Genome-wide characterization and expression profiling of EIN3/EIL family genes in Zea mays

Jyoti, Subroto Das; Azim, Jaber Bin; Robin, Arif Hasan Khan

doi:10.1016/j.plgene.2020.100270

Cited by 14 publications

(12 citation statements)

References 91 publications

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“…Based on phylogenetic analysis, the EIN3/EIL proteins were classified into three groups named A, B, and C, (Figure 2; Supplementary Figures S1-S3; Supplementary Data S3-S5), which is consistent with previous reports of EIN3/EIL proteins in angiosperms (Filiz et al, 2017;He et al, 2020;Jyoti et al, 2021). Moreover, as shown in Figure 2, group C EIN3/EIL proteins were only found in angiosperm and were divided into two subgroups: monocot (C1) and dicot (C2).…”

Section: Identification and Phylogenetic Analysis Of Ein3/eil Protein...supporting

confidence: 86%

Origin, Expansion, and Divergence of ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE Transcription Factors During Streptophytes Evolution

et al. 2022

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The transition of plants to land required several regulatory adaptive mechanisms. Little is known about these mechanisms, but they no doubt involved the evolution of transcription factor (TF) families. ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) transcription factors (TFs) are core components of the ethylene signaling pathway that play important roles in almost every aspect of plant development and environmental responses by regulating the transcription of numerous genes. However, the evolutionary history of EIN3/EIL TFs, which are present in a wide range of streptophytes, is still not clear. Here, to explore the evolution and functions of EIN3/EIL TFs, we performed phylogenetic analysis of these TFs and investigated their gene and protein structures as well as sequence features. Our results suggest that the EIN3/EIL TF family was already was already present in the ancestor of streptophyte algae. Phylogenetic analysis divided the EIN3/EIL TFs into three groups (Group A–C). Analysis of gene and protein structure revealed that most of the structural features of these TFs had already formed in ancient lineages. Further investigation suggested that all groups have undergone several duplication events related to whole-genome duplications in plants, generating multiple, functionally diverse gene copies. Therefore, as plants colonized terrestrial habitats and evolved key traits, the EIN3/EIL TF family expanded broadly via multiple duplication events, which could have promoted their fundamental neo- and sub-functionalization to help plants adapt to terrestrial life. Our findings shed light on the functional evolution of the EIN3/EIL TF family in the streptophytes.

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Section: Identification and Phylogenetic Analysis Of Ein3/eil Protein...supporting

confidence: 86%

Origin, Expansion, and Divergence of ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE Transcription Factors During Streptophytes Evolution

et al. 2022

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“…Similarly, scaffold was determined for one of the EIL genes identified in P. mume (Cao et al, 2017) and G. hirsutum (Salih et al, 2020). In this study, the Pvul-EIL genes were shown to be unevenly distributed in the chromosomes of P. vulgaris, similar to previous studies on diverse plant species (Filiz et al, 2017;Jyoti et al, 2021;.…”

Section: Identification Chromosomal Localization and Duplication Anal...supporting

confidence: 84%

“…Similarly, in a study conducted by Salih et al, (2020) on cotton species, it was determined that some EIL genes did not contain introns (Salih et al, 2020). In other studies, it was observed that EIL genes mostly include exons (Cao et al, 2017;Jyoti et al, 2021;Salih et al, 2020). Furthermore, the EIL gene structures of G. max and A. thaliana were examined, and it was shown that the majority of EIL genes only had exons (Figure 2).…”

Section: Gene Structure Motif Analysis Homology Modeling and Phylogen...mentioning

confidence: 77%

“…Based on this analysis, all Pvul-EILs were predicted to be localized in the nucleus (Table 1). Similarly, EIL proteins from G. max , T. aestivum (Yi-Qin et al, 2020), P. trichocarpa (Filiz et al, 2017), and Z. mays (Jyoti et al, 2021) species have also been reported to be localized in the nucleus. Instability index values of all Pvul-EIL members except Pvul-EIL-1 were found to be above 40.…”

Section: Identification Chromosomal Localization and Duplication Anal...mentioning

confidence: 92%

“…In this study, 11 EIL genes/proteins were identified and these EIL genes were named from Pvul-EIL-1 to Pvul-EIL-11 (Table 1). The number of EIL genes in P. vulgaris was found to be more than Arabidopsis thaliana (n = 6) (Chao et al, 1997), Prunus mume (n = 5), Prunus persica (n = 4), Fragaria vesca (n = 5) (Cao et al, 2017), Zea mays (n = 9) (Jyoti et al, 2021), but less than the number of members identified in Gossypium hirsutum (n = 18) (Salih et al, 2020), Glycine max (n = 12) and Triticum aestivum (n = 21) (Yi-Qin et al, 2020).…”

Section: Identification Chromosomal Localization and Duplication Anal...mentioning

confidence: 99%

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EIN3/EIL (Ethylene Insensitive3 / Ethylene Insensitive3 Like) Protein Family in Phaseolus vulgaris: Identification, Evolution and Expression Analysis within the Genome

Akbulut

Şafak

Okay

et al. 2023

Turkish JAF Sci.Tech.

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Ethylene insensitive-3 (EIN3) / Ethylene insensitive-3-like (EIL) protein family is a small family of transcription factors specific to plants that play role in plant growth and development under various environmental conditions. In this study, various bioinformatics approaches were used to make an in-depth identification of the EIN3/EIL family at both the gene and protein levels. So, 11 Pvul-EIL genes were identified and their approximate locations were determined. Various biochemical and physicochemical properties of EIL proteins in Phaseolus vulgaris have been described. It was determined that Pvul-EIL proteins had a length of 447-651 amino acids and a molecular weight of 51.08-70.68 kDa. All duplications occurring in the Pvul-EIL genome were segmental type. It was observed that conserved motif, gene structure and phylogeny analyses all yielded similar results. For instance, it has been understood that genes with same motif type and number have similar gene structures and were located under the same branch in the phylogenetic tree. Pvul-EIL protein homology modeling showed that DNA binding properties and protein structure were similar to Arabidopsis EIN3. According to cis-element analysis, Pvul-EIL genes are engaged in a wide range of functions, including tissue-specific, stress, and hormone-sensitive expression. Additionally, RNAseq data was used to perform a comparative expression analysis of EIL genes. Various Pvul-EIL gene expression levels were detected under salt and drought stress. This is the first study to check the gene expression levels in P. vulgaris using in-silico detection and characterization of EIL genes. Therefore, obtained results can form the basis for future studies.

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Reduction of ethylene biosynthesis in sugarcane induces growth and investment in the non-enzymatic antioxidant apparatus

et al. 2022

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Genome-wide characterization and expression profiling of EIN3/EIL family genes in Zea mays

Cited by 14 publications

References 91 publications

Origin, Expansion, and Divergence of ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE Transcription Factors During Streptophytes Evolution

Origin, Expansion, and Divergence of ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE Transcription Factors During Streptophytes Evolution

EIN3/EIL (Ethylene Insensitive3 / Ethylene Insensitive3 Like) Protein Family in Phaseolus vulgaris: Identification, Evolution and Expression Analysis within the Genome

Reduction of ethylene biosynthesis in sugarcane induces growth and investment in the non-enzymatic antioxidant apparatus

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