State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
BMC Genomics. 2022 Jan 10;23(1):40. doi: 10.1186/s12864-021-08248-z.
RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton.
Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes.
Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton.
RADIALIS（RAD）属于 MYB 基因家族，调节包括金鱼草花的背腹不对称和番茄果实蛋白发育在内的多种功能。RAD 基因含有 SNF2_N 超家族结构域。在此，我们从拟南芥和五种棉花物种中全面鉴定了 68 个 RAD 基因。
系统发育分析将 RAD 基因分为五个亚组。基因结构、蛋白基序和保守氨基酸残基表明，GhRAD 基因在进化过程中高度保守。染色体定位信息显示，GhRAD 基因在不同染色体上不均匀分布。共线性和选择压力分析表明，G. hirsutum 和 G. barbadense 中 RAD 基因家族扩张，并受到纯化选择压力的影响。此外，观察到多种生长和胁迫相关启动子顺式作用元件。组织特异性表达水平表明，大多数 GhRAD 基因在根和花中高度表达（GhRAD2、GhRAD3、GhRAD4 和 GhRAD11）。接下来，GhRAD 基因受到植物激素胁迫（JA、BL 和 IAA）的调控。此外，Ghi-miRN1496、Ghi-miR1440、Ghi-miR2111b、Ghi-miR2950a、Ghi-miR390a、Ghi-miR390b 和 Ghi-miR7495 是靶向大多数 GhRAD 基因的 miRNAs。
本研究表明，RAD 基因在进化上是保守的，可能参与不同的发育过程和激素应激反应。本研究提供的数据可为棉花 RAD 基因的进一步研究提供基础。
