Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus

Abstract

AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.

Systematical Characterization of the AT-Hook Gene Family in Juglans regia L. and the Functional Analysis of the JrAHL2 in Flower Induction and Hypocotyl Elongation

“…Clade-A contained 20 JrAHLs, and it was also classified into Type-I, harboring the Clade-A PPC domain and the Type-I AT-hook motifs in their putative protein sequence ( Figure 2 right panel). The higher abundance of Type I members (54%) in walnut is also consistent with observations in other land plants [ 25 , 27 , 31 ]. There were 17 JrAHL members in Clade-B, which all harbored the Clade-B PPC domain.…”

“…In recent years, the AHL gene family has been identified and analyzed in several species, such as Arabidopsis, soybean ( Glycine max ) [ 25 ], cotton ( Gossypium raimondii ) [ 26 ], Brassica napus [ 27 ], grape ( Vitis vinifera ) [ 28 ], carrot ( Daucus carota subsp. sativus ) [ 29 ], and so on.…”

Phylogenomics-Based Reconstruction and Molecular Evolutionary Histories of Brassica Photoreceptor Gene Families

“…However, none of the Brassica PHR members contains the aforementioned copies in any of the tetraploids or their progenitors, suggesting PHR genes were lost on a large scale, possibly due to functional redundancy between the replicates after the triploidization. The large-scale loss/genome contraction was also noted for other gene families like AHLs , EXPs, and flowering-time genes in Brassica [ 25 , 29 , 30 ]. In particular, heavy gene losses have occurred for CRY3 and PHYD subfamilies in all the Brassica species.…”

“…Like EXP [ 25 ], AHL [ 29 ], and Homeobox (HB) gene families of Brassica, segmental duplication is the driving force in the expansion of the PHR gene families. The most recent segmental duplication occurred in B. napus (for BnUVR8 like 2: BnUVR8 like 2-1, BnUVR8 like 2: BnUVR8 like 2-2) was 3.7 MYA.…”

Differential chromatin binding preference is the result of the neo‐functionalization of the TB1 clade of TCP transcription factors in grasses

“…One of the major driving forces for gene neo‐functionalization after duplication events is the fixation of adaptive residues (Ohno, 1970; Conant & Wolfe, 2008). There is a vast literature showing the incidence of positive selection in plant TFs (Viola et al ., 2012; Wu et al ., 2014; Bartlett et al ., 2016; Derbyshire et al ., 2021; Zhang et al ., 2021), even including TB1 ‐like genes from the TCP family (Gübitz et al ., 2003; Martín‐Trillo et al ., 2011). However, the implication of adaptive evolution in the binding preference of TFs to chromatin remains largely unknown.…”