Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava

Abstract

The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.

Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus

“…Additionally, some BnSRS genes contained stress-responsive, drought-inducibility, cell cycle regulation, and other related elements in the promoter region (Figure 6). These results suggest that BnSRS genes may play a crucial role in regulating hormone responses and in response to stresses, as well as growth and development, which is consistent with the SRS gene family in Cassava [61] and cotton [8].…”

“…Only the expression of BnSRS18 showed a significant increase, with a nearly 2-fold up-regulation, while the expression of BnSRS21 showed a substantial decrease, with a nearly 3-fold down-regulation (Figure 8B). These results suggested that the BnSRS genes play an important role in response to a variety of stresses, as in other species [6][7][8][9]61].…”

“…A total of 20 duplicated gene pairs were found in the BnSRS genes, with 2 pairs of both genes found within the A subgenome, 1 pair in the C subgenome, and the remaining 17 duplicated gene pairs between the 2 subgenomes (Figure 3 and Table S2). Upon analyzing these gene pairs, we found that all had non-synonymous to synonymous substitutions (Ka/Ks) values less than 1, similar to that in Cassava [61], indicating that they underwent purifying selection during the evolutionary process. In addition, 23 out of the 34 BnSRS genes had undergone WGD (whole genome duplication) or segmental, which indicated that the expansion of the BnSRS gene members mainly resulted from WGD or segmental events.…”