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Beyond the greenhouse: coupling environmental and salt stress response reveals unexpected global transcriptional regulatory networks in Salicornia bigelovii

View ORCID ProfileHouda Chelaifa, Manikandan Vinu, Massar Dieng, View ORCID ProfileYoussef Idaghdour, Ayesha Hasan, View ORCID ProfileHector H. Hernandez
doi: https://doi.org/10.1101/2020.03.17.995720
Houda Chelaifa
1Department of Biomedical Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
5Microbial Environmental and Chemical Ecology Laboratory, Khalifa University, Abu Dhabi, United Arab Emirates
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  • ORCID record for Houda Chelaifa
Manikandan Vinu
4Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Massar Dieng
4Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Youssef Idaghdour
4Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Ayesha Hasan
1Department of Biomedical Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
2Center for Membrane and Advanced Water Technology, Khalifa University, Abu Dhabi, United Arab Emirates
3Applied Genomic Laboratory, Khalifa University, Abu Dhabi, United Arab Emirates
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Hector H. Hernandez
1Department of Biomedical Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
2Center for Membrane and Advanced Water Technology, Khalifa University, Abu Dhabi, United Arab Emirates
5Microbial Environmental and Chemical Ecology Laboratory, Khalifa University, Abu Dhabi, United Arab Emirates
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  • For correspondence: hector.hernandez@ku.ac.ae
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Abstract

Soil salinity is an increasing threat to global food production systems. As such, there is a need for salt tolerant plant model systems in order to understand salt stress regulation and response. Salicornia bigelovii, a succulent obligatory halophyte, is one of the most salt tolerant plant species in the world. It possesses distinctive characteristics that make it a candidate plant model for studying salt stress regulation and tolerance, showing promise as an economical non-crop species that can be used for saline land remediation and for large-scale biofuel production. However, available S. bigelovii genomic and transcriptomic data are insufficient to reveal its molecular mechanism of salt tolerance. We performed transcriptome analysis of S. bigelovii flowers, roots, seeds and shoots tissues cultivated under desert conditions and irrigated with saline aquaculture effluent. We identified a unique set of tissue specific transcripts present in this non-model crop. A total of 66,943 transcripts (72.63%) were successfully annotated through the GO database with 18,321 transcripts (27.38%) having no matches to known transcripts. Excluding non-plant transcripts, differential expression analysis of 49,914 annotated transcripts revealed differentially expressed transcripts (DETs) between the four tissues and identified shoots and flowers as the most transcriptionally similar tissues relative to roots and seeds. The DETs between above and below ground tissues, with the exclusion of seeds, were primarily involved in osmotic regulation and ion transportation. We identified DETs between shoots and roots implicated in salt tolerance including SbSOS1, SbNHX, SbHKT6 upregulated in shoots relative to roots, while aquaporins (AQPs) were up regulated in roots. We also noted that DETs implicated in osmolyte regulation exhibit a different profile among shoots and roots. Our study provides the first report of a highly upregulated HKT6 from S. bigelovii shoot tissue. Furthermore, we identified two BADH transcripts with divergent sequence and tissue specific expression pattern. Overall, expression of the ion transport transcripts suggests Na+ accumulation in S. bigelovii shoots. Our data led to novel insights into transcriptional regulation across the four tissues and identified a core set of salt stress-related transcripts in S. bigelovii.

Footnotes

  • (1) In the 'Environmental Conditions' results section, ion concentrations were improperly labeled and have been changed from mg / L to g / L to reflect actual readings. (2) The deposited data information has been updated to include the Short Read Archive database Bioproject and Biosample ID. (3) In the 'Funding Section, we have added New York University Abu Dhabi research grant AD105 funding data. (4) Table 1 has been modified for clarity. (5) Figure 5 legend has been modified for clarity. (6) Figure 7 legend has been modified for clarity. (7) Tables S1 and S2 in supplemental data have been modified for clarity.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 20, 2020.
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Beyond the greenhouse: coupling environmental and salt stress response reveals unexpected global transcriptional regulatory networks in Salicornia bigelovii
Houda Chelaifa, Manikandan Vinu, Massar Dieng, Youssef Idaghdour, Ayesha Hasan, Hector H. Hernandez
bioRxiv 2020.03.17.995720; doi: https://doi.org/10.1101/2020.03.17.995720
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Beyond the greenhouse: coupling environmental and salt stress response reveals unexpected global transcriptional regulatory networks in Salicornia bigelovii
Houda Chelaifa, Manikandan Vinu, Massar Dieng, Youssef Idaghdour, Ayesha Hasan, Hector H. Hernandez
bioRxiv 2020.03.17.995720; doi: https://doi.org/10.1101/2020.03.17.995720

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