Full-Length Transcriptome Analysis of the Halophyte Nitraria sibirica Pall

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.

The first released available genome of the common ice plant (Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C3-CAM photosynthetic conversion, and halophilism

“…The richest PKinase subfamily was “receptor-like kinase/Pelle, DUF26, SD-1, LRR-VIII and VWA, a moss-specific new RLK subfamily (RLK-Pelle_DLSV)”, containing primarily receptor-type kinases, which was consistent with the transcriptome profiling in a halophyte, Nitraria sibrica ( Zhang et al 2022 ). It has been assumed to be involved in cell wall biosynthesis, adhesion, and developmental regulation.…”

A whole-genome shotgun assembly for genome characterization of the common ice plant (Mesembryanthemum crystallinum L.)

“…The richest PKinase subfamily was "receptor-like kinase/Pelle, DUF26, SD-1, LRR-VIII and VWA, a mossspeci c new RLK subfamily" (RLK-Pelle_DLSV), containing primarily receptor-type kinases, which was consistent with the transcriptome pro ling in a halophyte, Nitraria sibrica 29 . It has been assumed to be involved in cell wall biosynthesis, adhesion, and developmental regulation.…”

Integrating Full-Length and Second-Generation Transcriptomics to Reveal Differentially Expressed Genes Associated with the Development of Corydalis yanhusuo Tuber

“…The obtained fulllength transcripts from different tissues can provide more information about C. yanhusuo. The obtained full-length transcriptome data may provide more reliable and complete mRNA information in the organism [34,35]. A total of 63.11% of the unigenes were annotated with M. cordata.…”