Genomic dissection and transcriptional profiling of Cysteine-rich receptor-like kinases in five cereals and functional characterization of TaCRK68-A

Shumayla, .; Tyagi, Shivi; Sharma, Alok; Singh, Kashmir; Upadhyay, Santosh Kumar

doi:10.1016/j.ijbiomac.2019.05.016

Cited by 56 publications

(28 citation statements)

References 61 publications

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“…Superscript III First-Strand Synthesis Super-mix (Invitrogen, USA) was used for cDNA synthesis from one microgram of RNA. By using SYBR Green and gene-specific primers (Supplementary Table S1 ) of chosen TaMSL genes, qRT-PCR was done at CFX96 Real-Time PCR (BioRad, USA) by tracking already established protocol 67 . An ADP-ribosylation factor ( TaARF1 ) was taken for the internal control and the delta-delta CT method (2-ΔΔCT) was used for calculating the expression values 68 .…”

Section: Methodsmentioning

confidence: 99%

Genome-wide characterization and expression analysis suggested diverse functions of the mechanosensitive channel of small conductance-like (MSL) genes in cereal crops

Kaur

Taneja

Tyagi

et al. 2020

Sci Rep

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Mechanosensitive ion channels are pore-forming transmembrane proteins that allow ions to move down their electrochemical gradient in response to mechanical stimuli. They participate in many plant developmental processes including the maintenance of plastid shape, pollen tube growth, etc. Herein, a total of 11, 10, 6, 30, 9, and 8 MSL genes were identified in Aegilops tauschii, Hordeum vulgare, Sorghum bicolor, Triticum aestivum, Triticum urartu, and Zea mays, respectively. These genes were located on various chromosomes of their respective cereal, while MSLs of T. urartu were found on scaffolds. The phylogenetic analysis, subcellular localization, and sequence homology suggested clustering of MSLs into two classes. These genes consisted of cis-regulatory elements related to growth and development, responsive to light, hormone, and stress. Differential expression of various MSL genes in tissue developmental stages and stress conditions revealed their precise role in development and stress responses. Altered expression during CaCl2 stress suggested their role in Ca2+ homeostasis and signaling. The co-expression analysis suggested their interactions with other genes involved in growth, defense responses etc. A comparative expression profiling of paralogous genes revealed either retention of function or pseudo-functionalization. The present study unfolded various characteristics of MSLs in cereals, which will facilitate their in-depth functional characterization in future studies.

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Section: Methodsmentioning

confidence: 99%

Genome-wide characterization and expression analysis suggested diverse functions of the mechanosensitive channel of small conductance-like (MSL) genes in cereal crops

Kaur

Taneja

Tyagi

et al. 2020

Sci Rep

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“…The prediction of duplication events was based on !80% sequence similarity, which was conducted through the bidirectional BLAST search at e-value 10 À10 . Tandem and segmental gene duplication events were classified based on distance between paralogous gene pairs as suggested in the earlier studies (Shumayla et al, 2016(Shumayla et al, , 2019Sharma et al, 2020).…”

Section: Identification Of Duplication Eventsmentioning

confidence: 99%

Genome-wide characterization and expression and co-expression analysis suggested diverse functions of WOX genes in bread wheat

Rathour

Sharma

Kaur

et al. 2020

Heliyon

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WUSCHEL-related homeobox ( WOX ) genes belong to the homeobox superfamily, are plant-specific and play vital functions in the growth and development. Herein, we identified a total of 43 TaWOX genes in the allohexaploid (AABBDD) genome of Triticum aestivum L . These genes were distributed on the various chromosomes of each subgenome (A, B and D). The phylogenetic analysis showed the clustering of TaWOXs into three clades: ancient, intermediate and modern or WUS. The gene and protein structures including exon/intron organization, intron phases, and domain and motif distribution were found to be conserved in each phylogenetic clade. The subcellular localization was predicted as nuclear. The Ka/Ks analyses suggested the purifying selection of paralogous genes. The differential expression profiling of various TaWOXs in numerous tissue developmental stages and different layers of grains suggested their role in growth and development. Moreover, a few genes exhibited modulated expression during abiotic and biotic stress conditions, which revealed their roles in stress response. The occurrence of various cis- acting regulatory elements further confirmed their role in plant development and stress tolerance. The co-expression analyses suggested the interactions of these genes with other genes, involved in various processes including plant development, signalling and stress responses. The present study reported several characteristic features of TaWOX s genes that can be useful for further characterization in future studies.

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“…Duplication events were identified using a bidirectional blast hit approach with sequence similarity ≥80%. Duplication events (tandem and segmental) were differentiated on the basis of distance as per the previous studies [88].…”

Section: Methodsmentioning

confidence: 99%

“…The Superscript III First-Strand Synthesis Supermix (Invitrogen, USA) was used to synthesize the cDNA from one microgram of total RNA. A real-time qRT-PCR was performed with the gene-specific primers of selected genes using SYBR Green at the 7900 HT Fast Real-Time PCR System (Applied Biosystems) following the method established in our laboratory [21]. The fold expression change was calculated using the delta-…”

Section: Rna Isolation Cdna Synthesis and Qrt-pcrmentioning

confidence: 99%

Molecular characterization revealed the role of thaumatin-like proteins in stress response in bread wheat

Sharma

Upadhyay

2020

Preprint

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BackgroundPR superfamily, pathogenesis related (PR) proteins divided into P1-PR17 subfamilies, is involved in the defense mechanism of plants. Thaumatin-like proteins (TLPs) are part of PR-5 family that facilitates resistance against abiotic and biotic stress responses.ResultsIn the present study, a total of 26, 27, 39, 93 and 37 TLPs with conserved signature-motif were identified in Brachypodium distachyon, Oryza sativa, Sorghum bicolor, Triticum aestivum and Zea mays, respectively. They were phylogenetically divided into 10 different clades. Majority of genes possessed one to three exons. Physicochemical analysis suggested significant differences between small and long TLPs. Majority consisted of signal peptide and localized in extracellular region. Evolutionary analyses suggested the role of duplication events in the expansion of this gene family. Tissue-specific expression of certain genes suggested their role in development, while differential expression revealed their putative roles in stress-response. The occurrence of assorted set of cis-regulatory elements further suggested their diverse functions. Co-expression analysis depicted their interaction with several stress responsive genes.ConclusionsThe detailed characterization of TLP proteins in cereals depicted their importance in combating various biotic and abiotic challenges. This study would be useful in further characterization of individual TLP genes in each plant, and various crop improvement programs in future studies.

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Genomic dissection and transcriptional profiling of Cysteine-rich receptor-like kinases in five cereals and functional characterization of TaCRK68-A

Cited by 56 publications

References 61 publications

Genome-wide characterization and expression analysis suggested diverse functions of the mechanosensitive channel of small conductance-like (MSL) genes in cereal crops

Genome-wide characterization and expression analysis suggested diverse functions of the mechanosensitive channel of small conductance-like (MSL) genes in cereal crops

Genome-wide characterization and expression and co-expression analysis suggested diverse functions of WOX genes in bread wheat

Molecular characterization revealed the role of thaumatin-like proteins in stress response in bread wheat

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