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Genome-wide identification of the LSD1/JmjC gene family, in longan, and their molecular evolution and expression during early somatic embryogenesis(PDF)

Chinese Journal of Applied & Environmental Biology[ISSN:1006-687X/CN:51-1482/Q]

2021 05
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Genome-wide identification of the LSD1/JmjC gene family, in longan, and their molecular evolution and expression during early somatic embryogenesis
SHEN Xu CHEN Xiaohui CHEN Rongzhu XU Xiaoping LI Xiaofei NI Shanshan ZHANG Jing JIANG Mengqi LIN Yuling & LAI Zhongxiong?
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
longan histone demethylation DlLSD1/DlJmjC gene family bioinformatics stress response somatic embryogenesis molecular evolution

Histone demethylation modification is an important method of modifying chromatin. The lysine-specific demethylase1 (LSD1) and Jumonji C (JmjC)-containing proteins are two histone demethylases that have been reported as being involved in plant growth, reproductive development, and disease resistance. However, the function of LSD1/JmjC in longan remains unclear. We used the embryogenic callus (EC), incomplete compact proembryogenic cultures (ICpEC), and globe embryos (GE) in early somatic embryogenesis (SE) of the longan cultivar ‘Honghezi’, and utilized bioinformatic methods and real-time quantitative PCR to analyze the roles of DlLSD1/DlJmjC genes during early SE in longan. The results showed that there are 4 DlLSD1 and 18 DlJmjC genes on the longan genome; phylogenetic tree analysis showed that these genes were divided into LSD1, KDM3/JMJD1, KDM4/JMJD2, KDM5/JARID and JmjC domain only groups based on their structural and phylogenetic features. Whole genomic duplication (WGD) and segmental duplication events played an important role in the expansion of the longan DlLSD1/DlJmjC gene family, while synteny and phylogenetic analyses provided insights into the evolutionary characteristics of the DlLSD1/DlJmjC genes in longan. Predictions of protein-protein interactions have shown that DlJMJ11, DlJMJ12, and DlJMJ13 have a strong correlation, and promoter analysis found that the genes DlLDL1, DlJMJ11, DlJMJ12, DlJMJ14, DlJMJ16-1, DlJMJ17, and DlJMJ32 have a high number of stress and hormone response elements, suggesting their important roles in stress and hormone regulatory networks. Expression profiles derived from transcriptome data and qRT-PCR analysis showed that the expression of DlJMJ14 and DlJMJ17 was significantly and gradually upregulated during the differentiation of ECs into GEs, but DlJMJ26 and DlLDL1 were significantly and gradually downregulated. DlJMJ11, DlJMJ12, DlJMJ14, DlJMJ17, and DlLDL1 all responded to the regulation of salicylic acid (SA) and methyl jasmonate (MeJA), while the expression of DlJMJ12 and DlLDL1 was inhibited by abscisic acid (ABA) and gibberellin A3 (GA3); DlJMJ12 was also inhibited by SA and MeJA. Moreover, the expression levels of DlJMJ11, DlJMJ14, DlJMJ17, and DlLDL1 were significantly upregulated at 4 h of SA and MeJA treatment while DlJMJ11, DlJMJ12, DlJMJ17, and DlLDL1 all responded to the regulation of low temperatures. Of the latter, DlJMJ11 and DlLDL1 both also responded to the regulation of high temperatures while the expression of DlJMJ12 and DlJMJ17 was inhibited under the same conditions. This study indicated that DlLSD1 is highly conserved, compared to DlJmjC, during the process of evolution and that DlLSD1/DlJmjC may be involved in the embryonic development and somatic embryogenesis in longan as they responded to the regulation of hormones and abiotic stressors.


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