New Insights into Structure and Function Predictions of TIFY Genes in Barley: A Genome-Wide Comprehensive Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genome-Wide Identification of TIFY Gene Family Members
2.2. Multiple Sequence Alignment and Phylogenetic Tree Construction
2.3. Analysis of Gene Structure, Conserved Motif and Cis-Acting Element
2.4. Analysis of Chromosomal Location, Gene Duplication and Gene Synteny
2.5. In Silico Expression Analysis of Barley TIFY Genes
3. Results
3.1. Identification of TIFY Genes in Barley
3.2. Multiple Sequence Alignment, Phylogenetic Analysis and Classification of the Barley TIFY Genes
3.3. Gene Structure and Protein Motif Analyses of HvTIFY
3.4. Cis-Acting Element Analysis of TIFY Gene Family Members in Barley
3.5. Chromosomal Location and Duplication Analyses of TIFY Gene Family Members in Barley
3.6. Synteny and Evolutionary Analyses of Barley TIFY Genes and Other Plant TIFYs
3.7. Expression Pattern Analysis of Barley TIFY Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
TF | Transcription factor |
AA | Amino acids |
MW | Molecular weight |
pI | Isoelectric point |
CDS | Coding sequences |
MSA | Multiple sequence alignments |
ARE | Anaerobic induction element |
LTR | Low-temperature responsiveness element |
MBS | MYB binding site |
ABRE | Abscisic acid responsiveness |
chr | Chromosome |
kDa | Kilodaltons |
Ka | Nonsynonymous |
Ks | Synonymous |
JA | Jasmonic acid |
JAZ | Jasmonate ZIM-Domain |
ZIM/ZML | Zinc-finger inflorescence meristem/ZIM-like |
PPD | PEAPOD |
CCT | CONSTANS, CO-like and TOC1 |
BLAST | Basic local alignment search tool |
HMM | Hidden Markov model |
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Li, J.; Xu, X.; Wang, H.; Zhang, Y. New Insights into Structure and Function Predictions of TIFY Genes in Barley: A Genome-Wide Comprehensive Analysis. Agronomy 2024, 14, 1663. https://doi.org/10.3390/agronomy14081663
Li J, Xu X, Wang H, Zhang Y. New Insights into Structure and Function Predictions of TIFY Genes in Barley: A Genome-Wide Comprehensive Analysis. Agronomy. 2024; 14(8):1663. https://doi.org/10.3390/agronomy14081663
Chicago/Turabian StyleLi, Jianjian, Xiwen Xu, Haoran Wang, and Yuan Zhang. 2024. "New Insights into Structure and Function Predictions of TIFY Genes in Barley: A Genome-Wide Comprehensive Analysis" Agronomy 14, no. 8: 1663. https://doi.org/10.3390/agronomy14081663