001, China

    Xiaolong Huang, Yanjing Liu & Yin Yi

  3. School of Life Sciences, Guizhou Normal University, Huaxi District, Guiyang, 550001, Guizhou, China

    Xiaolong Huang & Yanjing Liu

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Correspondence to Huiqing Yan.

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Huang, X., Yan, H., Liu, Y. et al. Genome-wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN-in Physcomitrella patens and stress responses. Genes Genom 42, 651–662 (2020). https://doi.org/10.1007/s13258-020-00931-x

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