Unlocking the secrets of black raspberry resilience: genome-wide discovery and analysis of bZIP transcription factors

Transcription factors (TFs) like basic leucine zippers (bZIPs) play vital roles in various plant biological regulation, including stress responses. However, their presence in the Rubus species has received limited attention, especially regarding the function and interactions of bZIP groups S1 and C in the Rubus genus. The current challenge lies in deepening our knowledge of these bZIP networks in non-model plants, which could inform breeding strategies and improve crop resilience.

In February 2024, Fruit Research published a research entitled by “Heterodimeric interaction of the C/S1 basic leucine zipper transcription factors in black raspberry: a genome-wide identification and comparative analysis”.

In this study, researchers combined protein signature files from the Pfam database and a plant-specific Hidden Markov Model (HMM) to identify bZIP members. As a result, 49 candidate bZIP coding genes in both black and red raspberries were identified. These genes were confirmed to encode proteins with characteristic Basic Region (BR) and Leucine Zipper (LZ) domains, varying in length from 137 to 706 amino acids and molecular weights from 15.9 to 76.3 kDa. Phylogenetic analysis classified these into 13 phylogenetic clades, revealing interspecies clustering and suggesting an evolutionary conservation pre-dating species divergence. Additionally, genome-wide analyses revealed significant expansions or contractions in gene families, with gene duplication, especially dispersed and segmental duplications, playing a crucial role in the evolution of bZIP genes in Rubus. Comparative genomic analyses among ten Rosaceae species demonstrated a closer evolutionary relationship among roses, raspberries, and strawberries, and identified the Rubus genome as undergoing chromosomal rearrangements like those in wild strawberries.

Gene ontology annotation and expression analysis of RobZIP genes across different tissues highlighted their involvement in a wide array of cellular processes, including nitrogen metabolism and stress responses. The study also delved into the dimerization properties of the identified bZIPs, predicting potential protein interactions and validating them through yeast two-hybrid assays. Overall, this research not only provided insights into the functional redundancy and specific roles of bZIP TFs in Rubus but also underlined the evolutionary dynamics shaping their diversity across the Rosaceae family. Overall, likely due to stringent selection criteria, this research offers a foundational understanding of the bZIP gene family’s contribution to the regulatory networks within and beyond the Rubus genus, paving the way for future studies on their functional mechanisms and interactions.

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References

DOI

10.48130/frures-0024-0001

Original Source URL

Authors

Ximeng Lin^1,2, Mei Huang¹, Jinwei He¹, Ailing Min¹, Ying Zhou¹, Wendie Ma¹, Xunju Liu³, Xiaorong Wang^1,4, Haoru Tang¹ & Qing Chen^1,4,* 

Affiliations

¹College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China

²College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China

³University Bordeaux, INRAe, Biologie du Fruit et Pathologie, UMR 1332, av. Edouard Bourlaux, Villenave d’Ornon 33140, France

⁴Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Chengdu 611130, China

^*Corresponding author

About Qing Chen

Professor, College of Horticulture, Sichuan Agricultural University. His main research interests are in horticultural plant genetic breeding, with raspberries and strawberries as the research targets, focusing on fruit flavonoid metabolism, sugar synthesis (concentrating on the relationship with pigment synthesis in flavonoids) as well as the biosynthesis of fruit cuticle and the relationship between structure and function of the cell wall.