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龙眼体细胞胚胎发生过程中 NAC 转录因子基因家族的全基因组鉴定和综合分析及表达模式

Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression patterns during somatic embryogenesis in Dimocarpus longan Lour.

机构信息

Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan.

出版信息

Plant Physiol Biochem. 2020 Dec;157:169-184. doi: 10.1016/j.plaphy.2020.10.009. Epub 2020 Oct 13.

Abstract

The NAM, ATAF1/2, and CUC2 form a huge plant-specific gene family of NAC TFs that are involved in the growth, development, and regulation of biotic and abiotic stress responses. Although the draft genome of longan (Dimocarpus longan Lour.) has been published, however the comprehensive data regarding the functions, evolution, and expression patterns of the NAC family are still unavailable. In this study, a comprehensive analysis of the NAC transcription factor family in longan was performed, and a total of 114 NAC genes were found. We investigated the NAC gene family exploring the phylogeny, domain conservation, intron/exon, motifs, cis-regulatory elements, protein-protein interaction, and expression profiles of RNA-seq samples in different tissues and early somatic embryogenesis of longan. Phylogenetic analysis showed that the genes with similar gene structure and motif distribution were clustered in the same group. Cis-element identification indicates the possible role of NAC genes in biological and physiological processes. Protein-protein interaction identified the DlNACs homologous with Arabidopsis proteins. We further investigated the expression pattern of DlNAC genes in different tissues (pulp, stem, large fruit, young fruit, and flower) during somatic embryogenesis at embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), and globular embryos (GE) stages. The qRT-PCR results showed that the DlNAC genes were expressed higher at EC and GE stage compared with ICpEC stage. In conclusion, our results provide insight into the evolution, diversity, and characterization of NAC genes in the longan and provide a base for understanding their biological roles and molecular mechanisms in plants.

摘要

NAM、ATAF1/2 和 CUC2 形成了一个庞大的植物特异性 NAC TF 基因家族,它们参与生长、发育以及生物和非生物胁迫反应的调节。尽管龙眼(Dimocarpus longan Lour.)的草案基因组已经发布,但是关于 NAC 家族的功能、进化和表达模式的综合数据仍然不可用。在本研究中,对龙眼 NAC 转录因子家族进行了全面分析,共发现 114 个 NAC 基因。我们通过对 NAC 基因家族的研究,探讨了其系统发育、结构域保守性、内含子/外显子、基序、顺式调控元件、蛋白质-蛋白质相互作用以及不同组织和早期龙眼体细胞胚胎发生的 RNA-seq 样本的表达谱。系统发育分析表明,具有相似基因结构和基序分布的基因聚类在同一组中。顺式元件鉴定表明 NAC 基因可能在生物和生理过程中发挥作用。蛋白质-蛋白质相互作用确定了与拟南芥蛋白同源的 DlNACs。我们进一步研究了 DlNAC 基因在体细胞胚胎发生过程中不同组织(果肉、茎、大果实、幼果和花)以及胚胎发生愈伤组织(EC)、不完全致密原胚培养物(ICpEC)和球形胚胎(GE)阶段的表达模式。qRT-PCR 结果表明,与 ICpEC 阶段相比,EC 和 GE 阶段的 DlNAC 基因表达更高。总之,我们的研究结果深入了解了龙眼 NAC 基因的进化、多样性和特征,为理解它们在植物中的生物学作用和分子机制提供了基础。

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