Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in four Ipomoea species

Si, Zengzhi; Wang, Lianjun; Qiao, Yunfeng; Roychowdhury, Rajib; Ji, Zhi-xin; Zhang, Kai; Han, Jinling

doi:10.3389/fpls.2022.960723

Cited by 6 publications

(6 citation statements)

References 75 publications

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“…Studies have found that some wild species are better able than cultivated species to resist biotic and abiotic stresses [ 73 , 74 , 75 ]. Therefore, the diploid relatives are valuable resources for the improvement of cultivated sweet potato [ 76 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses

Nie

Huo

Sun

et al. 2023

IJMS

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Phytochrome-interacting factors (PIFs) are essential for plant growth, development, and defense responses. However, research on the PIFs in sweet potato has been insufficient to date. In this study, we identified PIF genes in the cultivated hexaploid sweet potato (Ipomoea batatas) and its two wild relatives, Ipomoea triloba, and Ipomoea trifida. Phylogenetic analysis revealed that IbPIFs could be divided into four groups, showing the closest relationship with tomato and potato. Subsequently, the PIFs protein properties, chromosome location, gene structure, and protein interaction network were systematically analyzed. RNA-Seq and qRT-PCR analyses showed that IbPIFs were mainly expressed in stem, as well as had different gene expression patterns in response to various stresses. Among them, the expression of IbPIF3.1 was strongly induced by salt, drought, H2O2, cold, heat, Fusarium oxysporum f. sp. batatas (Fob), and stem nematodes, indicating that IbPIF3.1 might play an important role in response to abiotic and biotic stresses in sweet potato. Further research revealed that overexpression of IbPIF3.1 significantly enhanced drought and Fusarium wilt tolerance in transgenic tobacco plants. This study provides new insights for understanding PIF-mediated stress responses and lays a foundation for future investigation of sweet potato PIFs.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses

Nie

Huo

Sun

et al. 2023

IJMS

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“…These genome data contribute to the genetic study of sweet potatoes and genome evolution analysis in the Ipomoea species. In a previous study, some important enzyme-encoding genes (such as XTH, NBS, CDPK, SWEET, and SPL) [59][60][61][62][63] and TFs (such as GRAS, WRKY, bZIP, and MADS-box) [64][65][66][67][68] gene families were investigated in tuberous root development and the stress responses of Ipomoea species. However, a comprehensive and comparative molecular, evolutionary, and functional analysis of R2R3-MYB genes, which are indispensable for several developmental pathways and stress responses, is lacking in the Ipomoea species, even though the R2R3-MYB gene family has been identified in I. aquatica [69] and I. nil [70].…”

Section: Discussionmentioning

confidence: 99%

“…An interspecific collinearity analysis of R2R3-MYBs showed that a total of 1223 collinearity gene pairs were detected among hexaploid I. batatas and 5 other diploid Ipomoea species, but their collinearity relationships were not as good as expected. Given their species' phylogenetic relationships (Figure 5a), one reasonable explanation is that the hexaploid I. batatas genome might have undergone a larger chromosome rearrangement during the evolutionary process [60].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

Zhou

et al. 2023

Plants

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Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species.

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“…A total of 11 differentially expressed NBS genes were found in Tengfei and JK20 after infection by stem nematodes, and 19 differentially expressed NBS genes were found in Santiandao and JK274 after infection by C. fimbriata, respectively. These results will provide a reference for the exploration of sweet potato disease resistance genes [45]. Yan et al used sweet potato cv.…”

Section: Exploration Of Resistance Genes In Sweet Potato For Nematode...mentioning

confidence: 96%

Research Progress in the Mechanisms of Resistance to Biotic Stress in Sweet Potato

Yang,

Chen,

et al. 2023

Genes

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Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important food, feed, industrial raw materials, and new energy crops, and is widely cultivated around the world. China is the largest sweet potato producer in the world, and the sweet potato industry plays an important role in China’s agriculture. During the growth of sweet potato, it is often affected by biotic stresses, such as fungi, nematodes, insects, viruses, and bacteria. These stressors are widespread worldwide and have severely restricted the production of sweet potato. In recent years, with the rapid development and maturity of biotechnology, an increasing number of stress-related genes have been introduced into sweet potato, which improves its quality and resistance of sweet potato. This paper summarizes the discovery of biological stress-related genes in sweet potato and the related mechanisms of stress resistance from the perspectives of genomics analysis, transcriptomics analysis, genetic engineering, and physiological and biochemical indicators. The mechanisms of stress resistance provide a reference for analyzing the molecular breeding of disease resistance mechanisms and biotic stress resistance in sweet potato.

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Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in four Ipomoea species

Cited by 6 publications

References 75 publications

Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses

Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

Research Progress in the Mechanisms of Resistance to Biotic Stress in Sweet Potato

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