Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L.

Abstract

Basic leucine zipper (bZIP), a conserved transcription factor widely found in eukaryotes, has important regulatory roles in plant growth. To understand the information related to the bZIP gene family in walnut, 88 JrbZIP genes were identified at the genome-wide level and classified into 13 subfamilies (A, B, C, D, E, F, G, H, I, J, K, M, and S) using a bioinformatic approach. The number of exons in JrbZIPs ranged from 1 to 12, the number of amino acids in JrbZIP proteins ranged from 145 to 783, and the isoelectric point ranged from 4.85 to 10.05. The majority of JrbZIP genes were localized in the nucleus. The promoter prediction results indicated that the walnut bZIP gene contains a large number of light-responsive and jasmonate-responsive action elements. The 88 JrbZIP genes were involved in DNA binding and nucleus and RNA biosynthetic processes of three ontological categories, molecular functions, cellular components and biological processes. The codon preference analysis showed that the bZIP gene family has a stronger bias for AGA, AGG, UUG, GCU, GUU, and UCU than other codons. Moreover, the transcriptomic data showed that JrbZIP genes might play an important role in floral bud differentiation. The results of a protein interaction network map and kegg enrichment analysis indicated that bZIP genes were mainly involved in phytohormone signaling, anthocyanin synthesis and flowering regulation. qRT-PCR demonstrated the role of the bZIP gene family in floral bud differentiation. Co-expression network maps were constructed for 29 walnut bZIP genes and 6 flowering genes, and JrCO (a homolog of AtCO) was significantly correlated (p < 0.05) with 13 JrbZIP genes in the level of floral bud differentiation expression, including JrbZIP31 (homolog of AtFD), and JrLFY was significantly and positively correlated with JrbZIP10,11,51,59,67 (p < 0.05), and the above results suggest that bZIP family genes may act together with flowering genes to regulate flower bud differentiation in walnut. This study was the first genome-wide report of the walnut bZIP gene family, which could improve our understanding of walnut bZIP proteins and provide a solid foundation for future cloning and functional analyses of this gene family.

Comprehensive Identification and Analyses of the GRF Gene Family in the Whole-Genome of Four Juglandaceae Species

“…We also identified binding sites for many important transcription factors, NAC [ 42 ], ERF [ 43 ], bHLH (Basic/Helix-loop-Helix) [ 44 ], among other TFBSs associated with plant growth and development, these different TFBSs may provide valuable clues for studying how plants affect growth and development by regulating the spatiotemporal expression of Juglandaceae 14-3-3. The weak codon preference of Juglandaceae family GRF genes is influenced by a combination of natural selection pressure and base mutations, and translational selection plays a dominant role in codon usage against mutational pressure, which is largely consistent with our previous studies within the walnut bZIP family [ 45 ].…”

The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response

“…In angiosperms, most plant genomes contain more than 40 bZIP genes ( Baloglu et al., 2014 ; Liu and Chu, 2015 ). In this research we identified 45 LchibZIP genes, less than rose with 48 bZIP genes ( Li et al., 2022b ), Juglans regia L. has 88 bZIP genes ( Zhang et al., 2022 ), and Sedum plumbizincicola has 92 bZIP genes ( Lu et al., 2022 ).…”

“…Deeper analysis showed that, 10 LchibZIPs were duplicated through segmental duplications, and only four gene pairs through tandem duplication, as demonstrated by synteny analysis of the LchibZIPs. Similarly, in Juglans regia L. bZIP genome, one pair of tandem repeats and 46 pairs of fragment repeats were identified ( Zhang et al., 2022 ). In the pear bZIP genome, 12 pairs of tandem repeats and 65 pairs of fragment repeats were identified ( Ma et al., 2021 ).…”

Comprehensive analysis of bZIP transcription factors in passion fruit

“… 8 About 17 bZIPs in yeast, 27 in fruit flies, 31 in nematodes, and 56 in humans have been discovered, 9 whereas in plants, more bZIPs were found, 127 in Arabidopsis thaliana , 216 in Zea mays , 210 in Nicotiana tabacum , 214 in Populus trichocarpa , 47 in Vitis vinifera , 70 in Solanum lycopersicum , 88 in Juglans regia, 135 in Malus domestica , and 352 in Glycine max , etc., also have been reported. 10 , 11 , 12 …”