Dataset Information

Genome-Wide Identification and Expression Analysis of the Sucrose Synthase Gene Family in Sweet Potato and Its Two Diploid Relatives.

ABSTRACT: Sucrose synthases (SUS; EC 2.4.1.13) encoded by a small multigene family are the central system of sucrose metabolism and have important implications for carbon allocation and energy conservation in nonphotosynthetic cells of plants. Though the SUS family genes (SUSs) have been identified in several plants, they have not been explored in sweet potato. In this research, nine, seven and seven SUSs were identified in the cultivated sweet potato (Ipomoea batatas, 2n = 6x = 90) as well as its two diploid wild relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30), respectively, and divided into three subgroups according to their phylogenetic relationships. Their protein physicochemical properties, chromosomal localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction network and expression patterns were systematically analyzed. The results indicated that the SUS gene family underwent segmental and tandem duplications during its evolution. The SUSs were highly expressed in sink organs. The IbSUSs especially IbSUS2, IbSUS5 and IbSUS7 might play vital roles in storage root development and starch biosynthesis. The SUSs could also respond to drought and salt stress responses and take part in hormone crosstalk. This work provides new insights for further understanding the functions of SUSs and candidate genes for improving yield, starch content, and abiotic stress tolerance in sweet potatoes.

SUBMITTER: Jiang Z

PROVIDER: S-EPMC10420203 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Genome-Wide Identification and Expression Analysis of the Sucrose Synthase Gene Family in Sweet Potato and Its Two Diploid Relatives.

Jiang Zhicheng Z Zhang Huan H Gao Shaopei S Zhai Hong H He Shaozhen S Zhao Ning N Liu Qingchang Q

International journal of molecular sciences 20230806 15

Sucrose synthases (SUS; EC 2.4.1.13) encoded by a small multigene family are the central system of sucrose metabolism and have important implications for carbon allocation and energy conservation in nonphotosynthetic cells of plants. Though the SUS family genes (SUSs) have been identified in several plants, they have not been explored in sweet potato. In this research, nine, seven and seven SUSs were identified in the cultivated sweet potato (Ipomoea batatas, 2n</i ...[more]

PMID: 37569874

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Project description:NAC (NAM, ATAF1/2, and CUC2) proteins play a pivotal role in modulating plant development and offer protection against biotic and abiotic stresses. Until now, no systematic knowledge of NAC family genes is available for the food security crop, sweet potato. Here, a comprehensive genome-wide survey of NAC domain-containing proteins identified 130 ItbNAC and 144 ItfNAC genes with full length sequences in the genomes of two diploid wild relatives of cultivated sweet potato, Ipomoea triloba and Ipomoea trifida, respectively. These genes were physically mapped onto 15 I. triloba and 16 I. trifida chromosomes, respectively. Phylogenetic analysis divided all 274 NAC proteins into 20 subgroups together with NAC transcription factors (TFs) from Arabidopsis. There were 9 and 15 tandem duplication events in the I. triloba and I. trifida genomes, respectively, indicating an important role of tandem duplication in sweet potato gene expansion and evolution. Moreover, synteny analysis suggested that most NAC genes in the two diploid sweet potato species had a similar origin and evolutionary process. Gene expression patterns based on RNA-Seq data in different tissues and in response to various hormone, biotic or abiotic treatments revealed their possible involvement in organ development and response to various biotic/abiotic stresses. The expression of 36 NAC TFs, which were upregulated in the five tissues and in response to mannitol treatment, was also determined by real-time quantitative polymerase chain reaction (RT-qPCR) in hexaploid cultivated sweet potato exposed to drought stress. Those results largely corroborated the expression profile of mannitol treatment uncovered by the RNA-Seq data. Some significantly up-regulated genes related to drought stress, such as ItbNAC110, ItbNAC114, ItfNAC15, ItfNAC28, and especially ItfNAC62, which had a conservative spatial conformation with a closely related paralogous gene, ANAC019, may be potential candidate genes for a sweet potato drought tolerance breeding program. This analysis provides comprehensive and systematic information about NAC family genes in two diploid wild relatives of cultivated sweet potato, and will provide a blueprint for their functional characterization and exploitation to improve the tolerance of sweet potato to abiotic stresses.

Project description:BackgroundIn recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato.ResultsHere, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results.ConclusionsThis study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

Dataset Information

Genome-Wide Identification and Expression Analysis of the Sucrose Synthase Gene Family in Sweet Potato and Its Two Diploid Relatives.

Publications

Genome-Wide Identification and Expression Analysis of the Sucrose Synthase Gene Family in Sweet Potato and Its Two Diploid Relatives.

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