Genomic Survey, Gene Expression, and Interaction Analysis Suggest Diverse Roles of ARF and Aux/IAA Proteins in Solanaceae

Kumar, Rahul; Agarwal, Priyanka; Pareek, Amit; Tyagi, Akhilesh K.; Sharma, Arun Kumar

doi:10.1007/s11105-015-0856-z

Cited by 31 publications

(28 citation statements)

References 70 publications

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“…However, the presence of two homologs each for SlMET1, SlCMT3, and SlDRM5 in pepper supported the earlier observations that expansion of these genes might have occurred through unequal gene duplication events, postSolanum-Capsicum speciation, resulting in different gene repertoires even in closely related species (Kim et al 2014, Wu et al 2009). The evolution of DMTase gene family members was further studied by comparing the gene structures of tomato syntelogs in potato and pepper, as studied previously for other genes in tomato (Kumar et al 2015). This analysis revealed that while tomato and potato homologs were conserved Fig.…”

Section: Discussionmentioning

confidence: 95%

“…A name search and hidden Markov model (HMM) analysis methods were employed against the genomic and protein datasets of tomato, Solanum pennellii, potato, eggplant, pepper, and Nicotiana benthamiana to identify DMTase genes (Kumar et al , 2015. The respective Bprotein.fasta^files were downloaded from either BENSEMBL Plants( http://plants.ensembl.org/index.html), BPhytozome v11.0( http://www.phytozome.net/), or SGN repository databases and searched for HMM profile of DMTases.…”

Section: Identification Of Dmtases In Solanaceaementioning

confidence: 99%

“…Tomato plants (Solanum lycopersicum cv Pusa Ruby) were grown under a daily photoperiodic regime of 16-h light/8-h dark in a greenhouse, as described earlier (Kumar et al 2015). For cold treatment, soil-grown 2-week-old seedlings were subjected to either 4°C for 8 and 24 h, whereas heat treatment was given by subjecting seedlings to 2 and 8 h at 40°C.…”

Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

“…nature.com/nature/journal/v475/n7355/extref/nature10158-s1.pdf) (Xu et al 2011). Expression profiles of tomato DMTases under heat, cold, and salt stresses were studied by employing the quantitative real-time PCR (qPCR) (Kumar et al 2015). GAPDH and SAND genes were used as an internal control for qPCR analysis.…”

Section: Gene Expression Analysismentioning

confidence: 99%

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Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Kumar

Chauhan

Khurana

2016

Funct Integr Genomics

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DNA methyltransferase (DMTase) enzymes contribute to plant development and stress responses by de novo establishment and subsequent maintenance of DNA methylation during replication. However, the molecular mechanism underlying this activity remains obscure, especially in crop species. Using DMTase homolog complement in six Solanaceae species, we demonstrated here that their number remained conserved in Solanum lineage, whereas it was expanded in both pepper and Nicotiana benthamiana. Non-synonymous vs synonymous (Ka/Ks) substitution ratio revealed that most of the Solanaceous DMTase homologs undergo purifying selection. The genomic sequences of tomato DMT homologs in its wild relative, Solanum pennellii, remained highly conserved in their exons and methyltransferase domains. Structure analysis further revealed highly similar folding of DMTase homologs and conservation in the residues participating in protein-protein interaction in Solanum lineage, whereas a considerable diversification was observed of pepper homologs. Transcript profiling of DMTases highlighted both similar and distinct expression patterns of tomato homologs in other species during fruit development and stress responses. Overall, our analysis provides a strong basis for in-depth exploration of both conserved as well as distinct functions of tomato DMTase homologs in other economically important Solanaceae species.

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Section: Discussionmentioning

confidence: 95%

Section: Identification Of Dmtases In Solanaceaementioning

confidence: 99%

Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

Section: Gene Expression Analysismentioning

confidence: 99%

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Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Kumar

Chauhan

Khurana

2016

Funct Integr Genomics

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“…In the case of cold and heat stresses, 1 µg RNA each from the two stages of treatments were mixed in equimolar concentration before cDNA preparation. The expression of gene was quantified by SYBR‐green‐based standard method following the methodology reported earlier (Kumar et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

Evolutionary Profiling of Group II Pyridoxal‐Phosphate‐Dependent Decarboxylases Suggests Expansion and Functional Diversification of Histidine Decarboxylases in Tomato

Kumar

Jiwani²,

Pareek³

et al. 2016

The Plant Genome

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Pyridoxal phosphate (PLP)-dependent enzymes are one of the most important enzymes involved in plant N metabolism. Here, we explored the evolution of group II PLP-dependent decarboxylases (PLP_deC), including aromatic L-amino acid decarboxylase, glutamate decarboxylase, and histidine decarboxylase in the plant lineage. Gene identification analysis revealed a higher number of genes encoding PLP_deC in higher plants than in lower plants. Expression profiling of PLP_deC orthologs and syntelogs in Arabidopsis thaliana (L.) Heynh., pepper (Capsicum annuum L.), and tomato (Solanum lycopersicum L.) pointed toward conserved as well as distinct roles in developmental processes such as fruit maturation and ripening and abiotic stress responses. We further characterized a putative promoter of tomato ripeningassociated gene (SlHDC10) operating in a complex regulatory circuit. Our analysis provides a firm basis for further in-depth exploration of the PLP_deC gene family, particularly in the economically important Solanaceae family.

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Auxins in potato: molecular aspects and emerging roles in tuber formation and stress resistance

et al. 2019

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Genomic Survey, Gene Expression, and Interaction Analysis Suggest Diverse Roles of ARF and Aux/IAA Proteins in Solanaceae

Cited by 31 publications

References 70 publications

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Evolutionary Profiling of Group II Pyridoxal‐Phosphate‐Dependent Decarboxylases Suggests Expansion and Functional Diversification of Histidine Decarboxylases in Tomato

Auxins in potato: molecular aspects and emerging roles in tuber formation and stress resistance

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