Abstract
The three amino acid loop extension (TALE) are essential transcription factors that regulate the differentiation of meristem in plant growth and development. Several studies on the TALE family in plants, including Arabidopsis, rice, and others, have been carried out. However, little is known about the TALE family in walnut. In this study, the genome-wide identification and expression analysis of the TALE gene family was studied comprehensively in walnut. Based on the specific structure of the TALE domain, a total of thirty walnut TALE genes were identified. According to different domains structure and phylogenetic relationships, the JrTALE gene family could be divided into two subfamilies, namely BELL and KNOX. Conserved protein motifs analysis showed that JrTALE contained similar motif structures in the same phylogenetic branch. The JrTALE gene family members had a weak overall codon bias, preferring to use synonymous codons ending in A/U. Expression pattern analysis of the JrTALE family genes showed that JrTALE17 and JrTALE18 were differentially expressed in female and male flower buds. We confirmed that JrTALE3, JrTALE5, JrTALE7, JrTALE10, JrTALE15 and JrTALE22 were differentially expressed between different stages of flower bud development by real-time quantitative PCR (qRT-PCR). This study provides valuable information about the TALE family in the transitional development of walnut flower buds, laying the foundation for a better understanding of the TALE family in walnut.
Highlights
The three amino acid loop extension (TALE) are essential transcription factors that regulate the differentiation of meristem in the plant growth and development. there's a lot of journalism of the TALE family in plants, such as Arabidopsis, rice, and others. there's no report on the TALE family in walnut
Sixty-nine JrTALEs were identified in the genome-wide. the physicochemical properties, phylogenetic relationships, gene structure, promoter cis-acting elements, and protein interactions were systematically analyzed by bioinformatics methods
This study provides valuable information about the TALE family in the transitional development of walnut flower buds, which lay the foundation for further understanding of TALE family genes and in walnut
Summary
Plant materialsAll samples of this study were collected from walnut (Juglans regia L.), which trees were grown under natural conditions in the southern part of the Xinjiang Uyghur Autonomous Region, China.. male and female flower buds were collected before, during, after the flower transition period (FB / MB-1, FB / MB-2, and FB / MB-3). Downloaded the latest protein sequence file (GCF_001411555.1_wgs.5d_protein.faa.gz) of the walnut genome from the NCBI website(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/411/555/GCF_001411555.1_wgs.5d/GCF_001411555.1_wgs.5d_protein.faa.gz). The hidden Markov models (HMM) family (PF07526, PF05920, PF03790, PF03791, PF03789) were obtained from the Pfam online (http://pfam.xfam.org/) [47]. Based on hmmer3.0, the HMM model was used to retrieve the protein sequence of walnut [48,49] (with a threshold value of E ≤ 1e-20), redundant sequences were removed, and the TALE gene family of walnut was identified initially. The candidate TALE members were uploaded to the CDD (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and SMART [50] (http://smart.embl-heidelberg.de/) online websites to further confirm that if they contained the proper TALE domain (remove sequences without TALE domain). The sequence was submitted to the ProtParam (https://www.expasy.org/protparam/) tool to predict its protein information, such as amino acid length, molecular weight, isoelectric point, and so on. The sequence was submitted to the ProtParam (https://www.expasy.org/protparam/) tool to predict its protein information, such as amino acid length, molecular weight, isoelectric point, and so on. the subcellular localization information of JrTALE protein was predicted by the online software ProtComp 9.0 (http://linux1.softberry.com/berry.phtml? topic=protcomppl&group=programs&subgroup=proloc)
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