MDSi: Multi-omics Database for Setaria italica

Li, Xukai; Hou, Siyu; Feng, Minghui; Xia, Rui; Li, Jiawei; Tang, Sha; Han, Yuanhuai; Gao, Jianhua; Wang, Xingchun

doi:10.1186/s12870-023-04238-3

Cited by 15 publications

(5 citation statements)

References 34 publications

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“…Co-expression analysis can help find genes that were closely co-regulated during the physiological process. Based on the MDSI database ( Li et al., 2023 ), we constructed co-expression networks centered on the SiDIR10, SiDIR19, SiDIR20, SiDIR22, SiDIR27, and SiDIR36 . As shown in Figure 9 , we obtained a total of six co-expression networks.…”

Section: Resultsmentioning

confidence: 99%

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Genome-wide identification and expression profiling analysis of DIR gene family in Setaria italica

Gong,

Li,

Zhu

et al. 2023

Front. Plant Sci.

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Dirigent (DIR) proteins play essential roles in regulating plant growth and development, as well as enhancing resistance to abiotic and biotic stresses. However, the whole-genome identification and expression profiling analysis of DIR gene family in millet (Setaria italica (Si)) have not been systematically understood. In this study, we conducted genome-wide identification and expression analysis of the S. italica DIR gene family, including gene structures, conserved domains, evolutionary relationship, chromosomal locations, cis-elements, duplication events, gene collinearity and expression patterns. A total of 38 SiDIR members distributed on nine chromosomes were screened and identified. SiDIR family members in the same group showed higher sequence similarity. The phylogenetic tree divided the SiDIR proteins into six subfamilies: DIR-a, DIR-b/d, DIR-c, DIR-e, DIR-f, and DIR-g. According to the tertiary structure prediction, DIR proteins (like SiDIR7/8/9) themselves may form a trimer to exert function. The result of the syntenic analysis showed that tandem duplication may play the major driving force during the evolution of SiDIRs. RNA-seq data displayed higher expression of 16 SiDIR genes in root tissues, and this implied their potential functions during root development. The results of quantitative real-time PCR (RT-qPCR) assays revealed that SiDIR genes could respond to the stress of CaCl2, CdCl, NaCl, and PEG6000. This research shed light on the functions of SiDIRs in responding to abiotic stress and demonstrated their modulational potential during root development. In addition, the membrane localization of SiDIR7/19/22 was confirmed to be consistent with the forecast. The results above will provide a foundation for further and deeper investigation of DIRs.

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Section: Resultsmentioning

confidence: 99%

“…Gene expression level data of different tissues were downloaded from MDSi: Multi-omics Database for S. italica ( http://foxtail-millet.biocloud.net/page/tools/expressionVisualization ) ( Yang et al., 2020 ; Li et al., 2023 ). The heatmap was generated by TBtools software ( Chen et al., 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification and expression profiling analysis of DIR gene family in Setaria italica

Gong,

Li,

Zhu

et al. 2023

Front. Plant Sci.

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“…The foxtail millet genome, proteome, coding sequences, and GFF annotation file were downloaded from MDSi, Multi-omics Database for S. italica (http://foxtail-millet.biocloud. net/home, accessed on 26 November 2021) [33]. CLE peptide sequences of Arabidopsis (https://www.arabidopsis.org/, accessed on 26 November 2021), maize (https://maizegdb.…”

Section: Genome-wide Identification Of Sicle Genes In Foxtail Milletmentioning

confidence: 99%

“…To comprehensively understand the functions of SiCLE genes in foxtail millet, we conducted an analysis of the transcript levels of the 41 SiCLE genes in various tissues (root, stem, leaf, panicle, and spikelet) at different growth stages (three days after germination, one-tip-two-leaf stage, heading stage, filling stage, and panicle differentiation stage) in the Jingu 21 variety. We utilized publicly available transcriptome data from MDSi [33] for our analysis. The TPM values of the SiCLE genes are listed in Table S4, and a heatmap was generated to display the expression patterns of the SiCLE genes (Figure 6).…”

Section: Expression Pattern Analysis Of Sicle Genes In Different Tissuesmentioning

confidence: 99%

Genome-Wide Identification and Characterization of CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Foxtail Millet (Setaria italica L.)

Ren,

Chen,

Chen

et al. 2023

Genes

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The CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) genes encode signaling peptides that play important roles in various developmental and physiological processes. However, the systematic identification and characterization of CLE genes in foxtail millet (Setaria italica L.) remain limited. In this study, we identified and characterized 41 SiCLE genes in the foxtail millet genome. These genes were distributed across nine chromosomes and classified into four groups, with five pairs resulting from gene duplication events. SiCLE genes within the same phylogenetic group shared similar gene structure and motif patterns, while 34 genes were found to be single-exon genes. All SiCLE peptides harbored the conserved C-terminal CLE domain, with highly conserved positions in the CLE core sequences shared among foxtail millet, Arabidopsis, rice, and maize. The SiCLE genes contained various cis-elements, including five plant hormone-responsive elements. Notably, 34 SiCLE genes possessed more than three types of phytohormone-responsive elements on their promoters. Comparative analysis revealed higher collinearity between CLE genes in maize and foxtail millet, which may be because they are both C4 plants. Tissue-specific expression patterns were observed, with genes within the same group exhibiting similar and specific expression profiles. SiCLE32 and SiCLE41, classified in Group D, displayed relatively high expression levels in all tissues except panicles. Most SiCLE genes exhibited low expression levels in young panicles, while SiCLE6, SiCLE24, SiCLE25, and SiCLE34 showed higher expression in young panicles, with SiCLE24 down-regulated during later panicle development. Greater numbers of SiCLE genes exhibited higher expression in roots, with SiCLE7, SiCLE22, and SiCLE36 showing the highest levels and SiCLE36 significantly down-regulated after abscisic acid (ABA) treatment. Following treatments with ABA, 6-benzylaminopurine (6-BA), and gibberellic acid 3 (GA3), most SiCLE genes displayed down-regulation followed by subsequent recovery, while jasmonic acid (JA) and indole-3-acetic acid (IAA) treatments led to upregulation at 30 min in leaves. Moreover, identical hormone treatments elicited different expression patterns of the same genes in leaves and stems. This comprehensive study enhances our understanding of the SiCLE gene family and provides a foundation for further investigations into the functions and evolution of SiCLE genes in foxtail millet.

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“…Notably, xiaomi shares several unique features with Arabidopsis thaliana, including reduced size and shortened life cycle. Furthermore, a highly e cient Agrobacterium-mediated genetic transformation system, a high-quality genome assembly and an online multi-omics database were developed (Yang et al 2020;Li et al 2023), laying a robust foundation for establishing foxtail millet as a C 4 model plant. In 2013, Diao's group constructed a haplotype map of foxtail millet (Jia et al 2013), providing an overview of the genomic variations of foxtail millet.…”

mentioning

confidence: 99%

Identification and characterization of four novel xiaomi alleles to facilitate foxtail millet as a C4 model plant

Shan,

Duan,

Shen

et al. 2024

Plant Growth Regul

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Diverse genetic background is essential for genetic analysis and functional genomics research in model plants. In this paper, named xiaomi3, xiaomi4, xiaomi5, and xiaomi6, were identi ed and characterized in different genetic backgrounds. These mutants exhibited an extremely early heading phenotype, with heading occurring around 30-40 days after sowing under natural long-day conditions. Signi cant reductions in plant height, leaf length, leaf width, panicle length, and panicle diameter were observed in the mutants compared to their corresponding wild-types. Notably, these mutants displayed diverse panicle architectures and hull colors, effectively preventing seed mixing between them. Subsequent investigation under controlled short-day and long-day conditions con rmed the signi cant early heading phenotype of the mutants. Molecular characterization revealed mutations in the Phytochrome C (SiPHYC) gene, including transposon insertions and a frame shift mutation, were responsible for the extremely early heading phenotype. RNA-sequencing (RNA-Seq) analysis identi ed 19 differentially expressed genes associated with the extremely early heading phenotype. Additionally, genome-wide InDels and SNPs were identi ed, providing valuable resources for marker-assisted breeding and genetic studies. These ndings advance our comprehension of the genetic and molecular mechanisms underlying SiPHYC mediated photoperiod owering, and provide valuable resources that will push xiaomi as a C 4 model plant.

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MDSi: Multi-omics Database for Setaria italica

Cited by 15 publications

References 34 publications

Genome-wide identification and expression profiling analysis of DIR gene family in Setaria italica

Genome-wide identification and expression profiling analysis of DIR gene family in Setaria italica

Genome-Wide Identification and Characterization of CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Foxtail Millet (Setaria italica L.)

Identification and characterization of four novel xiaomi alleles to facilitate foxtail millet as a C4 model plant

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