Genome-wide Member Identification, Phylogeny and Expression Analysis of PEBP Gene Family in Wheat and Its Progenitors

Overview

Journal PeerJ

Specialties Biology
Environmental Health
General Medicine

Date 2020 Dec 28

PMID 33362967

Citations 8

Authors

Lei Dong

Yue Lu

Shubing Liu

Affiliations

Soon will be listed here.

Abstract

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all genes have been identified or analyzed in common wheat ( L.) and its progenitors. In this study, we identified the genes in common wheat, , and by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 genes were identified in common wheat, , and , respectively. Phylogenetic analysis classified the genes into four subfamilies (, , and ); the subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more genes than other chromosomes. The genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of genes than segmental duplication. Furthermore, transcriptome analysis revealed that genes showed tissue/organ-specific expression profiles and some genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (, , , and ) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

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References

Liu Y, Yang K, Wei X, Wang X . Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution. New Phytol. 2016; 212(3):730-744. DOI: 10.1111/nph.14066. View

Ryu J, Park C, Seo P . The floral repressor BROTHER OF FT AND TFL1 (BFT) modulates flowering initiation under high salinity in Arabidopsis. Mol Cells. 2011; 32(3):295-303. PMC: 3887636. DOI: 10.1007/s10059-011-0112-9. View

Jiao Y, Li J, Tang H, Paterson A . Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. Plant Cell. 2014; 26(7):2792-802. PMC: 4145114. DOI: 10.1105/tpc.114.127597. View

Meng X, Muszynski M, Danilevskaya O . The FT-like ZCN8 Gene Functions as a Floral Activator and Is Involved in Photoperiod Sensitivity in Maize. Plant Cell. 2011; 23(3):942-60. PMC: 3082274. DOI: 10.1105/tpc.110.081406. View

Wang Z, Zhou Z, Liu Y, Liu T, Li Q, Ji Y . Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis. Plant Cell. 2015; 27(2):323-36. PMC: 4456927. DOI: 10.1105/tpc.114.135103. View

Shewry P, Hey S . The contribution of wheat to human diet and health. Food Energy Secur. 2016; 4(3):178-202. PMC: 4998136. DOI: 10.1002/fes3.64. View

Kikuchi R, Kawahigashi H, Ando T, Tonooka T, Handa H . Molecular and functional characterization of PEBP genes in barley reveal the diversification of their roles in flowering. Plant Physiol. 2009; 149(3):1341-53. PMC: 2649388. DOI: 10.1104/pp.108.132134. View

Avni R, Nave M, Barad O, Baruch K, Twardziok S, Gundlach H . Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science. 2017; 357(6346):93-97. DOI: 10.1126/science.aan0032. View

Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T . Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol. 2002; 43(10):1096-105. DOI: 10.1093/pcp/pcf156. View

10.

Gursky V, Kozlov K, Nuzhdin S, Samsonova M . Dynamical Modeling of the Core Gene Network Controlling Flowering Suggests Cumulative Activation From the Gene Homologs in Chickpea. Front Genet. 2018; 9:547. PMC: 6262361. DOI: 10.3389/fgene.2018.00547. View

11.

Jang S, Torti S, Coupland G . Genetic and spatial interactions between FT, TSF and SVP during the early stages of floral induction in Arabidopsis. Plant J. 2009; 60(4):614-25. DOI: 10.1111/j.1365-313X.2009.03986.x. View

12.

Gu Z, Cavalcanti A, Chen F, Bouman P, Li W . Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol. 2002; 19(3):256-62. DOI: 10.1093/oxfordjournals.molbev.a004079. View

13.

Chautard H, Jacquet M, Schoentgen F, Bureaud N, Benedetti H . Tfs1p, a member of the PEBP family, inhibits the Ira2p but not the Ira1p Ras GTPase-activating protein in Saccharomyces cerevisiae. Eukaryot Cell. 2004; 3(2):459-70. PMC: 387632. DOI: 10.1128/EC.3.2.459-470.2004. View

14.

Pnueli L, Carmel-Goren L, Hareven D, Gutfinger T, Alvarez J, Ganal M . The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development. 1998; 125(11):1979-89. DOI: 10.1242/dev.125.11.1979. View

15.

Shannon S, Meeks-Wagner D . A Mutation in the Arabidopsis TFL1 Gene Affects Inflorescence Meristem Development. Plant Cell. 1991; 3(9):877-892. PMC: 160057. DOI: 10.1105/tpc.3.9.877. View

16.

Kardailsky I, Shukla V, Ahn J, Dagenais N, Christensen S, Nguyen J . Activation tagging of the floral inducer FT. Science. 1999; 286(5446):1962-5. DOI: 10.1126/science.286.5446.1962. View

17.

Taoka K, Ohki I, Tsuji H, Furuita K, Hayashi K, Yanase T . 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature. 2011; 476(7360):332-5. DOI: 10.1038/nature10272. View

18.

Lynch M, Conery J . The evolutionary fate and consequences of duplicate genes. Science. 2000; 290(5494):1151-5. DOI: 10.1126/science.290.5494.1151. View

19.

Bradley D, Ratcliffe O, Vincent C, Carpenter R, Coen E . Inflorescence commitment and architecture in Arabidopsis. Science. 1997; 275(5296):80-3. DOI: 10.1126/science.275.5296.80. View

20.

Hu B, Jin J, Guo A, Zhang H, Luo J, Gao G . GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2014; 31(8):1296-7. PMC: 4393523. DOI: 10.1093/bioinformatics/btu817. View