Genome-Wide Identification and Expression Analysis of Expansin Gene Family in the Storage Root Development of Diploid Wild Sweetpotato Ipomoea trifida

Abstract

Expansins play important roles in root growth and development, but investigation of the expansin gene family has not yet been reported in Ipomoea trifida, and little is known regarding storage root (SR) development. In this work, we identified a total of 37 expansins (ItrEXPs) in our previously reported SR-forming I. trifida cv. Y22 genome, which included 23 ItrEXPAs, 4 ItrEXPBs, 2 ItrEXLAs and 8 ItrEXLBs. The phylogenetic relationship, genome localization, subcellular localization, gene and protein structure, promoter cis-regulating elements, and protein interaction network were systematically analyzed to reveal the possible roles of ItrEXPs in the SR development of I. trifida. The gene expression profiling in Y22 SR development revealed that ItrEXPAs and ItrEXLBs were down-regulated, and ItrEXPBs were up-regulated while ItrEXLAs were not obviously changed during the critical period of SR expansion, and might be beneficial to SR development. Combining the tissue-specific expression in young SR transverse sections of Y22 and sweetpotato tissue, we deduced that ItrEXLB05, ItrEXLB07 and ItrEXLB08 might be the key genes for initial SR formation and enlargement, and ItrEXLA02 might be the key gene for root growth and development. This work provides new insights into the functions of the expansin gene family members in I. trifida, especially for EXLA and EXLB subfamilies genes in SR development.

Genome-Wide Systematic Characterisation and Expression Analysis of Expansin Gene Family Provides Insights into Their Promising Functions in Tuberous Root Development and Stress Response in Sweetpotato (Ipomoea batatas)

“…In this study, 59 IbEXPs genes were identified from Ipomoea batatas genome, while only 37 ItfEXP genes were identified in Ipomoea trifida, suggesting that the number expansion of EXP gene family has occurred in Ipomoea batatas compared with to its diploid wild relative [55]. These 59 IbEXPs genes were divided into four subfamilies, IbEXPA, IbEXPB, IbEXLA and IbEXLB, which were similar to other plant species.…”

“…And it also ensures the food security in a lot of developing countries on account of its adaptation in various environmental conditions [53]. In previous study, 37 EXP genes were identified from Ipomoea trifida, which is the most possible diploid wild relative species of sweetpotato [55]. However, the Ipomoea trifida genome does not adequately represent the whole sweetpotato genome information.…”

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato

“…The comparative genome-wide study was performed between four Ipomoea species to evaluate valine glutamine motif-containing genes and found 40 differentially expressed genes (DEGs) referring to various abiotic stresses [ 26 ]. The other genome-wide studies in different Ipomoea species were conducted for important TF families such as NAC ( NAM , ATAF , and CUC ) TFs family [ 27 ], hydroxycinnamate-CoA quinate hydroxycinnamoyl transferase gene family [ 28 ], DNA-binding with one finger (Dof) TF family [ 29 ], myeloblastosis (MYB) gene family [ 30 ], phytochrome-interacting factors [ 25 ], domain of unknown function gene family [ 31 ], two-component system genes [ 32 ], xyloglucan endotransglucosylase/hydrolase gene family [ 33 ], expansin gene family [ 34 ], glycine-rich RNA-binding proteins [ 35 ], WRKY TFs family [ 36 ], zinc-finger domain-containing stress-associated proteins [ 37 ], plant-specific GRAS TFs [ 38 ], APETALA2/ethylene responsive factor (AP2/ERF) TFs family [ 38 ], jasmonate-ZIM (JAZ) TF family [ 39 ], and bZIP TF family [ 10 ]. These studies provide new insights for understanding the different TFs families-mediated stress responses and lays the foundation for future functional investigation of sweet potato TFs families.…”

Evolution and Expression of the Expansin Genes in Emmer Wheat

“…Expansin family genes have been found to contain two domains (DPBB_1 and Pollen_allerg_1), and show four subfamilies: EXPA (α-expansin), EXPB (β-expansin), EXLA (expansin-like A), and EXLB (expansin-like B) [ 19 , 20 , 21 ]. The differential number of expansin genes contained in many plants, such as 34 in Arabidopsis thaliana , 38 in rice ( Oryza sativa ), 37 in sweet potato ( Ipomoea batatas ), 82 in moso Bamboo ( Phyllostachys edulis ), 56, 58, and 60 in Brassica rapa , Brassica oleracea and Brassica nigra , 30 in jujube ( Ziziphus jujuba ), 36 in potato ( Solanum tuberosum ), 75 in wild soybean ( Glycine soja ), and so on [ 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. In bread wheat ( Triticum aestivum ), the genes number of expansin family has been found for several articles to be 87, 128, 241, and 104 [ 29 , 30 , 31 , 32 ].…”