Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

Abstract

Background Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees. Results To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume. Conclusions We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

Genome-wide analysis and identification of the PEBP genes of Brassica juncea var. Tumida

“…BjBFT1 was detected in all tissues but showed relatively high expression in the root, stem, and leaf. This finding is consistent with that of a previous study by Zhang et al [ 36 ] who stated that BFT expression is relatively high in the stem and leaf of Prunus yedoensis and Rosaceae occidentalis . In Arabidopsis sp., MFT4 plays a redundant role in flowering [ 9 ].…”

“…Regarding the structural composition of PEBP , all PEBP genes were found to have four exons and three introns, except BjMFT1 and BjPYBHB1 ; this finding is consistent with that of Zhang et al [ 36 ] who identified the PEBP gene family in nine Rosaceae trees species. The second and third exons of BjPEBP were noted to be short and the first and fourth exons were noted to be long; this finding is similar to that observed in Jatropha curcas [ 41 ].…”

“…The second and third exons of BjPEBP were noted to be short and the first and fourth exons were noted to be long; this finding is similar to that observed in Jatropha curcas [ 41 ]. The short motifs DPDxP (Asp-Pro-Asp-X-Pro) and GIHR (Gly-Ile-His-Arg) are highly conserved and represent the characteristic motifs of the PEBP protein family [ 36 ]. The conserved protein motif identifies motif1 and motif5 as the characteristic motifs of Brassica juncea var.…”

“…The PEBP family has been identified in various plants such as Moso Bamboo (gene number [n] = 6) [ 31 ], Oryza sativa ( n = 19) [ 11 ], Gossypium hirsutum ( n = 8) [ 32 ], common wheat ( n = 76, 38, 16, and 22) [ 33 ], Glycine max ( n = 27) [ 34 ], Vitis cinifera ( n = 5) [ 35 ], Rosaceae tree species ( n = 56) [ 36 ], rice ( n = 19) [ 11 ], and corn ( n = 25) [ 37 ].…”

Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume

“…Using the chilling hour model, we calculated total chilling hours (CH) required for cultivar "Subaitage" as approximately 320 CHs, which started to accumulate since October 12th, 2020 (Figure 1B). In P. mume, floral organ initiation was induced in late summer with floral primordium continuing to develop throughout winter (Zhang et al, 2021a). In early November, floral buds were maintained in endodormant state with floral organ primordiums, including sepal, petal, stamen, and pistil fully differentiated.…”