Genome-wide identification, characterization, and expression profiling of SPX gene family in wheat

Kumar, Anuj; Sharma, Mansi; Gahlaut, Vijay; Nagaraju, M.; Chaudhary, Shivam; Kumar, Avneesh; Tyagi, Pankaj; Gajula, Mnv Prasad; Singh, K. P.

doi:10.1016/j.ijbiomac.2019.08.105

Cited by 40 publications

(32 citation statements)

References 107 publications

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“…Multiple alignment of the SPX protein sequences from soybean, M. truncatula, common bean, Arabidopsis, rice, wheat, rapeseed, A. trichopoda, C. braunii, C. reinhardtii, C. crispus, C. merolae, G. sulphuraria, M. polymorpha, N. colorata, O. lucimarinus, P. somniferum, P. patens, and S. moellendorffii, as well as proteins from mouse, human, and Caenorhabditis elegans as an out-group, followed by phylogenetic analysis revealed four distinct clades of SPX proteins, SPX, EXS, MFS, and RING (Figure 2). This topology and distinct separation of four classes are consistent with previous studies on SPX gene family [3,12,13,27,34]. SPX…”

Section: Phylogenetic Treesupporting

confidence: 92%

“…The role of SPX domain-containing proteins in Pi homeostasis in Arabidopsis, rice, rapeseed, and wheat and to some extent in soybean and common bean were studied previously [3,13,27,[29][30][31]35]. While an evolutionary analysis of SPX-EXS [47] and SPX-MFS [24] classes has been reported, as far as we know, the evolution of all classes of SPX gene family from algae to higher plants has not been explored.…”

Section: Discussionmentioning

confidence: 99%

“…The amino acid sequences of identified SPX proteins in our surveyed species and Arabidopsis as reviewed in [6], rice [6], wheat [3], and Brassica napus [27] were downloaded from EnsemblPlants…”

Section: Phylogeny Analysis and Identification Of Conserved Motifsmentioning

confidence: 99%

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New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

Nezamivand-Chegini¹,

Ebrahimie

Tahmasebi

et al. 2021

Preprint

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BackgroundSPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes.ResultsWe analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs.ConclusionThis comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1 and AtPHO1;H1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

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Section: Phylogenetic Treesupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

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New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

Nezamivand-Chegini¹,

Ebrahimie

Tahmasebi

et al. 2021

Preprint

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“…In order to check significant similarity between the predicted genes and their corresponding genes in rice, the predicted genes were superimposed based on statistical and probability scores and root-square deviation (RMSD) using FATCAT tool (flexible structure alignment by changing fragment pairs allowing twists) 66 . To perform the expression profiling patterns of the identified leaf rolling genes under drought stress RNA-seq expression data was accessed through Wheat expression Browser ( https://www.wheat-expression.com/ ) powered by expression Visualization and Integration Platform (expVIP) 67 , 68 .…”

Section: Methodsmentioning

confidence: 99%

QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat

Verma

Niranjana

Jha

et al. 2020

Sci Rep

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Leaf rolling is an important mechanism to mitigate the effects of moisture stress in several plant species. In the present study, a set of 92 wheat recombinant inbred lines derived from the cross between NI5439 × HD2012 were used to identify QTLs associated with leaf rolling under moisture stress condition. Linkage map was constructed using Axiom 35 K Breeder’s SNP Array and microsatellite (SSR) markers. A linkage map with 3661 markers comprising 3589 SNP and 72 SSR markers spanning 22,275.01 cM in length across 21 wheat chromosomes was constructed. QTL analysis for leaf rolling trait under moisture stress condition revealed 12 QTLs on chromosomes 1B, 2A, 2B, 2D, 3A, 4A, 4B, 5D, and 6B. A stable QTL Qlr.nhv-5D.2 was identified on 5D chromosome flanked by SNP marker interval AX-94892575–AX-95124447 (5D:338665301–5D:410952987). Genetic and physical map integration in the confidence intervals of Qlr.nhv-5D.2 revealed 14 putative candidate genes for drought tolerance which was narrowed down to six genes based on in-silico analysis. Comparative study of leaf rolling genes in rice viz., NRL1, OsZHD1, Roc5, and OsHB3 on wheat genome revealed five genes on chromosome 5D. Out of the identified genes, TraesCS5D02G253100 falls exactly in the QTL Qlr.nhv-5D.2 interval and showed 96.9% identity with OsZHD1. Two genes similar to OsHB3 viz. TraesCS5D02G052300 and TraesCS5D02G385300 exhibiting 85.6% and 91.8% identity; one gene TraesCS5D02G320600 having 83.9% identity with Roc5 gene; and one gene TraesCS5D02G102600 showing 100% identity with NRL1 gene were also identified, however, these genes are located outside Qlr.nhv-5D.2 interval. Hence, TraesCS5D02G253100 could be the best potential candidate gene for leaf rolling and can be utilized for improving drought tolerance in wheat.

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“…The specific primers for SSRs were designed by Primer3 [ 91 ] and screened by e-PCR [ 92 ]. The potential MiRNAs targeting TaSCPL genes were predicted according to previously described methods [ 93 ]. Briefly, the psRNATarget server [ 57 ] was used to predict MiRNA, and MirBase 22.0 ( http://www.mirbase.org/ ) [ 94 ] was used to query the specific information of miRNAs.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response

Zhang

Zhao

et al. 2021

BMC Genomics

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Background The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family members have not yet been performed in wheat. Results In this study, we identified a total of 210 candidate genes encoding SCPL proteins in wheat. According to their structural characteristics, it is possible to divide these members into three subfamilies: CPI, CPII and CPIII. We uncovered a total of 209 TaSCPL genes unevenly distributed across 21 wheat chromosomes, of which 65.7% are present in triads. Gene duplication analysis showed that ~ 10.5% and ~ 64.8% of the TaSCPL genes are derived from tandem and segmental duplication events, respectively. Moreover, the Ka/Ks ratios between duplicated TaSCPL gene pairs were lower than 0.6, which suggests the action of strong purifying selection. Gene structure analysis showed that most of the TaSCPL genes contain multiple introns and that the motifs present in each subfamily are relatively conserved. Our analysis on cis-acting elements showed that the promoter sequences of TaSCPL genes are enriched in drought-, ABA- and MeJA-responsive elements. In addition, we studied the expression profiles of TaSCPL genes in different tissues at different developmental stages. We then evaluated the expression levels of four TaSCPL genes by qRT-PCR, and selected TaSCPL184-6D for further downstream analysis. The results showed an enhanced drought and salt tolerance among TaSCPL184-6D transgenic Arabidopsis plants, and that the overexpression of the gene increased proline and decreased malondialdehyde levels, which might help plants adapting to adverse environments. Our results provide comprehensive analyses of wheat SCPL genes that might work as a reference for future studies aimed at improving drought and salt tolerance in wheat. Conclusions We conducte a comprehensive bioinformatic analysis of the TaSCPL gene family in wheat, which revealing the potential roles of TaSCPL genes in abiotic stress. Our analysis also provides useful resources for improving the resistance of wheat.

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Genome-wide identification, characterization, and expression profiling of SPX gene family in wheat

Cited by 40 publications

References 107 publications

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat

Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response

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