Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China.
The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China.
Genes (Basel). 2022 Apr 8;13(4):661. doi: 10.3390/genes13040661.
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 under salt stress.
In this study, we used single-molecule real-time (SMRT) technology based on the PacBio Iso-Seq platform to obtain transcriptome data from under salt treatment for the first time, which is helpful for our in-depth analysis of the salt tolerance and molecular characteristics of .
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 under salt stress.
柽柳是盐碱地区的先锋树种之一，具有极强的耐盐性。然而，由于其基因组信息的缺乏，限制了对其在盐胁迫下分子机制的进一步探索。
本研究首次利用基于 PacBio Iso-Seq 平台的单分子实时（SMRT）技术，从盐胁迫下的获取转录组数据，有助于我们深入分析的耐盐性和分子特征。
从 19.26 Gb 的原始数据中，我们共获得了 234508 条平均读长为 2121 bp 的圆形一致序列（CCS）。此外，基于转录物聚类分析，获得了 93713 个一致的同工型，包括 92116 个高质量同工型。去除冗余序列后，从高质量同工型中获得了 49240 个非冗余转录本。总共获得了 37261 个 SSRs、1816 个 LncRNAs 和 47314 个 CDSs，其中 40160 个携带完整的 ORFs。基于我们的转录组数据，我们还分析了 H-PPase 的编码基因，生物信息学和功能分析的结果表明，通过 SMRT 技术获得的全长转录本进行基因预测是可靠和有效的。总之，我们通过 SMRT 技术获得的研究数据为进一步分析在盐胁迫下的调控网络和分子机制提供了更可靠和准确的信息。
