Genome-wide identification and bioinformatics analysis of auxin response factor genes in highbush blueberry

Abstract

Auxin response factors (ARFs) are a transcription factor family that regulates the expression of auxin phase-responsive genes. Here, we performed a genome-wide investigation of the tetraploid blueberry (Vaccinium corymbosum cv. ‘Draper’) genome sequence. Physical and chemical properties, phylogenetic evolution, gene structure, conservative motifs, chromosome location, and cis-acting elements of blueberry ARF genes were comprehensively evaluated. A total of 70 blueberry ARF genes (VcARF) were found in its genome, which could be divided into six subfamilies. VcARF genes were unevenly distributed on 40 chromosomes and were observed to encode protein sequences ranging in length from 162 to 1117 amino acids. Their exon numbers range from 2 to 22. VcARF promoter regions contain multiple functional domains associated with light signaling, aerobic metabolism, plant hormones, stress, and cell cycle regulation. More family members of VcARF genes were discovered in blueberry than in previously studied plants, likely because of the occurrence of whole-genome duplication and/or tandem duplication. VcARF expression patterns were analyzed at different stages of fruit development, and VcARF3, VcARF4, VcARF14, VcARF37, and VcARF52 were observed to play important roles. VcARF3 and VcARF4 appeared to function as repressors, while VcARF14 acted as an essential factor in fruit firmness differences between firm and soft flesh cultivars.