背景:B3基因家族,最大的植物特异性转录因子之一,在植物生长中起着重要的作用,种子发育,和荷尔蒙。然而,B3基因家族,尤其是REM亚家族,尚未进行系统和功能研究。
结果:在这项研究中,我们对五种茄科植物的B3基因进行了全基因组重新注释,拟南芥,和水稻,最后预测了1039个B3基因,包括231个(22.2%)新注释的基因。我们在辣椒物种中发现了惊人的REM基因丰富(辣椒,辣椒,和辣椒)。比较基序分析显示,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基因被包括在特定的亚组(G8)中。染色体定位和进化分析表明,G8亚组基因主要是通过辣椒和其他茄科之间的物种形成后,在1号和3号染色体上进行了辣椒特异性的最近串联复制而进化的。RNA-seq分析提示了盐下REM基因的潜在功能,热,冷,和辣椒中的甘露醇胁迫条件(C.annuum)。
结论:我们的研究提供了辣椒REM基因家族的进化和功能见解。
BACKGROUND: 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.
RESULTS: 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).
CONCLUSIONS: Our study provides evolutionary and functional insights into the REM gene family in pepper.