Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea.
BMC Plant Biol. 2024 Mar 19;24(1):201. doi: 10.1186/s12870-024-04897-w.
The B3 gene family, one of the largest plant-specific transcription factors, plays important roles in plant growth, seed development, and hormones. However, the B3 gene family, especially the REM subfamily, has not been systematically and functionally studied.
In this study, we performed genome-wide re-annotation of B3 genes in five Solanaceae plants, Arabidopsis thaliana, and Oryza sativa, and finally predicted 1,039 B3 genes, including 231 (22.2%) newly annotated genes. We found a striking abundance of REM genes in pepper species (Capsicum annuum, Capsicum baccatum, and Capsicum chinense). Comparative motif analysis revealed that REM and other subfamilies (ABI3/VP1, ARF, RAV, and HSI) consist of different amino acids. We verified that the large number of REM genes in pepper were included in the specific subgroup (G8) through the phylogenetic analysis. Chromosome location and evolutionary analyses suggested that the G8 subgroup genes evolved mainly via a pepper-specific recent tandem duplication on chromosomes 1 and 3 after speciation between pepper and other Solanaceae. RNA-seq analyses suggested the potential functions of REM genes under salt, heat, cold, and mannitol stress conditions in pepper (C. annuum).
Our study provides evolutionary and functional insights into the REM gene family in pepper.
B3 基因家族是最大的植物特异性转录因子之一，在植物生长、种子发育和激素中发挥重要作用。然而，B3 基因家族，特别是 REM 亚家族，尚未得到系统和功能研究。
本研究对五个茄科植物（拟南芥、水稻）中的 B3 基因进行了全基因组重新注释，最终预测了 1039 个 B3 基因，包括 231 个（22.2%）新注释基因。我们发现辣椒物种（辣椒、辣椒和辣椒）中 REM 基因的丰度惊人。比较基序分析表明，REM 和其他亚家族（ABI3/VP1、ARF、RAV 和 HSI）由不同的氨基酸组成。通过系统发育分析，我们验证了辣椒中大量的 REM 基因包含在特定的亚组（G8）中。染色体定位和进化分析表明，G8 亚组基因在辣椒和其他茄科植物分化后，主要通过染色体 1 和 3 上的辣椒特异性近期串联重复进化而来。RNA-seq 分析表明，REM 基因在辣椒（辣椒）中可能在盐、热、冷和甘露醇胁迫条件下发挥作用。
本研究为辣椒 REM 基因家族提供了进化和功能方面的见解。
