Genome-Wide Analysis and Characterization of SABATH Gene Family in Phaseolus vulgaris Genotypes Subject to Melatonin under Drought and Salinity Stresses

AYGÖREN, Ahmed Sidar; Güneş, Ebru; Muslu, Selman; KASAPOĞLU, Ayşe Gül; Yiğider, Esma; Aydın, Murat; Büyük, İlker; İlhan, Emre

doi:10.1007/s11105-022-01363-5

Cited by 9 publications

(4 citation statements)

References 64 publications

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“…Gene duplication, including tandem and segmental duplications, is one of the essential driving strengths in the evolution of genomes (Kasapoğlu et al, 2022). When Ka/Ks<1, it indicates purifying selection, when Ka/Ks=1, it indicates natural selection, and when Ka/Ks>1, it indicates positive selection during the evolution of the gene sequence (İlhan, 2018;Aygören et al, 2022;Oner et al, 2022). As a result of our research, the Ka/Ks ratios of segmentally duplicated genes were found to be less than 1.…”

Section: Discussionmentioning

confidence: 60%

Genome-Wide Analysis and Characterization of FBA (Fructose 1,6-bisphosphate aldolase) Gene Family of Phaseolus vulgaris L

Uçar,

Alım,

Kasapoğlu

et al. 2024

Journal of Agricultural Production

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Fructose-1,6-biphosphate aldolase (FBA) genes have important roles in plant stress responses. At the same time, these genes positively affect growth and development in plants. FBA is involved in gluconeogenesis, glycolysis, and the Calvin-Benson cycle, and it is an enzyme that plays an important role in signal transduction of these stages. This study aims to determine and characterize the FBA gene family in the bean genome. As a result of the study, 7 Pvul-FBA genes were determined in the bean (Phaseolus vulgaris L.) genome. The highest amino acid number of Pvul-FBA proteins was determined in the Pvul-FBA-1 gene (1374), and the highest molecular weight (43.03 kDa) was determined in the Pvul-FBA-7 gene. Again, the highest isoelectric point (8.03) was determined in the Pvul-FBA-3 gene. It has been determined that the Pvul-FBA-6/Pvul-FBA-7 genes are segmental duplicated genes. The main four groups were obtained according to the phylogenetic analysis consisting of FBA proteins of three plants (P. vulgaris, Glycine max, and Arabidopsis thaliana). As a result of interproscan analysis, Motif-1, 2, 3, 4 and 5 were found to contain the fructose-bisphosphate aldolase domain. According to in silico gene expression analysis, it was determined that the expression rates of Pvul-FBA genes increased or decreased under salt and drought stress conditions. Synteny analyses of FBA genes in common bean and A. thaliana plants showed that these three plants have a relationship in terms of FBA genes. The results of this research will allow a better designation of the molecular structure of the FBA gene family in common bean.

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Section: Discussionmentioning

confidence: 60%

Genome-Wide Analysis and Characterization of FBA (Fructose 1,6-bisphosphate aldolase) Gene Family of Phaseolus vulgaris L

Uçar,

Alım,

Kasapoğlu

et al. 2024

Journal of Agricultural Production

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“…Expression levels of PvMADS genes under drought stresses were calculated using RNA-seq data from the sequence reading archive (SRA) by Illumina sequencing. SRA data with accession numbers SRR8284481 (drought stress leaf) and SRR8284480 (control leaf) were used as previously described by Aygören et al ( 2023 ). Hierarchical clustering heatmaps were created using TBtools.…”

Section: Methodsmentioning

confidence: 99%

“…The stress-exposed plants were observed to be shorter than the control group plants; their leaves were curved and pale, and their weights continuously dropped because of water loss. Followingly, the plants were sampled and were crushed with liquid nitrogen in a mortar and then stored at − 80 °C (Büyük and Aras 2017 ; Aygören et al 2023 ).…”

Section: Methodsmentioning

confidence: 99%

Omics approaches to understand the MADS-box gene family in common bean (Phaseolus vulgaris L.) against drought stress

Okay,

Kırlıoğlu,

Durdu

et al. 2024

Protoplasma

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MADS-box genes are known to play important roles in diverse aspects of growth/devolopment and stress response in several plant species. However, no study has yet examined about MADS-box genes in P. vulgaris. In this study, a total of 79 PvMADS genes were identified and classified as type I and type II according to the phylogenetic analysis. While both type I and type II PvMADS classes were found to contain the MADS domain, the K domain was found to be present only in type II PvMADS proteins, in agreement with the literature. All chromosomes of the common bean were discovered to contain PvMADS genes and 17 paralogous gene pairs were identified. Only two of them were tandemly duplicated gene pairs (PvMADS-19/PvMADS-23 and PvMADS-20/PvMADS-24), and the remaining 15 paralogous gene pairs were segmentally duplicated genes. These duplications were found to play an important role in the expansion of type II PvMADS genes. Moreover, the RNAseq and RT-qPCR analyses showed the importance of PvMADS genes in response to drought stress in P. vulgaris.

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“…Additionally, the HMMER database was used to scan the presence of the KCS domain with the sequence information. KCS protein parameters were established by the earlier investigation by Aygören et al (2023).…”

Section: Identification and Characterization Of Kcs Genes In P Vulgarismentioning

confidence: 99%

Genome-wide Analysis and Functional Identification of KCS Gene Family under Drought and Salt Stresses in Phaseolus vulgaris L

YILMAZ,

YÜCE,

AYGÖREN

et al. 2023

Journal of Agricultural Production

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β-ketoacyl-CoA synthase (KCS) is an important enzyme that catalyzes the biosynthesis of very-long-chain fatty acids (VLCFAs). In this study, the genome-wide analysis and functional characterization of the KCS gene family members in common bean (Phaseolus vulgaris L.) plants were conducted, and the response of the identified gene family to abiotic stresses was evaluated. In this study, 19 KCS genes were identified and characterized in the P. vulgaris genome. The molecular weights of these KCS proteins ranged from 49.14 kDa to 60.57 kDa, their amino acid lengths varied from 437 to 534, and their pI values ranged from 8.81 to 9.47, indicating a basic nature. Segmental and tandem duplications were observed in the Pvul-KCS gene family. Phylogenetic analysis revealed that Pvul-KCS proteins clustered into three main groups with Arabidopsis thaliana and Glycine max species. Comparative mapping analysis was also conducted with A. thaliana and G. max. Expression profile comparisons indicated that these genes had different expression levels in common bean varieties and played a role in the plant’s response to biotic and abiotic stresses. This study provides important insights into the biological functions of KCS genes in Phaseolus vulgaris and offers valuable information for improving drought and salt stress tolerance in common beans.

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Genome-Wide Analysis and Characterization of SABATH Gene Family in Phaseolus vulgaris Genotypes Subject to Melatonin under Drought and Salinity Stresses

Cited by 9 publications

References 64 publications

Genome-Wide Analysis and Characterization of FBA (Fructose 1,6-bisphosphate aldolase) Gene Family of Phaseolus vulgaris L

Genome-Wide Analysis and Characterization of FBA (Fructose 1,6-bisphosphate aldolase) Gene Family of Phaseolus vulgaris L

Omics approaches to understand the MADS-box gene family in common bean (Phaseolus vulgaris L.) against drought stress

Genome-wide Analysis and Functional Identification of KCS Gene Family under Drought and Salt Stresses in Phaseolus vulgaris L

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