Dataset Information

Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida.

ABSTRACT:

Background

The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved transcription factor families. In addition to being involved in growth and development, bZIP transcription factors also play an important role in plant adaption to abiotic stresses.

Results

A total of 41 bZIP genes that encode 66 proteins were identified in Ipomoea trifida. They were distributed on 14 chromosomes of Ipomoea trifida. Segmental and tandem duplication analysis showed that segmental duplication played an important role in the ItfbZIP gene amplification. ItfbZIPs were divided into ten groups (A, B, C, D, E, F, G, H, I and S groups) according to their phylogenetic relationships with Solanum lycopersicum and Arabidopsis thaliana. The regularity of the exon/intron numbers and distributions is consistent with the group classification in evolutionary tree. Prediction of the cis-acting elements found that promoter regions of ItfbZIPs harbored several stress responsive cis-acting elements. Protein three-dimensional structural analysis indicated that ItfbZIP proteins mainly consisted of α-helices and random coils. The gene expression pattern from transcriptome data and qRT-PCR analysis showed that ItfbZIP genes expressed with a tissue-specific manner and differently expressed under various abiotic stresses, suggesting that the ItfbZIPs were involved in stress response and adaption in Ipomoea trifida.

Conclusions

Genome-wide identification, gene structure, phylogeny and expression analysis of bZIP gene in Ipomoea trifida supplied a solid theoretical foundation for the functional study of bZIP gene family and further facilitated the molecular breeding of sweet potato.

SUBMITTER: Yang Z

PROVIDER: S-EPMC6482516 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BACKGROUND:Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. RESULTS:Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. CONCLUSIONS:We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

Project description:MADS-box gene, one of the largest transcription factor families in plants, is a class of transcription factors widely present in eukaryotes. It plays an important role in plant growth and development and participates in the growth and development of flowers and fruits. Sweet potato is the seventh most important food crop in the world. Its tuberous roots, stems, and leaves contain a large number of proteins, lipids, carotenoids, anthocyanins, conjugated phenolic acids, and minerals, which have high edible, forage, and medicinal value, and is also an important energy crop. At present, MADS-box genes in sweet potato have rarely been reported, and there has been no study on the genome-wide identification and classification of MADS-box genes in Ipomoea batatas. This study provided the first comprehensive analysis of sweet potato MADS-box genes. We identified 95 MADS-box genes, analyzed the structure and protein of sweet potato MADS-box genes, and categorized them based on phylogenetic analysis with Arabidopsis MADS-box proteins. Chromosomal localization indicated an unequal number of MADS-box genes in all 14 chromosomes except LG3, with more than 10 MADS-box genes located on chromosomes LG7, LG11, and LG15. The MADS domain and core motifs of the sweet potato MADS-box genes were identified by motif analysis. We identified 19 MADS-box genes with collinear relationships and analyzed duplication events. Cis-acting elements, such as light-responsive, auxin-responsive, drought-inducible, and MeJA-responsive elements, were found in the promoter region of the MADS-box genes in sweet potato, which further indicates the basis of MADS-box gene regulation in response to environmental changes and hormones. RNA-seq suggested that sweet potato MADS-box genes exhibit tissue-specific expression patterns, with 34 genes highly expressed in sweet potato flowers and fruits, and 19 genes highly expressed in the tuberous root, pencil root, or fibrous root. qRT-PCR again validated the expression levels of the 10 genes and found that IbMADS1, IbMADS18, IbMADS19, IbMADS79, and IbMADS90 were highly expressed in the tuberous root or fibrous root, and IbMADS18, IbMADS31, and IbMADS83 were highly expressed in the fruit. In this study, the molecular basis of MADS-box genes of sweet potato was analyzed from various angles. The effects of MADS-box genes on the growth and development of sweet potato were investigated, which may provide a certain theoretical basis for molecular breeding of sweet potato.

Project description:BackgroundCytochrome P450 monooxygenases (CYP450s) play a crucial role in various biochemical reactions involved in the synthesis of antioxidants, pigments, structural polymers, and defense-related compounds in plants. As sweet potato (Ipomoea batatas L.) holds significant economic importance, a comprehensive analysis of CYP450 genes in this plant species can offer valuable insights into the evolutionary relationships and functional characteristics of these genes.ResultsIn this study, we successfully identified and categorized 95 CYP450 genes from the sweet potato genome into 5 families and 31 subfamilies. The predicted subcellular localization results indicate that CYP450s are distributed in the cell membrane system. The promoter region of the IbCYP450 genes contains various cis-acting elements related to plant hormones and stress responses. In addition, ten conserved motifs (Motif1-Motif10) have been identified in the IbCYP450 family proteins, with 5 genes lacking introns and only one exon. We observed extensive duplication events within the CYP450 gene family, which may account for its expansion. The gene duplication analysis results showed the presence of 15 pairs of genes with tandem repeats. Interaction network analysis reveals that IbCYP450 families can interact with multiple target genes and there are protein-protein interactions within the family. Transcription factor interaction analysis suggests that IbCYP450 families interact with multiple transcription factors. Furthermore, gene expression analysis revealed tissue-specific expression patterns of CYP450 genes in sweet potatoes, as well as their response to abiotic stress and plant hormones. Notably, quantitative real-time polymerase chain reaction (qRT‒PCR) analysis indicated the involvement of CYP450 genes in the defense response against nonbiological stresses in sweet potatoes.ConclusionsThese findings provide a foundation for further investigations aiming to elucidate the biological functions of CYP450 genes in sweet potatoes.