Genome-wide analysis of VPE family in four Gossypium species and transcriptional expression of VPEs in the upland cotton seedlings under abiotic stresses

• Published in: Functional & integrative genomics 2022-04, Vol.22 (2), p.179-192
• Main Authors: Zhu, Liufang, Wang, Xueping, Tian, Juan, Zhang, Xinxin, Yu, Tingting, Li, Yun, Li, Dahui
• Format: Article
• Language: English
• Subjects: Abiotic stress; Animal Genetics and Genomics; Apoptosis; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Cell Biology; Cell death; Chromosomes; Genomes; Gossypium; Gossypium hirsutum; Life Sciences; Microbial Genetics and Genomics; Original Article; Phylogeny; Plant Genetics and Genomics; Seedlings; Species; Synteny; Transcription; Waterlogging
• ISSN: 1438-793X; 1438-7948
• DOI: 10.1007/s10142-021-00818-4

Vacuolar processing enzymes (VPEs) play important roles in plant development, programmed cell death, and the responsiveness to biotic and abiotic stresses. To characterize the VPE s in upland cotton ( Gossypium hirsutum ), the VPE gene family within four Gossypium species, consisting of G. hirsutum , G. barbadense , G. arboreum , and G. raimondii , together with Arabidopsis thaliana , was comparatively analyzed at the genome-wide level. As a result, a total of 43 VPE s were identified, including 13 GhVPE s, 12 GbVPE s, 7 GaVPE s, and 7 GrVPE s, which are evenly distributed with one gene on a chromosome from four Gossypium species, respectively. The phylogenetic tree showed that the identified VPE s within the four Gossypium species could be categorized into β-type, δ-type, and γ-type VPE clades. Collinearity analysis presented 36 of intraspecies VPE -pairs and 152 of interspecies VPE -pairs, respectively, which are included in synteny blocks on chromosome. These results indicate that VPE duplication events have accorded well with the whole genome duplication. And expression profiles of GhVPE s in G. hirsutum seedlings demonstrated that the GhVPEs from the same clade are not necessarily identical in the pattern of transcriptional expression. Upon abiotic stresses (i.e., waterlogging and salt treatments), three GhVPE s (i.e., Ghir_A05G004610 , Ghir_A09G011870 , and Ghir_D09G011410 ) were significantly upregulated in their expression amounts, respectively. The GhVPE genes that presented inducible expression under some abiotic stresses may be applied to the improvement of resilience to abiotic stresses for the cultivated cottons.