Genome Wide Identification and Annotation of NGATHA
Transcription Factor Family in Crop Plants

J 2022

Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants

SALAVA, Hymavathi, Sravankumar THULA, Adria SANS SÁNCHEZ, Tomasz NODZYNSKI, Fatemeh MAGHULY et. al.

Základní údaje

Originální název

Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants

Autoři

SALAVA, Hymavathi, Sravankumar THULA (356 Indie, domácí), Adria SANS SÁNCHEZ (724 Španělsko, domácí), Tomasz NODZYNSKI (616 Polsko, garant, domácí) a Fatemeh MAGHULY

Vydání

International Journal of Molecular Sciences, Basel, Multidisciplinary Digital Publishing Institute, 2022, 1422-0067

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.600

Kód RIV

RIV/00216224:14740/22:00128573

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.3390/ijms23137063

UT WoS

000822132700001

Klíčová slova anglicky

transcription factor; NGATHA (NGA); phylogenetic analysis; evolution; plant development

Štítky

CF PLANT, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 3. 4. 2023 10:52, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against Arabidopsis thaliana in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (Brachypodium distachyon, Oryza sativa L. japonica, and Sorghum bicolor) family members in comparison with A. thaliana. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter cis-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes.

Návaznosti

GJ20-20860Y, projekt VaV

Název: Odhalení nových regulátorů vnitrobuněčného transportu zapojených do stresové reakce rostlin.

Investor: Grantová agentura ČR, Unravelling novel intracellular trafficking regulators involved in plant stress response.

Citovat

SALAVA, Hymavathi, Sravankumar THULA, Adria SANS SÁNCHEZ, Tomasz NODZYNSKI a Fatemeh MAGHULY. Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants. International Journal of Molecular Sciences. Basel: Multidisciplinary Digital Publishing Institute, 2022, roč. 23, č. 13, s. 7063-7084. ISSN 1422-0067. Dostupné z: https://dx.doi.org/10.3390/ijms23137063.

@article{2253405,
   author = {Salava, Hymavathi and Thula, Sravankumar and Sans Sánchez, Adria and Nodzynski, Tomasz and Maghuly, Fatemeh},
   article_location = {Basel},
   article_number = {13},
   doi = {http://dx.doi.org/10.3390/ijms23137063},
   keywords = {transcription factor; NGATHA (NGA); phylogenetic analysis; evolution; plant development},
   language = {eng},
   issn = {1422-0067},
   journal = {International Journal of Molecular Sciences},
   title = {Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants},
   url = {https://www.mdpi.com/1422-0067/23/13/7063},
   volume = {23},
   year = {2022}
}

TY  - JOUR
ID  - 2253405
AU  - Salava, Hymavathi - Thula, Sravankumar - Sans Sánchez, Adria - Nodzynski, Tomasz - Maghuly, Fatemeh
PY  - 2022
TI  - Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants
JF  - International Journal of Molecular Sciences
VL  - 23
IS  - 13
SP  - 7063
EP  - 7063
PB  - Multidisciplinary Digital Publishing Institute
SN  - 14220067
KW  - transcription factor
KW  - NGATHA (NGA)
KW  - phylogenetic analysis
KW  - evolution
KW  - plant development
UR  - https://www.mdpi.com/1422-0067/23/13/7063
N2  - The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against Arabidopsis thaliana in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (Brachypodium distachyon, Oryza sativa L. japonica, and Sorghum bicolor) family members in comparison with A. thaliana. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter cis-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes.
ER  -

SALAVA, Hymavathi, Sravankumar THULA, Adria SANS SÁNCHEZ, Tomasz NODZYNSKI a Fatemeh MAGHULY. Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants. \textit{International Journal of Molecular Sciences}. Basel: Multidisciplinary Digital Publishing Institute, 2022, roč.~23, č.~13, s.~7063-7084. ISSN~1422-0067. Dostupné z: https://dx.doi.org/10.3390/ijms23137063.

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