Abstract
TALE (Three Amino-acid Loop Extension) transcription factors belong to a large gene family in plants and are also widespread in other Eukaryotes, including animals. We have in detail studied TALE genes in the economically important crop plant pineapple (Ananas comosus) but also compared these gene sequences with other plant TALE-genes. Using the webtool HMMER we found 18 TALE gene sequences in the pineapple genome, 33 genes in rice genome and 27 genes in Arabidopsis thaliana genome, 25 genes in Brachypodium distachyon genome, 22 genes in Vitis vinifera genome and 36 genes in Populus trichocarpa genome. The found TALE genes in pineapple genome were assigned to four groups (A, B, C, and D) based on similarity. The 18 TALE genes in pineapple were located on 11 of the 25 chromosomes. Structural heterogeneity was observed for the pineapple TALE genes and number of introns varied from 1 to 3 while the number of exons was 2–4. The pineapple TALE genes showed tissue specific expression. AcoTALE1 and AcoTALE15 were highly expressed in roots while AcoTALE16, AcoTALE2, and AcoTALE18 were highly expressed in fruit tissues. AcoTALE4 and AcoTALE7 were highly expressed at two different stages of stamen development. Abiotic shock treatment revealed that AcoTALE17 and AcoTALE8 were moderately upregulated by cold shock while heat shock firmly upregulated AcoTALE16 and AcoTALE5. AcoTALE2, AcoTALE4, AcoTALE12 and AcoTALE16 was highly expressed in response to salt shock while AcoTALE5 and AcoTALE12 was upregulated in response to osmotic (mannitol) shock. None of the TALE gene was differentially regulated in response to sudden darkness. Our study, identifying these TALE transcription factors and their involvement in different stress responses lays a foundation for the possible use of genetic modifications of TALE genes for pineapple crop improvements.
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Abbreviations
- TFs:
-
Transcription factors
- ORF:
-
Open reading frame
- IP:
-
Isoelectric point
- RNA-Seq:
-
RNA sequencing
- qRT-PCR:
-
Quantitative real-time PCR
- NaCl:
-
Sodium chloride
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Acknowledgments
This work was supported by the 100 Talent Programs of Fujian Province and NSFC (U1605212).
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H. Ali performed experiments, data analysis and manuscript writing, Y. Liu and W. Li carried out bioinformatics assistance, U. Ali and I. Ali organized figures, H.J. Ashraf and Y. Jie worked on qRT-PCR, SM. Azam helped and observed RNA-Seq analysis. S. Olsson and Y. Qin conceived the study. H. Ali and S. Olsson wrote the manuscript.
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Communicated by: Hongwei Cai
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Ali, H., Liu, Y., Azam, S.M. et al. Genome Wide Identification and Expression Profiles of TALE Genes in Pineapple (Ananas comosus L). Tropical Plant Biol. 12, 304–317 (2019). https://doi.org/10.1007/s12042-019-09232-4
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DOI: https://doi.org/10.1007/s12042-019-09232-4