Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

BACKGROUND

The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies.

RESULTS

In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments.

CONCLUSIONS

Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.

Full-Length Transcriptome Analysis of the Halophyte Nitraria sibirica Pall

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.

Improvement of a Traditional Orphan Food Crop, Portulaca oleracea L. (Purslane) Using Genomics for Sustainable Food Security and Climate-Resilient Agriculture

Purslane (Portulaca oleracea L.) is a popular orphan crop used for its nutritional properties in various parts of the world. It is considered one of the richest terrestrial sources of omega-3 and omega-6-fatty acids (ω-3 and 6-FAs) suggesting its importance for human health. This ethnomedicinal plant is also an important part of traditional healing systems among the indigenous people. Many studies have indicated its tolerance against multiple stresses and found that it easily grows in a range of environmental gradients. It has also been considered one of the important biosaline crops for the future. Despite its huge nutritional, economic, and medicinal importance, it remains neglected to date. Most of the studies on purslane were focused on its ethnomedicinal, phytochemical, pharmacological, and stress-tolerance properties. Only a few studies have attempted genetic dissection of the traits governing these traits. Purslane being an important traditional food crop across the globe can be valorized for a sustainable food security in the future. Therefore, this review is an attempt to highlight the distribution, domestication, and cultivation of purslane and its importance as an important stress-tolerant food and a biosaline crop. Furthermore, identification of genes and their functions governing important traits and its potential for improvement using genomics tools for smart and biosaline agriculture has been discussed.