SMART v1.0: A Database for Small Molecules with Functional Implications in Plants

Lei, Beilei; Song, Minggui; Li, Xiyang; Dang, Xiaoxue; Qin, Runwen; Zhu, S. H.; An, Xiaoyan; Liu, Qinchang; Yao, Xiaojun; Nie, Yanming; Ma, Chuang

doi:10.1007/s12539-021-00480-1

Cited by 5 publications

(3 citation statements)

References 25 publications

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“…embl-heide lberg. de/) 51 to predict the structure of the sequence obtained in the previous step, knock out sequences that do not contain the typical SBP binding domain of MsSPL proteins, the rest of the protein sequence is regarded as a member of the MsSPL family.…”

Section: Discussionmentioning

confidence: 99%

Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses

Wang

Ruan

Zhu

et al. 2023

Sci Rep

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The SQUAMOSA promoter binding-like protein (SPL) is a specific transcription factor that affects plant growth and development. The SPL gene family has been explored in various plants, but information about these genes in alfalfa is limited. This study, based on the whole genome data of alfalfa SPL, the fundamental physicochemical properties, phylogenetic evolution, gene structure, cis-acting elements, and gene expression of members of the MsSPL gene family were analyzed by bioinformatics methods. We identified 82 SPL sequences in the alfalfa, which were annotated into 23 genes, including 7 (30.43%) genes with four alleles, 10 (43.47%) with three, 3 (13.04%) with two, 3 (13.04%) with one allele. These SPL genes were divided into six groups, that are constructed from A. thaliana, M. truncatula and alfalfa. Chromosomal localization of the identified SPL genes showed arbitary distribution. The subcellular localization predictions showed that all MsSPL proteins were located in the nucleus. A total of 71 pairs of duplicated genes were identified, and segmental duplication mainly contributed to the expansion of the MsSPL gene family. Analysis of the Ka/Ks ratios indicated that paralogs of the MsSPL gene family principally underwent purifying selection. Protein–protein interaction analysis of MsSPL proteins were performed to predict their roles in potential regulatory networks. Twelve cis-acting elements including phytohormone and stress elements were detected in the regions of MsSPL genes. We further analyzed that the MsSPLs had apparent responses to abiotic stresses such as drought and salt and the biotic stress of methyl jasmonate. These results provide comprehensive information on the MsSPL gene family in alfalfa and lay a solid foundation for elucidating the biological functions of MsSPLs. This study also provides valuable on the regulation mechanism and function of MsSPLs in response to biotic and abiotic stresses.

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Section: Discussionmentioning

confidence: 99%

Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses

Wang

Ruan

Zhu

et al. 2023

Sci Rep

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“…We removed redundant and incomplete sequences, and the remaining sequences containing the protein kinase domain (PF07690) were considered candidate NRT2 members. To further ensure the existence of NRT2 conserved structures, we reconfirmed the structures of the candidate members using the online software SMART (http://smart.embl-heidelberg.de/) 53 , HMMER (https://www.ebi.ac.uk/Tools/hmmer/) 54 and Pfam (http://pfam.xfam.org/). Finally, we obtained the members of the M. sativa NRT2 gene family, and analyzed the physicochemical properties of these genes using ExPASy (https://web.expasy.org/protparam/) 55 .…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification of high-affinity nitrate transporter 2 (NRT2) gene family in alfalfa (Medicago sativa)

Luo,

Nan

2024

Preprint

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The high-affinity nitrate transporter 2 (NRT2) proteins plays an important role in nitrate uptake and transport in plants. In this study, the NRT2s gene family was systematically analyzed in alfalfa. We showed that a total of three NRT2 members were identified from the genome database, according to their chromosomal location, they were named MsNRT2.1-2.3. The phylogenetic tree revealed that NRT2 proteins were categorized into two main subgroups, which was further confirmed by their gene structure and conserved motifs. Three MsNRT2 genes distributed on 2 chromosomes. Furthermore, we studied the expression pattern of MsNRT2 gene in six tissues based on RNA-sequencing data from the Short Read Archive (SRA) database of NCBI, and the results showed that MsNRT2 gene was widely expressed in six tissues. After treatment with drought, salt, abscisic acid (ABA) and salicylic acid (SA), We used quantitative RT-PCR to analyze the expression levels of MsNRT2 genes and the results showed that most of the MsNRT2 genes responded to these stresses. However, the individual genes play a major role under the different treatment conditions. In summary, MsNRT2 plays an irreplaceable role in the growth, development and stress response of alfalfa, and this study provides valuable information and theoretical basis for future research on MsNRT2 function.

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“…The six AtIQM and eight OsIQM protein sequences were used as query sequences to search against the kiwifruit protein databases using the BLASTP program, with an e-value of 1 × e −50 as the threshold. The conserved domains of candidate sequences were annotated using the SMART (http://smart.emblheidelberg.de/, accessed on 20 November 2023) [33] and Pfamscan (https://www.ebi.ac.uk/Tools/pfa/pfamscan/, accessed on 20 November 2023) databases [34]. Members of the kiwifruit IQM family were identified based on the presence of the complete IQ motif.…”

Section: Identification Of Kiwifruit Iqm Proteinsmentioning

confidence: 99%

Genome-Wide Identification of the IQM Gene Family and Their Transcriptional Responses to Abiotic Stresses in Kiwifruit (Actinidia eriantha)

Xu,

Zhang,

Ling

et al. 2024

Genes

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IQM is a plant-specific calcium-binding protein that plays a pivotal role in various aspects of plant growth response to stressors. We investigated the IQM gene family and its expression patterns under diverse abiotic stresses and conducted a comprehensive analysis and characterization of the AeIQMs, including protein structure, genomic location, phylogenetic relationships, gene expression profiles, salt tolerance, and expression patterns of this gene family under different abiotic stresses. Based on phylogenetic analysis, these 10 AeIQMs were classified into three distinct subfamilies (I–III). Analysis of the protein motifs revealed a considerable level of conservation among these AeIQM proteins within their respective subfamilies in kiwifruit. The genomic distribution of the 10 AeIQM genes spanned across eight chromosomes, where four pairs of IQM gene duplicates were associated with segmental duplication events. qRT-PCR analysis revealed diverse expression patterns of these AeIQM genes under different hormone treatments, and most AeIQMs showed inducibility by salt stress. Further investigations indicated that overexpression of AeIQMs in yeast significantly enhanced salt tolerance. These findings suggest that AeIQM genes might be involved in hormonal signal transduction and response to abiotic stress in Actinidia eriantha. In summary, this study provides valuable insights into the physiological functions of IQMs in kiwifruit.

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SMART v1.0: A Database for Small Molecules with Functional Implications in Plants

Cited by 5 publications

References 25 publications

Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses

Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses

Genome-wide identification of high-affinity nitrate transporter 2 (NRT2) gene family in alfalfa (Medicago sativa)

Genome-Wide Identification of the IQM Gene Family and Their Transcriptional Responses to Abiotic Stresses in Kiwifruit (Actinidia eriantha)

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