scholarly journals An updated census of the maize TIFY family

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247271
Author(s):  
Pingdong Sun ◽  
Yannan Shi ◽  
Aga Guido Okwana Valerio ◽  
Eli James Borrego ◽  
Qingyun Luo ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Family Members ◽  
Specific Gene ◽  
Ecological Analysis ◽  
Crop Species ◽  
Conserved Domains ◽  
Important Crop ◽  
Ear Motif ◽  
Domain Protein

The TIFY gene family is a plant-specific gene family encoding a group of proteins characterized by its namesake, the conservative TIFY domain and members can be organized into four subfamilies: ZML, TIFY, PPD and JAZ (Jasmonate ZIM-domain protein) by presence of additional conserved domains. The TIFY gene family is intensively explored in several model and agriculturally important crop species and here, yet the composition of the TIFY family of maize has remained unresolved. This study increases the number of maize TIFY family members known by 40%, bringing the total to 47 including 38 JAZ, 5 TIFY, and 4 ZML genes. The majority of the newly identified genes were belonging to the JAZ subfamily, six of which had aberrant TIFY domains, suggesting loss JAZ-JAZ or JAZ-NINJA interactions. Six JAZ genes were found to have truncated Jas domain or an altered degron motif, suggesting resistance to classical JAZ degradation. In addition, seven membranes were found to have an LxLxL-type EAR motif which allows them to recruit TPL/TPP co-repressors directly without association to NINJA. Expression analysis revealed that ZmJAZ14 was specifically expressed in the seeds and ZmJAZ19 and 22 in the anthers, while the majority of other ZmJAZs were generally highly expressed across diverse tissue types. Additionally, ZmJAZ genes were highly responsive to wounding and JA treatment. This study provides a comprehensive update of the maize TIFY/JAZ gene family paving the way for functional, physiological, and ecological analysis.

Identification and expression analysis of LEA gene family members in cucumber genome

2016 ◽  
Vol 80 (2) ◽  
pp. 225-241 ◽  
Author(s):  
Yasemin Celik Altunoglu ◽  
Pinar Baloglu ◽  
Esra Nurten Yer ◽  
Sefa Pekol ◽  
Mehmet Cengiz Baloglu
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Family Members ◽  
Lea Gene ◽  
Cucumber Genome

scholarly journals Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

Cell Research ◽  
2006 ◽  
Vol 16 (5) ◽  
pp. 507-518 ◽  
Author(s):  
Danhua Jiang ◽  
Changsong Yin ◽  
Aiping Yu ◽  
Xiaofan Zhou ◽  
Wanqi Liang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Mirna Gene ◽  
Family Members

scholarly journals Identification and expression analysis of bovine ANGPTL gene family

2010 ◽  
Vol 56 (4) ◽  
pp. 445-453 ◽  
Author(s):  
Zhengbing Guan ◽  
Guolin Cai ◽  
Junyong Sun ◽  
Jian Lu
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Biological Activities ◽  
Expression Patterns ◽  
Family Members ◽  
Coiled Coil ◽  
Amino Acid Sequences ◽  
Pcr Analysis ◽  
Important Species ◽  
Real Time Quantitative Pcr

Abstract Encoded by seven genes, angiopoietin-like (ANGPTL) family members structurally similar to the angiogenic regulating factor angiopoietin are known to possess biological activities in angiogenesis and metabolism. Here we reports for the first time the identification and expression analysis of all the seven members of bovine ANGPTL gene family, which were designated bANGPTL1 to bANGPTL7 in order. The seven bANGPTL genes consist of 4-9 exons, span 3800-43000 bp and are located on different chromosomes. The deduced amino acid sequences of the members all possess an N-terminal coiled-coil domain and a C-terminal fibrinogen-like domain, both characteristics of angiopoietins. Phylogenetic analysis showed that the 32 identified ANGPTL homologs from 9 species could be classified into two major groups. Real-time quantitative PCR (Q-PCR) analysis revealed that the bANGPTL family members have different expression patterns. This study will be helpful for investigation on the biological role of the bANGPTL family in this economically important species. Furthermore, it provides an insight into the molecular evolution of the emerging ANGPTL family.

Comparative identification, characterization, and expression analysis of bZIP gene family members in watermelon and melon genomes

2018 ◽  
Vol 87 (2) ◽  
pp. 227-243 ◽  
Author(s):  
Necdet Mehmet Unel ◽  
Fadime Cetin ◽  
Yasin Karaca ◽  
Yasemin Celik Altunoglu ◽  
Mehmet Cengiz Baloglu
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Family Members

scholarly journals Identification and expression analysis of histone modification gene (HM) family during somatic embryogenesis of oil palm

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Lixia Zhou ◽  
Rajesh Yarra ◽  
Longfei Jin ◽  
Yaodong Yang ◽  
Hongxing Cao ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Histone Modification ◽  
Gene Family ◽  
Expression Analysis ◽  
Histone Modifications ◽  
Oil Palm ◽  
Large Scale ◽  
Elaeis Guineensis ◽  
Family Members ◽  
Evolutionary Relationship

Abstract Background Oil palm (Elaeis guineensis, Jacq.) is an important vegetable oil-yielding plant. Somatic embryogenesis is a promising method to produce large-scale elite clones to meet the demand for palm oil. The epigenetic mechanisms such as histone modifications have emerged as critical factors during somatic embryogenesis. These histone modifications are associated with the regulation of various genes controlling somatic embryogenesis. To date, none of the information is available on the histone modification gene (HM) family in oil palm. Results We reported the identification of 109 HM gene family members including 48 HMTs, 27 HDMs, 13 HATs, and 21 HDACs in the oil palm genome. Gene structural and motif analysis of EgHMs showed varied exon–intron organization and with conserved motifs among them. The identified 109 EgHMs were distributed unevenly across 16 chromosomes and displayed tandem duplication in oil palm genome. Furthermore, relative expression analysis showed the differential expressional pattern of 99 candidate EgHM genes at different stages (non-embryogenic, embryogenic, somatic embryo) of somatic embryogenesis process in oil palm, suggesting the EgHMs play vital roles in somatic embryogenesis. Our study laid a foundation to understand the regulatory roles of several EgHM genes during somatic embryogenesis. Conclusions A total of 109 histone modification gene family members were identified in the oil palm genome via genome-wide analysis. The present study provides insightful information regarding HM gene’s structure, their distribution, duplication in oil palm genome, and also their evolutionary relationship with other HM gene family members in Arabidopsis and rice. Finally, our study provided an essential role of oil palm HM genes during somatic embryogenesis process.

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