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© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

Background: Nitraria sibirica Pall. is one of the pioneer tree species in saline–alkali areas due to its extreme salt tolerance. However, the lack of information on its genome limits the further exploration of the molecular mechanisms in N. sibirica under salt stress. Methods: In this study, we used single-molecule real-time (SMRT) technology based on the PacBio Iso-Seq platform to obtain transcriptome data from N. sibirica under salt treatment for the first time, which is helpful for our in-depth analysis of the salt tolerance and molecular characteristics of N. sibirica. Results: Our results suggested that a total of 234,508 circular consensus sequences (CCSs) with a mean read length of 2121 bp were obtained from the 19.26 Gb raw data. Furthermore, based on transcript cluster analysis, 93,713 consensus isoforms were obtained, including 92,116 high-quality isoforms. After removing redundant sequences, 49,240 non-redundant transcripts were obtained from high-quality isoforms. A total of 37,261 SSRs, 1816 LncRNAs and 47,314 CDSs, of which 40,160 carried complete ORFs, were obtained. Based on our transcriptome data, we also analyzed the coding genes of H+-PPase, and the results of both bioinformatics and functional analyses indicated that the gene prediction via full-length transcripts obtained by SMRT technology is reliable and effective. In summary, our research data obtained by SMRT technology provides more reliable and accurate information for the further analysis of the regulatory network and molecular mechanism of N. sibirica under salt stress.

Details

Title
Full-Length Transcriptome Analysis of the Halophyte Nitraria sibirica Pall
Author
Zhang, Huilong 1   VIAFID ORCID Logo  ; Liu, Zhen 2 ; Hu, Aishuang 3 ; Wu, Haiwen 1 ; Zhu, Jianfeng 1 ; Wang, Fengzhi 2 ; Cao, Pingping 2 ; Yang, Xiuyan 1 ; Zhang, Huaxin 1 

 Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China; [email protected] (H.Z.); [email protected] (A.H.); [email protected] (H.W.); [email protected] (J.Z.); [email protected] (X.Y.); The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China 
 Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou 061001, China; [email protected] (Z.L.); [email protected] (F.W.); [email protected] (P.C.); Academy of Agriculture and Forestry Sciences, Cangzhou 061001, China 
 Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China; [email protected] (H.Z.); [email protected] (A.H.); [email protected] (H.W.); [email protected] (J.Z.); [email protected] (X.Y.); Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan 063299, China 
First page
661
Publication year
2022
Publication date
2022
Publisher
MDPI AG
e-ISSN
20734425
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2652995940
Copyright
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.