Molecular insights into the VIRESCENS amino acid sequence and its implication in anthocyanin production in red- and yellow-fruited cultivars of date palm

Abstract

This study examined the amino acid sequence of the VIRESCENS gene (VIR), which regulates the production of anthocyanin in 12 cultivars of the date palm (Phoenix dactylifera L.), grown in Al-Madinah Al-Munawarah of the Kingdom of Saudi Arabia. The gene products were amplified via polymerase chain reactions, amplifying both exons and introns. The products were sequenced for the reconstruction of a phylogenetic tree, which used the associated amino acid sequences. The ripening stages of Khalal, Rutab, and Tamar varied among the cultivars. Regarding VIR genotype, the red date had the wild-type gene (VIR⁺), while the yellow date carried a dominant mutation (VIR^IM), i.e., long terminal repeat retrotransposons (LTR-RTs). The DNA sequence of VIR^IM revealed that the insertion length of the LTR-RTs ranged between 386 and 476 bp. The R2 and R3 motifs in both VIR⁺ and VIR^IM were conserved. The C-terminus motifs S6A, S6B, and S6C were found in the VIR⁺ protein sequence. However, the amino acids at positions 123, 161, 166, and 168 differed between VIR⁺ and VIR^IM, and were not included in the C-terminus motifs. Within the VIR⁺ allele, the lysine at position 187 in the C-terminus was located immediately after S6B, with a protein binding score of 0.3, which was unique to the dark, red-fruited cultivars Ajwah, Anbarah, and Safawi. In the lighter, red-fruited cultivars, the presence of glutamic acid at the same position suggested that the anthocyanin regulation of date palm might be outside the R2 and R3 domains in the N-terminus.