Genome-Wide Analysis, Identification, and Characterization of the PFK Gene Family Members of Populus deltoides

Abstract

Plants produce two phosphorylated enzymes: pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP) and ATP-dependent phosphofructokinase (PFK). However, the characterization of phosphofructokinase (PFK) family members and their functions remains unexplored in Eastern Cottonwood (Populus deltoides). This study comprehensively analyzed 17 phosphofructokinase genes in the P. deltoides genome, including their gene structure, conserved domains, evolutionary relationships, and expression patterns. Genome-wide analysis of the poplar genome identified 11 genes belonging to PdPFK and 6 genes belonging to PdPFP. Phylogenetic, gene structure, and motif analyses revealed two main categories of PFK genes: PFK with eleven genes and PFP with six genes. Quantitative PCR (qPCR) analysis demonstrated that all 17 phosphofructokinase genes were induced in various tissues and developmental stages of P. deltoides. PFPs were strongly expressed throughout P. deltoides’ growth and development, notably in the roots, according to the transcript analysis. This genome-wide analysis provides insights into PFK and PFP genes and establishes a foundation for future investigations into the role of genes in P. deltoids.

Genome-wide identification of the PFK gene family and their expression analysis in Quercus rubra

“…Phylogenetic analysis with the PFK gene family members with other reported crops such as A. thaliana, P. deltoides, R. communis, O. sativa, and S. tuberosum has grouped Qurub.05G067500.1, Qurub.02 G097100.1, and Qurub.02G097100.2 with the PFPs of other model crops. Similar instances were observed in the crops, P. deltoides (Kim Frontiers in Genetics frontiersin.org et al, 2023), A. thaliana (Mustroph et al, 2007), R. communis (Podesta and Plaxton, 1994), O. sativa (Kato-Noguchi, 2002, and S. tuberosum (Kim et al, 2023), implying that they belonged to PFP family. The availability of the Q. rubra genome facilitated the investigation of the roles of PFKs and PFPs.…”

“…The genome and annotations for P. deltoides, A. thaliana, S. tuberosum, R. communis, and O. sativa were downloaded for comparative studies. P. deltoides genome was downloaded from Phytozome V13 (Kim et al, 2023) (Cui et al, 2007;Liu et al, 2014). We used BLASTP searches to examine tandem and segmental gene duplications in PFKs.…”

“…The evolution of sequencing technology over the last 10 years has enabled the sequencing of numerous plant genomes. Multiple other plant species have been reported to contain members of the PFK gene family, including poplar (Kim et al, 2023), rice (Mustroph et al, 2013), Arabidopsis (Mustroph et al, 2007), saccharum (Zhu et al, 2013), and spinach (Winkler et al, 2007). Gene duplication is a key process that provides novel evolutionary models of gene family expansion in eukaryotes (Ohno, 1970;Zhang, 2003).…”