Small Heat Shock Proteins, a Key Player in Grass Plant Thermotolerance

De novo assembly and annotation of the transcriptome of the endangered seagrass Zostera capensis: Insights from differential gene expression under thermal stress

Seagrasses are important marine ecosystem engineers but anthropogenic impacts and climate change have led to numerous population declines globally. In South Africa, Zostera capensis is endangered due to fragmented populations and heavy anthropogenic pressures on estuarine ecosystems that house the core of the populations. Addressing questions of how pressures such as climate change affect foundational species, including Z. capensis are crucial to supporting their conservation and underpin restoration efforts. Here we use ecological transcriptomics to study key functional responses of Z. capensis through quantification of gene expression after thermal stress and present the first reference transcriptome of Z. capensis. Four de novo reference assemblies (Trinity, IDBA-tran, RNAspades, SOAPdenovo) filtered through the EvidentialGene pipeline resulted in 153,755 transcripts with a BUSCO score of 66.1% for completeness. Differential expression analysis between heat stressed (32 °C for three days) and pre-warming plants identified genes involved in photosynthesis, oxidative stress, translation, metabolic and biosynthetic processes in the Z. capensis thermal stress response. This reference transcriptome is a significant contribution to the limited available genomic resources for Z. capensis and represents a vital tool for addressing questions around the species restoration and potential functional responses to warming marine environments.

Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response

Long non-coding RNAs (lncRNAs) regulate plant responses to abiotic stresses. However, the short reads produced by second-generation sequencing technology make it difficult to accurately explore full-length transcripts, limiting the study of lncRNAs. In this study, we used third-generation long-read sequencing technology with the PacBio Sequel and Illumina platform to explore the role of lncRNAs in the heat stress response of Populus x canadensis Moench trees. We using 382,034,416 short reads to correct 4,297,179 long reads by resulted in 66,657 full-length transcripts, representing 33,840 genes. Then, 753 putative lncRNAs were identified, including 658 sense lncRNAs (87.38%), 41 long intervening/intergenic non-coding RNAs (lincRNAs) (5.44%), 12 antisense lncRNAs (1.59%), and 42 sense intronic lncRNAs (5.58%). Using the criteria | log₂FC| ≥ 1 and q-value < 0.05, 3,493 genes and 78 lncRNAs were differentially expressed under the heat treatment. Furthermore, 923 genes were detected as targets of 43 differently expressed lncRNAs by cis regulation. Functional annotation demonstrated that these target genes were related to unfolded protein binding, response to stress, protein folding, and response to stimulus. Lastly, we identified a lncRNA–gene interaction network consisting of four lncRNAs and six genes [Heat Shock Protein 82 (HSP82), HSP83, Disease Resistance Protein 27 (DRL27), DnaJ family protein (DNJH), and two other predicted protein-coding genes], which showed that lncRNAs could regulate HSP family genes in response to heat stress in Populus. Therefore, our third-generation sequencing has improved the description of the P. canadensis transcriptome. The potential lncRNAs and HSP family genes identified here present a genetic resource to improve our understanding of the heat-adaptation mechanisms of trees.

Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones

Heat shock proteins (Hsps) play a key role for regulation of the changes during different stress conditions including salinity, drought, heavy metal and extreme temperature. Molecular based studies on the response mechanisms of forest trees to abiotic stresses started in 2006 when Populus trichocarpa genome sequence was completed as a model tree species. In recent years, bioinformatic analyzes have been carried out to determine functional gene regions of tree species. In this study, sHsp, Hsp40, Hsp60, Hsp90 and Hsp100 gene family members were identified in poplar genome. Some bioinformatics analyses were conducted, such as: identification of DNA/protein sequences, chromosomal localization, gene structure, calculation of genomic duplications, determination of phylogenetic groups, examination of protected motif regions, identification of gene ontology categories, modeling of protein 3D structure, determination of miRNA targeting genes, examination of sHsp, Hsp40, Hsp60, Hsp90 and Hsp100 gene family members in transcriptome data during salinity stress. As a result of bioinformatic analyzes made on P. trichocarpa genome; 60, 145, 49, 34, 12 and 90 genes belonging to members of sHsp, Hsp40, Hsp60, Hsp70, Hsp90 and Hsp100 protein families were firstly defined within the scope of this study. A total of 390 genes belonging to all Hsps gene families were characterized using different bioinformatics tools. In addition, salinity stress was applied to Populus tremula L. (Samsun) naturally grown in Turkey, Hybrid poplar species I-214 (Populus euramericana Dode. Guinier) and Black Poplar species (Populus nigra L.), Geyve and N.03.368.A clones. The expression levels of the selected Hsps genes were determined by the qRT-PCR method. After salt stress application in various poplar clones, expression levels of genes including PtsHsp-11, PtsHsp-21, PtsHsp-36, PtHsp40-113, PtHsp40-117, PtHsp60-31, PtHsp60-33, PtHsp60-38, PtHsp60-49, PtHsp70-09, PtHsp70-12, 33, PtHsp90-09, PtHsp90-12, PtHsp100-21, and PtHsp100-75 were increased. The role of the Hsps genes during salt stress has been revealed. Together with detailed bioinformatics analyses, gene expression analysis greatly contributes to understand functions of these gene family members. This research serves as a blueprint for future studies and offers a significant clue for the further study of the functions of this important gene family. Moreover, determined genes in this study can also be used for cloning studies in agricultural practices.

Transcriptional Profiling and Identification of Heat-Responsive Genes in Perennial Ryegrass by RNA-Sequencing

Perennial ryegrass (Lolium perenne) is one of the most widely used forage and turf grasses in the world due to its desirable agronomic qualities. However, as a cool-season perennial grass species, high temperature is a major factor limiting its performance in warmer and transition regions. In this study, a de novo transcriptome was generated using a cDNA library constructed from perennial ryegrass leaves subjected to short-term heat stress treatment. Then the expression profiling and identification of perennial ryegrass heat response genes by digital gene expression analyses was performed. The goal of this work was to produce expression profiles of high temperature stress responsive genes in perennial ryegrass leaves and further identify the potentially important candidate genes with altered levels of transcript, such as those genes involved in transcriptional regulation, antioxidant responses, plant hormones and signal transduction, and cellular metabolism. The de novo assembly of perennial ryegrass transcriptome in this study obtained more total and annotated unigenes compared to previously published ones. Many DEGs identified were genes that are known to respond to heat stress in plants, including HSFs, HSPs, and antioxidant related genes. In the meanwhile, we also identified four gene candidates mainly involved in C₄ carbon fixation, and one TOR gene. Their exact roles in plant heat stress response need to dissect further. This study would be important by providing the gene resources for improving heat stress tolerance in both perennial ryegrass and other cool-season perennial grass plants.