Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut (Juglans Regia L.)

Abstract

Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regia PAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

“…The WRKY gene family in walnut can be divided into four groups, similar to the classification of WRKY genes in Musa acuminate and Musa balbisiana , Castor bean, pineapple, soybean, C. sinensis , C. clementina and C. unshiu , Eucalyptus grandis , Quinoa, Dimocarpus longan , Raphanus sativus , potato, moso bamboo, G. raimondii and G. arboretum , Cassava, willow, Oryza officinalis , peach and Dendrobium officinale . The division of the family in such a manner suggests that the results of our classification were reasonable and reliable [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 ]. In view of the conserved motifs, motifs 5, 9, 1, 2, 8, 10 and 7 were the typical motifs of group I; motifs 1 and 2 were the typical motifs of group II; and motifs 4, 1 and 2 were the typical motifs of group III.…”

“…There is no previous study regarding the WRKY gene in common walnut ( J. regia ) [ 33 , 34 ]. In a recent publication of high-quality common walnut genome data, some gene families and transcript factors were reported in common walnut, such phenylalanine ammonialyase ( PAL) , F-box , fatty acid desaturase ( FAD) , heat stress transcription factors ( HSFs ), nascent polypeptide-associated complex protein ( NAC) and repressor of GAI; gibberellic acid-insensitive RGA and scarecrow SCR ( GRAS ) were also reported [ 35 , 36 , 37 , 38 , 39 , 40 ]. However, comprehensive information regarding the functional characterization of the WRKY gene family in common walnut is still unclear.…”

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

“…HMMsearch software and the TPS and TPP’s HMMs were used to search all possible TPS candidate sequences containing typical TPS and TPP domains under a Linux system ( Chen et al, 2019 ). Pfam ( Liu et al, 2019a ) and NCBI-CDD ( ) ( Yan, Li & Zhao, 2019 ) databases were used to manually confirm that the candidate sequences had complete TPS and TPP domains. The remaining genes were subsequently identified as members of the cucumber TPS family and were named according to their location on the cucumber’s chromosome.…”

Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

“…Subsequently, MEGA7.0 software (Molecular evolutionary genetics analysis, Pennsylvania State University: State College, PA, USA) was employed to construct an unrooted phylogenetic tree based on alignments using the neighbor-joining (NJ) method [42,43]. The neighbor-joining phylogenetic trees were constructed with pairwise deletion of 1000 bootstraps and a Poisson model [44].…”

“…Gene structure is an important factor for gene family evolution [29,43]. Intron positions always determine the gene coding sequence position and protein structure, and increased protein diversity through exon shuffling and alternative splicing causes an evolutionary advantage [63][64][65].…”