Phylogenetic Classification, Characterization and Expression of Goldon2-like (GLK) Transcription Factor Gene Family in Persian Walnut in Response to Phomopsis capsici Infection

Abstract

The G2-like (GLK) transcription factors are members of the GARP superfamily and control chloroplast biogenesis, photosynthesis development and stress responses in plants. However, they are yet to be characterized in a systematic manner in woody perennial species. In this work, we identified and characterized the GLK gene family at genome level in Persian walnut (Juglans regia L.) using the chromosome-scale Walnut 2.0 genome assembly (GCF_001411555.2). Forty-four non-redundant JrGLK genes were identified at the family level; of these, 43 with complete genomic coordinates were mapped and found unevenly distributed on 14 of the 16 walnut chromosomes, with the largest gene clusters on chromosomes 3 and 4. A total of 126 GLK protein sequences from J. regia, A. thaliana and O. sativa were subjected to maximum-likelihood phylogenetic analysis, which classified the family into 15 statistically supported groups. Members from A. thaliana and O. sativa were distributed across most groups, with no purely walnut-specific group reaching the support threshold, arguing against walnut-specific lineage expansion. Conserved motif and exon–intron structure analysis showed patterns concordant with this classification, with several groups distinguished by group-specific motif combinations. Promoter analysis of the 43 characterized genes revealed predicted occurrences of abscisic acid-, drought-, defense- and light-associated regulatory elements across the family, representing predicted motif occurrences rather than confirmed regulatory function. Synteny analysis identified 23 JrGLK genes with confirmed syntenic orthologs in A. thaliana and 23 in Populus trichocarpa, indicating evolutionary retention of GLK loci across dicotyledonous lineages. Transcriptomic analysis of plants infected with Phomopsis capsici identified 13 significantly differentially expressed JrGLK genes, six up-regulated and seven down-regulated, indicating a transcriptional response to infection. Together, these data provide a genomic resource for the GLK family in J. regia and a foundation for functional studies and molecular breeding in walnut and other Juglandaceae species.