Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species

Abstract

Background Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available. Results This study identified 55, 58, 50 and 47 VQ genes from sweetpotato (I. batatas), I.triflida, I. triloba and I. nil, respectively. The phylogenetic analysis revealed that the VQ genes formed eight clades (I–VII), and the members in the same group exhibited similar exon–intron structure and conserved motifs distribution. The distribution of the VQ genes among the chromosomes of Ipomoea species was disproportional, with no VQ genes mapped on a few of each species' chromosomes. Duplication analysis suggested that segmental duplication significantly contributes to their expansion in sweetpotato, I.trifida, and I.triloba, while the segmental and tandem duplication contributions were comparable in I.nil. Cis-regulatory elements involved in stress responses, such as W-box, TGACG-motif, CGTCA-motif, ABRE, ARE, MBS, TCA-elements, LTR, and WUN-motif, were detected in the promoter regions of the VQ genes. A total of 30 orthologous groups were detected by syntenic analysis of the VQ genes. Based on the analysis of RNA-seq datasets, it was found that the VQ genes are expressed distinctly among different tissues and hormone or stress treatments. A total of 40 sweetpotato differentially expressed genes (DEGs) refer to biotic (sweetpotato stem nematodes and Ceratocystis fimbriata pathogen infection) or abiotic (cold, salt and drought) stress treatments were detected. Moreover, IbVQ8, IbVQ25 and IbVQ44 responded to the five stress treatments and were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis. Conclusions Our study may provide new insights into the evolution of VQ genes in the four Ipomoea genomes and contribute to the future molecular breeding of sweetpotatoes.

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

“…Recently, a combined approach was adopted to study both biotic and abiotic stress responses in sweet potatoes and identified the role of IbPIF3.1 TF under drought and Fusarium wilt stresses [ 25 ]. 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 ].…”