Genome-wide Identification and Expression Analyses of the Homeobox Transcription Factor Family During Ovule Development in Seedless and Seeded Grapes

Overview

Journal Sci Rep

Specialty Science

Date 2017 Oct 5

PMID 28974771

Citations 19

Authors

Yunduan Li

Yanxun Zhu

Jin Yao

Songlin Zhang

Li Wang

Chunlei Guo

Steve van Nocker

Xiping Wang

Affiliations

Soon will be listed here.

Abstract

Seedless grapes are of considerable importance for the raisin and table grape industries. Previous transcriptome analyses of seed development in grape revealed that genes encoding homeobox transcription factors were differentially regulated in seedless compared with seeded grape during seed development. In the present study, we identified a total of 73 homeobox-like genes in the grapevine genome and analyzed the genomic content and expression profiles of these genes. Based on domain architecture and phylogenetic analyses grape homeobox genes can be classified into eleven subfamilies. An analysis of the exon-intron structures and conserved motifs provided further insight into the evolutionary relationships between these genes. Evaluation of synteny indicated that segmental and tandem duplications have contributed greatly to the expansion of the grape homeobox gene superfamily. Synteny analysis between the grape and Arabidopsis genomes provided a potential functional relevance for these genes. The tissue-specific expression patterns of homeobox genes suggested roles in both vegetative and reproductive tissues. Expression profiling of these genes during the course of ovule development in seeded and seedless cultivars suggested a potential role in ovule abortion associated with seedlessness. This study will facilitate the functional analysis of these genes and provide new resources for molecular breeding of seedless grapes.

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References

Abe M, Katsumata H, Komeda Y, Takahashi T . Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis. Development. 2002; 130(4):635-43. DOI: 10.1242/dev.00292. View

Gehring W, Affolter M, Burglin T . Homeodomain proteins. Annu Rev Biochem. 1994; 63:487-526. DOI: 10.1146/annurev.bi.63.070194.002415. View

Olsson A, Engstrom P, Soderman E . The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis. Plant Mol Biol. 2004; 55(5):663-77. DOI: 10.1007/s11103-004-1581-4. View

Plesch G, Stormann K, Torres J, Walden R, Somssich I . Developmental and auxin-induced expression of the Arabidopsis prha homeobox gene. Plant J. 1997; 12(3):635-47. DOI: 10.1046/j.1365-313x.1997.00635.x. View

Blanc G, Wolfe K . Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 2004; 16(7):1679-91. PMC: 514153. DOI: 10.1105/tpc.021410. View

Chan R, Gago G, Palena C, Gonzalez D . Homeoboxes in plant development. Biochim Biophys Acta. 1998; 1442(1):1-19. DOI: 10.1016/s0167-4781(98)00119-5. View

Muller K, Romano N, Gerstner O, Garcia-Maroto F, Pozzi C, Salamini F . The barley Hooded mutation caused by a duplication in a homeobox gene intron. Nature. 1995; 374(6524):727-30. DOI: 10.1038/374727a0. View

Malabarba J, Buffon V, Mariath J, Gaeta M, Dornelas M, Margis-Pinheiro M . The MADS-box gene Agamous-like 11 is essential for seed morphogenesis in grapevine. J Exp Bot. 2017; 68(7):1493-1506. DOI: 10.1093/jxb/erx025. View

Wang M, Yue H, Feng K, Deng P, Song W, Nie X . Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.). BMC Genomics. 2016; 17:668. PMC: 4994377. DOI: 10.1186/s12864-016-2993-7. View

10.

Kerstetter R, Vollbrecht E, Lowe B, Veit B, Yamaguchi J, Hake S . Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes. Plant Cell. 1994; 6(12):1877-87. PMC: 160568. DOI: 10.1105/tpc.6.12.1877. View

11.

Sawa S, Ohgishi M, Goda H, Higuchi K, Shimada Y, Yoshida S . The HAT2 gene, a member of the HD-Zip gene family, isolated as an auxin inducible gene by DNA microarray screening, affects auxin response in Arabidopsis. Plant J. 2002; 32(6):1011-22. DOI: 10.1046/j.1365-313x.2002.01488.x. View

12.

Wang L, Yin X, Cheng C, Wang H, Guo R, Xu X . Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines. Mol Genet Genomics. 2014; 290(3):825-46. DOI: 10.1007/s00438-014-0961-y. View

13.

Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A . The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449(7161):463-7. DOI: 10.1038/nature06148. View

14.

Schena M, Davis R . Structure of homeobox-leucine zipper genes suggests a model for the evolution of gene families. Proc Natl Acad Sci U S A. 1994; 91(18):8393-7. PMC: 44612. DOI: 10.1073/pnas.91.18.8393. View

15.

Schindler U, Beckmann H, Cashmore A . HAT3.1, a novel Arabidopsis homeodomain protein containing a conserved cysteine-rich region. Plant J. 1993; 4(1):137-50. DOI: 10.1046/j.1365-313x.1993.04010137.x. View

16.

Agalou A, Purwantomo S, Overnas E, Johannesson H, Zhu X, Estiati A . A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol Biol. 2007; 66(1-2):87-103. DOI: 10.1007/s11103-007-9255-7. View

17.

Desplan C, Theis J, Ofarrell P . The sequence specificity of homeodomain-DNA interaction. Cell. 1988; 54(7):1081-90. PMC: 2753412. DOI: 10.1016/0092-8674(88)90123-7. View

18.

Zhang Y, Gao M, Singer S, Fei Z, Wang H, Wang X . Genome-wide identification and analysis of the TIFY gene family in grape. PLoS One. 2012; 7(9):e44465. PMC: 3439424. DOI: 10.1371/journal.pone.0044465. View

19.

Pabo C, Sauer R . Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem. 1992; 61:1053-95. DOI: 10.1146/annurev.bi.61.070192.005201. View

20.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View