关键词: SPL基因家族, miR156, 全基因组复制, 串联复制, 功能分化

Abstract:

【Objective】Duplication and subsequent divergence of genes play important roles in driving the evolution of genomes and species. The SQUAMOSA promoter-binding-like (SPL) genes be long to a family of plant-specific transcription factors that regulate numerous fundamental aspects of plant growth and development as well as stress response. The SPL gene family provides an excellent system to analyze the evolutionary fate and consequences of duplicated genes. In this study, gene duplication and the functional divergence of the SPL gene family were analyzed in four model plants, including Vitis vinifera, Carica papaya, Populus trichocarpa and Arabidopsis thaliana. 【Method】The SPL genes of V. vinifera, C. papaya, P. trichocarpa and A. thaliana were identified by using the conserved SQUAMOSA-PROMOTER BINDING PROTEIN domain as the query, and a phylogenetic tree was constructed with the maximum likelihood method. Based on the genome collinearity within and between species, the SPL gene duplication patterns and differential retention were identified in the four plants. The K_a/K_s values were calculated for each retained SPL paralog and ortholog, and functional divergence of these genes was analyzed. 【Result】A total of 73 SPL genes were identified in the four investigated plants, and 42 of them were miR156 target genes. The phylogenetic analysis revealed that the 73 SPL genes were classified into nine major clades, with the miR156 targets being clustered in six major clades. The SPL genes in Clade I encoded two zinc finger motifs, namely C4 and C₂HC, while genes in the remaining clades encoded C3H and C₂HC. Large-scale duplication events (segmental or whole-genome duplication) have played important roles in SPL gene expansion. Based on whole-genome duplications in each species, there were theoretically 360 loci duplicated from 15 ancestral loci; however, 83.6% of them were lost or evolved into non-SPL genes. Among the retained SPL genes, 17 paralogous and 27 orthologous pairs were identified, and the K_a/K_s values of all paralogous and orthologous pairs were lower than 1. 【Conclusion】The SPL genes originating from the ancestor have differentially been retained and expanded in the genomes of the four model plants. Orthologous or paralogous SPL pairs are under strong purifying selection and show conserved structure and function, leading to strong functional conservation. Additionally, an emerging pattern of divergence, including expression bias, subfunctionalization, and neofunctionalization, was revealed among the paralogous SPL pairs. Our findings provide phylogenetic information for studying gene function and identifying species-specific genes.

Key words: SPL gene family, miR156, whole-genome duplication, tandem duplication, functional divergence