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Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato.
BMC Genomics. 2017 Sep 06; 18(1):695.BG

Abstract

BACKGROUND

Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum).

RESULTS

In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment.

CONCLUSION

Systematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes.

Authors+Show Affiliations

Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea. Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea. Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, South Korea.Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, South Korea.Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea. queen@sunchon.ac.kr. Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea. queen@sunchon.ac.kr.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28874115

Citation

Khatun, Khadiza, et al. "Genome-wide Analysis and Expression Profiling of Zinc Finger Homeodomain (ZHD) Family Genes Reveal Likely Roles in Organ Development and Stress Responses in Tomato." BMC Genomics, vol. 18, no. 1, 2017, p. 695.
Khatun K, Nath UK, Robin AHK, et al. Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato. BMC Genomics. 2017;18(1):695.
Khatun, K., Nath, U. K., Robin, A. H. K., Park, J. I., Lee, D. J., Kim, M. B., Kim, C. K., Lim, K. B., Nou, I. S., & Chung, M. Y. (2017). Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato. BMC Genomics, 18(1), 695. https://doi.org/10.1186/s12864-017-4082-y
Khatun K, et al. Genome-wide Analysis and Expression Profiling of Zinc Finger Homeodomain (ZHD) Family Genes Reveal Likely Roles in Organ Development and Stress Responses in Tomato. BMC Genomics. 2017 Sep 6;18(1):695. PubMed PMID: 28874115.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato. AU - Khatun,Khadiza, AU - Nath,Ujjal Kumar, AU - Robin,Arif Hasan Khan, AU - Park,Jong-In, AU - Lee,Do-Jin, AU - Kim,Min-Bae, AU - Kim,Chang Kil, AU - Lim,Ki-Byung, AU - Nou,Ill Sup, AU - Chung,Mi-Young, Y1 - 2017/09/06/ PY - 2017/05/18/received PY - 2017/08/21/accepted PY - 2017/9/7/entrez PY - 2017/9/7/pubmed PY - 2018/4/24/medline KW - Abiotic stress KW - Fruit development KW - Organ-specific expression KW - Phytohormone KW - Solanum lycopersicum KW - ZF-HD SP - 695 EP - 695 JF - BMC genomics JO - BMC Genomics VL - 18 IS - 1 N2 - BACKGROUND: Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum). RESULTS: In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment. CONCLUSION: Systematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/28874115/Genome_wide_analysis_and_expression_profiling_of_zinc_finger_homeodomain__ZHD__family_genes_reveal_likely_roles_in_organ_development_and_stress_responses_in_tomato_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4082-y DB - PRIME DP - Unbound Medicine ER -