In plants, PEBP genes are central regulators in determining the flowering time, plant architecture and seed germination. Animal PEBP proteins were reported to function as serine proteases or Raf kinase inhibitors, controlling cell growth and differentiation. Plant PEBP homologs share similar conserved motifs, except their C-terminal part is deleted. Mammalian PEBPs are globular proteins composed of a functional binding site for acetate, phosphate groups and phosphorylethanolamine. Phosphatidylethanolamine-binding proteins (PEBPs) form a superfamily of genes containing a PEBP domain, which is highly conserved across taxa, from bacteria and insects to mammals and plants. Therefore, it is important to study the flowering time control in perennial species and understand their adaptation mechanisms in synchronizing the timing of floral bud breaking and reproduction with local climate. Within the context of global climate change, warm winters and irregular occurrences of extreme weather have disrupted the timing of spring phenological events in tree species, increased the risk of frost damage, and caused abnormal fertility and poor fruit setting due to insufficient winter chill. Therefore, the blooming time of temperate woody perennials is mainly determined by intrinsic state of flower buds and external environment. However, in temperate tree species, flower buds initiate and develop during summer, undergo a short period of dormancy, exit dormancy after exposure to chilling temperatures and finally bloom in suitable environments. The flowering time in annual or biennials is largely determined by the timing of the transition from vegetative growth to reproductive growth. Proper timing of flowering is a key adaptive strategy in plant species, especially temperate woody perennials. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species. 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. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. 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. Codon usage analysis showed slightly biased codon usage across five gene lineages. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. 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. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. R-devel: tscount_1.4.1.zip, r-release: tscount_1.4.1.zip, r-oldrel: tscount_1.4.1.Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes.
Apsim r package citation series#
Tscount: An R Package for Analysis of Count Time Series Following Generalized Linear Models Matrix, xtable, gamlss.data, surveillance, gamlss, VGAM, acp, glarma, gamlss.util, KFAS, gcmr The conditional distribution can be Poisson or Negative Binomial. Models with the identity and with the logarithmic link function are allowed. Likelihood-based methods for model fitting and assessment, prediction and intervention analysis of count time series following generalized linear models are provided. CRAN - Package tscount tscount: Analysis of Count Time Series
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