Abstract
The three-amino-acid-loop-extension (TALE) gene family is a pivotal transcription factor that regulates the development of flower organs, flower meristem formation, organ morphogenesis and fruit development. A total of 17 genes of pomegranate TALE family were identified and analyzed in pomegranate via bioinformatics methods, which provided a theoretical basis for the functional research and utilization of pomegranate TALE family genes. The results showed that the PgTALE family genes were divided into eight subfamilies (KNOX-Ⅰ, KNOX-Ⅱ, KNOX-Ⅲ, BELL-Ⅰ, BELL-Ⅱ, BELL-Ⅲ, BELL-Ⅳ, and BELL-Ⅴ). All PgTALEs had a KNOX domain or a BELL domain, and their structures were conservative. The 1500 bp promoter sequence had multiple cis-elements in response to hormones (auxin, gibberellin) and abiotic stress, indicating that most of PgTALE were involved in the growth and development of pomegranates and stress. Function prediction and protein-protein network analysis showed that PgTALE may participate in regulating the development of apical meristems, flowers, carpels, and ovules. Analysis of gene expression patterns showed that the pomegranate TALE gene family had a particular tissue expression specificity. In conclusion, the knowledge of the TALE gene gained in pomegranate may be applied to other fruit as well.
Highlights
A homeobox (HB) encodes the transcriptional regulatory factors with homeodomain, which play considerable roles in the development of plants and animals [1]
Pomegranate genome sequences (ASM286412v1), protein sequences and transcriptome data were downloaded from NCBI, and the A. thaliana TALE protein sequence was downloaded from the A. thaliana database, E. grandis, Populus trichocarpa, Malus domestica, Vitis vinifera and Solanum lycopersicum TALE protein sequence were downloaded from the PlantTFDB database [6] (Fasta file S1, Table S1)
A. thaliana contains a member of the TALE gene family KNATM without homeodomain, we added a pomegranate gene homologous to KNATM [32], and the target protein domains were detected by SMART and CDD [43,44]
Summary
A homeobox (HB) encodes the transcriptional regulatory factors with homeodomain, which play considerable roles in the development of plants and animals [1]. Based on protein sequence and evolution, BELL and KNOX belong to the TALE gene family [7,8]. Studies have shown that the KNOX2 gene is involved in regulating the secondary growth of plant cell walls and plays a crucial regulatory role in the development of roots, stems, seed coats and heartwood [30,34,35,36]. Studying the function and regulatory mechanism of TALE genes in pomegranate helps regulate pomegranate growth patterns, flower and fruit development. The members of the TALE gene family were identified based on the genome sequence of ‘Taishanhong’, and their physical and chemical properties, protein structure, cis-elements, phylogenetic relationship, and gene tissue expression were analyzed. Through the systematic identification of PgTALE, the result lays a foundation for further study of the function of TALE genes in pomegranate
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