Genome‐wide identification and expression analysis of heat shock protein gene family in cassava

Abstract

Heat shock proteins are important molecular chaperones that are involved in plant growth and stress responses. However, members of the Hsp family have been poorly studied in cassava. In this study, 225 MeHsp genes were identified in the cassava genome, and their genetic structures exhibited relatively conserved features within each subfamily. The 225 MeHsp genes showed random chromosomal distribution, and at least 74 pairs of segmentally duplicated MeHsp genes. Eleven tandemly duplicated MeHsp genes were identified. Cis‐element analysis revealed the importance of MeHsps in plant adaptations to the environment. The prediction of protein interactions suggested that MeHsp70‐20 may play a critical regulatory role in the interactive network. Furthermore, the expression profiles of MeHsps in different tissues and cell subsets were analyzed using bulk transcriptomics and single‐cell transcriptomic data. Several subfamily genes exhibited unique expression patterns in the transcriptome and were selected for detailed analysis of the single‐cell transcriptome. Quantitative real‐time polymerase chain reaction (qRT‐PCR) revealed the expression patterns of these genes under temperature stress, further supporting the prediction of cis‐acting elements. This study provides valuable information for understanding the functional characteristics of MeHsp genes and the evolutionary relationships between MeHsps.

Identification of the 4CL family in cassava and expression pattern analysis of the Me4CL32 gene

“…The latest genome (M. esculenta v8.1) [21] and annotation les were downloaded from National Center for Biotechnology Information (NCBI) (https:ftp.ncbi.nlm, nih.gov/genomes/all/GCF/001/659/605/GCF_001655965.2_M.esculenta_v8); subsequently, we extracted the full-length sequence of representative cassava protein-based on the information derived from the genome and annotation les. We acquired the corresponding hidden Markov Model from the Pfam protein family database to identify members of the 4CL protein subfamily [22]. Using HMMer3.0 software with default parameters, we conducted a search against the full-length cassava protein sequence, selecting all proteins with an E-value 10 − 2 .…”

Genome-wide analysis and expression of the aquaporin gene family in Avena sativa L.

“…All AQP have a conserved hourglass structure, which comprises six transmembrane (TM) helices (TM1-TM6) formed by six a-helix bundles and five loops (Loops A-E) (TÖrnroth-Horsefield et al, 2006). Plant AQP can not only mediate the transport of water between plant tissues but also act as an ion-selective permeable membranes to effectively mediate the transmembrane transport of other small molecules, nutrient elements, and metal ions, among others, in plants and effectively improve the stress tolerance of plant by affecting the operation of small-molecule solutes such as ions, gases, and heavy metals in the plant body (Yuan, 2022). The overexpression of AtTIP5;1 in A. thaliana enhances the tolerance to boron toxicity (Pang et al, 2010); Mutations in AtNIP3;1 or AtNIP7;1 improve the tolerance to arsenate toxicity (Xu et al, 2015;Lindsay and Maathuis, 2016); and AtPIP1;2 can mediate CO 2 transport (Boudichevskaia et al, 2015).…”