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Genome-wide analysis of Fragaria vesca three-amino-acid-loop-extension (TALE) genes

Year 2021, Volume: 30 Issue: 2, 79 - 85, 15.12.2021

Gizem Kabak Seray Şehsuvar Sıla Turgut Şeyma Gökdemir

https://doi.org/10.38042/biotechstudies.977788
Cited By: 1

Abstract

The present study is aimed to identify and characterize the three-amino-acid-loop- extension (TALE) genes in Fragaria vesca as bioinformatics. TALE superclass homeoproteins have important roles in regulating certain signal pathways in the plant system. However, there is no knowledge about the role of TALE genes in Fragaria vesca. According to this study, a total of 18 candidate FvescaTale genes were identified. Identification of motifs, exon and intron analysis, genome mapping, localization in the cell, three-dimensional modeling, and ontology analysis were made according to these genes. This bioinformatic analysis revealed that FvescaTale genes might play an important role in stress response for Fragaria vesca cultivars and suggests that these genes could be used as functional markers for in silico analysis for future studies.

Keywords

TALE Fragaria vesca Genome-wide identification

References

  • Akam, M. (1993). Evolutionary conservation of developmental mechanisms: edited by Allan Spradling, Wiley-Liss, 1993. $98.00 (xii+ 219 pages) ISBN 0 471 58843 1.
  • Ariel, F. D., Manavella, P. A., Dezar, C. A., & Chan, R. L. (2007). The true story of the HD-Zip family. Trends in Plant Science, 12(9), 419–426. https://doi.org/10.1016/j.tplants.2007.08.003
  • Burglin, T. R. (1997). Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. Nucleic Acids Res. 25:4173–4180. https://doi.org/10.1093/nar/25.21.4173
  • Chen, H. (2003). Interacting Transcription Factors from the Three-Amino Acid Loop Extension Superclass Regulate Tuber Formation. Plant Physiology, 132(3), 1391–1404. https://doi.org/10.1104/pp.103.022434 Darrow, G. M. (1966). The strawberry. History, breeding and physiology. The strawberry. History, breeding and physiology. https://doi.org/10.1104/pp.103.022434
  • Hamant, O., & Pautot, V. (2010). Plant development: a TALE story. Comptes rendus biologies, 333(4), 371-381. https://doi.org/10.1016/j.crvi.2010.01.015
  • Hay, A., & Tsiantis, M. (2010). KNOX genes: versatile regulators of plant development and diversity. Development, 137(19), 3153–3165. https://doi.org/10.1242/dev.030049
  • Hirano, K., Kondo, M., Aya, K., Miyao, A., Sato, Y., Antonio, B. A., Namiki, N., Nagamura, Y., & Matsuoka, M. (2013). Identification of transcription factors involved in rice secondary cell wall formation. Plant and CellPhysiology, 54(11), 1791-1802. https://doi.org/10.1093/pcp/pct122
  • Li, Y., Pi, M., Gao, Q., Liu, Z., & Kang, C. (2019). Updated annotation of the wild strawberry Fragaria vesca V4 genome. Horticulture Research, 6(1). https://doi.org/10.1038/s41438-019-0142-6
  • Liu, Y., You, S., Taylor-Teeples, M., Li, W. L., Schuetz, M., Brady, S. M., & Douglas, C. J. (2014). BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 interact and regulate secondary cell wall formation via repression of REVOLUTA. The Plant Cell, 26(12), 4843-4861. https://doi.org/10.1105/tpc.114.128322
  • Ma, Q., Wang, N., Hao, P., Sun, H., Wang, C., Ma, L., Wang, H., Zhang, X., Wei, H., & Yu, S. (2019). Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis. BMC plant biology, 19(1), 1-20. https://doi.org/10.1186/s12870-019-2026-1
  • Morino, Y., Hashimoto, N., & Wada, H. (2017). Expansion of TALE homeobox genes and the evolution of spiralian development. Nature ecology & evolution, 1(12), 1942- 1949. https://doi.org/10.1038/s41559-017-0351-z
  • Reiser, L., Modrusan, Z., Margossian, L., Samach, A., Ohad, N., Haughn, G. W., & Fischer, R. L. (1995). The BELL1 gene encodes a homeodomain protein involved in pattern formation in the Arabidopsis ovule primordium. Cell, 83(5), 735-742. https://doi.org/10.1016/0092-8674(95)90186-8
  • Rutjens, B., Bao, D., Van Eck‐Stouten, E., Brand, M., Smeekens, S., & Proveniers, M. (2009). Shoot apical meristem function in Arabidopsis requires the combined activities of three BEL1‐like homeodomain proteins. The Plant Journal, 58(4), 641-654. https://doi.org/10.1111/j.1365- 313X.2009.03809.x
  • Shulaev, V., Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., ... & Folta, K. M. (2011). The Genome of Woodland Strawberry (Fragaria Vesca). Nature Genetics, 43(2), 109-16. https://doi.org/10.1038/ng.740

Year 2021, Volume: 30 Issue: 2, 79 - 85, 15.12.2021

Gizem Kabak Seray Şehsuvar Sıla Turgut Şeyma Gökdemir

https://doi.org/10.38042/biotechstudies.977788
Cited By: 1

Abstract

References

  • Akam, M. (1993). Evolutionary conservation of developmental mechanisms: edited by Allan Spradling, Wiley-Liss, 1993. $98.00 (xii+ 219 pages) ISBN 0 471 58843 1.
  • Ariel, F. D., Manavella, P. A., Dezar, C. A., & Chan, R. L. (2007). The true story of the HD-Zip family. Trends in Plant Science, 12(9), 419–426. https://doi.org/10.1016/j.tplants.2007.08.003
  • Burglin, T. R. (1997). Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. Nucleic Acids Res. 25:4173–4180. https://doi.org/10.1093/nar/25.21.4173
  • Chen, H. (2003). Interacting Transcription Factors from the Three-Amino Acid Loop Extension Superclass Regulate Tuber Formation. Plant Physiology, 132(3), 1391–1404. https://doi.org/10.1104/pp.103.022434 Darrow, G. M. (1966). The strawberry. History, breeding and physiology. The strawberry. History, breeding and physiology. https://doi.org/10.1104/pp.103.022434
  • Hamant, O., & Pautot, V. (2010). Plant development: a TALE story. Comptes rendus biologies, 333(4), 371-381. https://doi.org/10.1016/j.crvi.2010.01.015
  • Hay, A., & Tsiantis, M. (2010). KNOX genes: versatile regulators of plant development and diversity. Development, 137(19), 3153–3165. https://doi.org/10.1242/dev.030049
  • Hirano, K., Kondo, M., Aya, K., Miyao, A., Sato, Y., Antonio, B. A., Namiki, N., Nagamura, Y., & Matsuoka, M. (2013). Identification of transcription factors involved in rice secondary cell wall formation. Plant and CellPhysiology, 54(11), 1791-1802. https://doi.org/10.1093/pcp/pct122
  • Li, Y., Pi, M., Gao, Q., Liu, Z., & Kang, C. (2019). Updated annotation of the wild strawberry Fragaria vesca V4 genome. Horticulture Research, 6(1). https://doi.org/10.1038/s41438-019-0142-6
  • Liu, Y., You, S., Taylor-Teeples, M., Li, W. L., Schuetz, M., Brady, S. M., & Douglas, C. J. (2014). BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 interact and regulate secondary cell wall formation via repression of REVOLUTA. The Plant Cell, 26(12), 4843-4861. https://doi.org/10.1105/tpc.114.128322
  • Ma, Q., Wang, N., Hao, P., Sun, H., Wang, C., Ma, L., Wang, H., Zhang, X., Wei, H., & Yu, S. (2019). Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis. BMC plant biology, 19(1), 1-20. https://doi.org/10.1186/s12870-019-2026-1
  • Morino, Y., Hashimoto, N., & Wada, H. (2017). Expansion of TALE homeobox genes and the evolution of spiralian development. Nature ecology & evolution, 1(12), 1942- 1949. https://doi.org/10.1038/s41559-017-0351-z
  • Reiser, L., Modrusan, Z., Margossian, L., Samach, A., Ohad, N., Haughn, G. W., & Fischer, R. L. (1995). The BELL1 gene encodes a homeodomain protein involved in pattern formation in the Arabidopsis ovule primordium. Cell, 83(5), 735-742. https://doi.org/10.1016/0092-8674(95)90186-8
  • Rutjens, B., Bao, D., Van Eck‐Stouten, E., Brand, M., Smeekens, S., & Proveniers, M. (2009). Shoot apical meristem function in Arabidopsis requires the combined activities of three BEL1‐like homeodomain proteins. The Plant Journal, 58(4), 641-654. https://doi.org/10.1111/j.1365- 313X.2009.03809.x
  • Shulaev, V., Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., ... & Folta, K. M. (2011). The Genome of Woodland Strawberry (Fragaria Vesca). Nature Genetics, 43(2), 109-16. https://doi.org/10.1038/ng.740
There are 14 citations in total.

Details

Primary Language English
Subjects Horticultural Production
Journal Section Research Articles
Authors

Gizem Kabak This is me

Seray Şehsuvar This is me

Sıla Turgut This is me

Şeyma Gökdemir

Publication Date December 15, 2021
Published in Issue Year 2021 Volume: 30 Issue: 2

Cite

APA Kabak, G., Şehsuvar, S., Turgut, S., Gökdemir, Ş. (2021). Genome-wide analysis of Fragaria vesca three-amino-acid-loop-extension (TALE) genes. Biotech Studies, 30(2), 79-85. https://doi.org/10.38042/biotechstudies.977788

Cited By

Genome-Wide Classification and Evolutionary Analysis of the KNOX Gene Family in Plants
Horticulturae
https://doi.org/10.3390/horticulturae9111174
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