Article
Plant Sciences
Ramya Parakkunnel, K. Bhojaraja Naik, Girimalla Vanishree, C. Susmita, Supriya Purru, K. Udaya Bhaskar, KV. Bhat, Sanjay Kumar
Summary: The evolutionary dynamics of AP2/ERF and WRKY genes in the sesame pan-genome were extensively studied. These genes showed massive variation in terms of copy numbers, genome location, domain structure, exon-intron structure, and protein parameters. They play vital roles in defense response and stress signal pathways, and exhibit different characteristics and functions among different gene families.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Huiying Meng, Yunjuan Chen, Tingting Li, Huazhong Shi, Shuojun Yu, Yang Gao, Zhiqiang Wang, Xu Wang, Jian-Kang Zhu, Yechun Hong, Zhen Wang
Summary: The transcription factor AP2 plays a crucial role in ABA-mediated inhibition of seed germination through its interaction with ABI5. AP2 also interacts with SnRK2.2, SnRK2.3, and SnRK2.6, suggesting its multifaceted role in the ABA signaling pathway. These findings highlight the importance of the interactions of AP2 with SnRK2s and ABI5 in ABA signaling control of seed germination.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
K. Mohamed Shafi, Ramanathan Sowdhamini
Summary: This study identified and analysed potential cold stress response genes across ten Rosaceae family members, revealing differences in TFBS patterns among species and gene families, even among functionally related genes. Different combinations of transcription factors may play a role in the regulation and expression of genes within the same family.
Article
Biochemistry & Molecular Biology
Liangyu Guo, Shuo Wang, Yuqi Nie, Yirong Shen, Xiaoxue Ye, Wenwu Wu
Summary: Most eudicot plants did not undergo recent whole-genome duplication (R-WGD), but they were still able to adapt to environmental changes. In this study, researchers found that the AP2/ERF transcription factor family was retained after R-WGDs in some eudicot plants and showed exceptional response to cold stimulation. By comparing plants with and without R-WGD, the study revealed convergent expansions of the AP2/ERF III and IX subfamilies through independent duplications and tandem duplications (TDs) after R-WGDs. These expansions coincided with times of global cooling, particularly around and/or after the Cretaceous-Paleogene (K-Pg) boundary. The co-retention and expansion of AP2/ERF III C-repeat binding factor (CBF) duplicates contributed to rewiring of cold-specific regulatory networks in different eudicot lineages.
PLANT COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Jing Zhang, Jiayao Liao, Qiqi Ling, Yan Xi, Yexiong Qian
Summary: The study identified 214 ZmAP2/ERF genes in maize and categorized them into different families and subfamilies based on domain similarities. Analysis revealed the potential roles of these genes in plant growth, development, and responses to abiotic stresses, laying a foundation for further exploring their function and regulatory mechanisms.
Article
Biochemistry & Molecular Biology
Yunxiao Zhao, Minyan Wang, Yicun Chen, Ming Gao, Liwen Wu, Yangdong Wang
Summary: In this study, the AP2/ERF gene LcERF134 was identified as an activator for the accumulation of citral and other monoterpenes in Litsea cubeba. The overexpression of LcERF134 significantly increased monoterpene production by inducing the expression of key genes involved in the monoterpene biosynthesis pathway. This research offers insight into how to enhance the flavor of L. cubeba essential oil.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Plant Sciences
Jin-Wook Choi, Hyeon Ho Choi, Young-Soo Park, Min-Jeong Jang, Seungill Kim
Summary: This study provides a comprehensive investigation of the AP2/ERF gene family in Solanaceae plants, revealing their importance in abiotic stress response and development. A total of 2,195 AP2/ERF genes were identified, including 368 newly discovered genes, in eight Solanaceae species. Phylogenetic and chromosomal analyses showed gene expansion and species-specific differentiation within ERF subgroups. Transcriptome analyses suggested a putative role of these genes in abiotic stress response in peppers and tomatoes.
Article
Genetics & Heredity
Duan Wu, Ke Zhang, Chun-yu Li, Guan-Wen Xie, Ming-ting Lu, Yong Qian, Ya-ping Shu, Qi Shen
Summary: This study identified 212 AP2/ERF family members in the genome of Perilla and analyzed their characteristics. Transcriptome sequencing revealed up-regulated key enzyme genes involved in oil biosynthesis in high-oil and high-ALA varieties. Using WGCNA, significant correlations were found between 36 AP2/ERFs and 90 lipid metabolism genes, and 12 AP2/ERFs were identified as hub genes. Gene expression analysis identified three AP2/ERFs potentially playing a significant role in the regulation of oil accumulation in Perilla.
Article
Biochemistry & Molecular Biology
Xiaolin Zhu, Baoqiang Wang, Wenyu Liu, Xiaohong Wei, Xian Wang, Xuefeng Du, Haixun Liu
Summary: This study identified 148 AP2/ERF genes in quinoa and analyzed their characteristics and functions. The results showed that these genes play important roles in plant growth and development, especially in response to drought stress. Understanding the mechanisms of these genes' response to drought stress provides a solid foundation for further research on quinoa's drought resistance.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Plant Sciences
Yanfei Pei, Jun Zhang, Peng Wu, Li Ye, Duofeng Yang, Jiedan Chen, Jie Li, Yan Hu, Xiefei Zhu, Xiaoping Guo, Tianzhen Zhang
Summary: The floral nectary, important for plant reproduction and evolution, also plays a role in insect-resistant breeding. Research on the GoNe gene in cotton has revealed its crucial role in the formation of both floral and extrafloral nectaries, possibly independent of CRC and STY genes.
Article
Horticulture
Naiyu Wang, Yuchen Sun, Rong Lian, Zhixiong Guo, Yuan Yu, Tengfei Pan, Wenqin She
Summary: Pummelo exocarp color is determined by carotenoid metabolism. This study identified 8 AP2/ERF genes related to carotenoid metabolism, and found that 3 of them showed correlation with pummelo exocarp color through qRT-PCR and color parameter measurements.
SCIENTIA HORTICULTURAE
(2023)
Review
Plant Sciences
Ying Wu, Xiang Li, Jinnan Zhang, Haiqing Zhao, Shaolin Tan, Wanhao Xu, Jiaqi Pan, Fan Yang, Erxu Pi
Summary: This review focuses on the Ethylene Responsive Factor (ERF) subfamily, which is the largest group of proteins in the plant AP2/ERF superfamily. The ERFs have been extensively studied for their role in regulating plant resistances to various abiotic stresses. The review summarizes the molecular mechanisms of ERF regulation and their impact on stress responsive gene transcription. However, there is limited comprehensive annotation of the interacting proteins and target genes of ERFs. Future research prospects include investigating the mechanisms of stress signal transmission to ERFs and the transcriptional regulation of stress responsive genes by ERFs.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Fang Hu, Yunxiang Zhang, Jinping Guo
Summary: This study identified 145 AP2/ERF genes in yellow horn, classified into different subfamilies, with 87 transcription factors lacking introns, showing high collinearity and important roles under cold stress. Additionally, the expression patterns of eight XsAP2/ERF transcription factors in different tissues and stress treatments were confirmed using RT-qPCR.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Yu Ge, Xiaoping Zang, Ying Yang, Tao Wang, Weihong Ma
Summary: The study systematically analyzed AP2/ERF family members in avocado and identified 10 highly expressed PaAP2/ERF genes potentially related to fatty acid accumulation in avocado fruit. This analysis provides a foundation for future studies on the functions of AP2/ERF associated with fatty acid accumulation.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Genetics & Heredity
Ran Wan, Jinhui Song, Zhenyang Lv, Xingcheng Qi, Xuemeng Han, Qiang Guo, Sa Wang, Jiangli Shi, Zaihai Jian, Qingxia Hu, Yanhui Chen
Summary: Pomegranate is a valuable fruit with economic, ecological, and health benefits. This study identified and characterized 116 PgAP2/ERF genes in pomegranate, revealing their roles in fruit development and postharvest preservation. The expression of several PgAP2/ERFs was associated with pomegranate seed hardness, and many differentially expressed genes were identified as potential regulators of fruit development. Additionally, the study found that certain genes were involved in pomegranate postharvest preservation. These findings contribute to our understanding of the PgAP2/ERF gene family and provide insights into the candidate genes associated with pomegranate fruit development and postharvest preservation.
Article
Plant Sciences
Harold Suarez-Baron, Juan F. Alzate, Favio Gonzalez, Soraya Pelaz, Barbara A. Ambrose, Natalia Pabon-Mora
Summary: This study assessed the expression patterns of key genes involved in trichome development in the magnoliid Aristolochia fimbriata, revealing differences in gene expression in floral organs compared to vegetative tissues. The findings suggest a simpler genetic mechanism governing trichome development in flowers of early-divergent angiosperms. The results imply that the canonical trichome gene expression is more conserved in vegetative tissues than in floral organs across angiosperms.
Article
Evolutionary Biology
Barbara A. Ambrose, Tynisha L. Smalls, Cecilia Zumajo-Cardona
Summary: The MADS-box genes form a large transcription factor family that evolved through duplication and functional diversification, with the type II classic MADS-box genes being key developmental regulators in flowering plants. Our study focused on the evolution of type II classic MADS-box genes in land plants, particularly in lycophytes, and found that they have diverse expression patterns during plant development, indicating neofunctionalization and subfunctionalization after duplication events.
EVOLUTION & DEVELOPMENT
(2021)
Editorial Material
Plant Sciences
Natalia Pabon-Mora
Summary: Plants are versatile organisms, with the ability to regenerate, reproduce in different ways, and display a wide range of shapes and colors. The author selected a unique flowering image to study as a system for understanding the development of holoparasitic plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Cecilia Zumajo-Cardona, Natalia Pabon-Mora, Barbara A. Ambrose
Summary: The study reveals that the euAP2 gene plays a crucial role in vascular plants, initially contributing to spore and sporangium development and later being recruited for ovule, fruit, and floral organ development. The protein sequences of euAP2 are highly conserved, with changes in their function during development likely attributed to alterations in regulatory regions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Sarita Munoz-Gomez, Harold Suarez-Baron, Juan F. Alzate, Favio Gonzalez, Natalia Pabon-Mora
Summary: Flavonoids, carotenoids, betalains, and chlorophylls are plant pigments responsible for floral color, with anthocyanins largely responsible for red, purple, pink, and blue colors. The R2R3-MYB genes act as upstream regulatory factors of the anthocyanin biosynthetic pathway, with species-specific duplications in core eudicots and local duplications in Aristolochiaceae. The expression of these genes in different developmental stages and plant organs largely overlaps with red and purple pigments, indicating their role in anthocyanin and flavonoid synthesis.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Sebastian Martinez-Salazar, Favio Gonzalez, Juan F. Alzate, Natalia Pabon-Mora
Summary: Floral spurs are key innovations in angiosperms, shifting floral symmetry from radial to bilateral. This study on Tropaeolum longifolium identified candidate genes involved in adaxial-abaxial differential growth during spur formation. Evolutionary analysis revealed specific duplications and losses of critical genes in Brassicales, shedding light on genetic mechanisms behind spur formation and floral symmetry.
AMERICAN JOURNAL OF BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Adriana M. Gallego, Luisa F. Rojas, Wilmar G. Valencia, Lucia Atehortua, Aura I. Urrea, Andrew S. Fister, Mark J. Guiltinan, Siela N. Maximova, Natalia Pabon-Mora
Summary: The study showed that under white light exposure, cacao cells grew and synthesized an increased content of PAs. Transition to blue light further increased PAs content, activating genes associated with stress response. Exposure to blue light led to a decrease in PAs content associated with ROS-mediated stress pathways.
Article
Evolutionary Biology
Carolina Rodriguez-Pelayo, Barbara A. Ambrose, Alejandra Vasco, Juan F. Alzate, Natalia Pabon-Mora
Summary: LFY genes may play a role in the development of gametophytes and sporophytes in bryophytes and ferns, and have functions related to floral meristem differentiation in gymnosperms and flowering plants.
Article
Plant Sciences
Carolina Rodriguez-Pelayo, Barbara A. Ambrose, Alejandra Vasco, Juan F. Alzate, Natalia Pabon-Mora
Summary: This study provides a phylogenetic framework for PEBP genes and investigates their expression patterns in selected lycophytes and ferns. The results indicate that PEBP genes are involved in reproductive transitions and spore production in these plants, suggesting their important roles in meristem maintenance and sporangium development.
INTERNATIONAL JOURNAL OF PLANT SCIENCES
(2022)
Article
Evolutionary Biology
Cecilia Zumajo-Cardona, Barbara A. Ambrose
Summary: This study analyzed the transcriptome of two Ephedra species with different seed morphologies, revealing differentially expressed genes involved in seed development. The results also supported the hypothesis that the extra envelopes covering the seeds of Gnetales are not genetically similar to integument. The study highlights the importance of studying less explored species like gymnosperms in understanding plant evolution.
Article
Plant Sciences
D. Blaine Marchant, Guang Chen, Shengguan Cai, Fei Chen, Peter Schafran, Jerry Jenkins, Shengqiang Shu, Chris Plott, Jenell Webber, John T. Lovell, Guifen He, Laura Sandor, Melissa Williams, Shanmugam Rajasekar, Adam Healey, Kerrie Barry, Yinwen Zhang, Emily Sessa, Rijan R. Dhakal, Paul G. Wolf, Alex Harkess, Fay-Wei Li, Clemens Roessner, Annette Becker, Lydia Gramzow, Dawei Xue, Yuhuan Wu, Tao Tong, Yuanyuan Wang, Fei Dai, Shuijin Hua, Hua Wang, Shengchun Xu, Fei Xu, Honglang Duan, Guenter Theissen, Michael R. McKain, Zheng Li, Michael T. W. McKibben, Michael S. Barker, Robert J. Schmitz, Dennis W. Stevenson, Cecilia Zumajo-Cardona, Barbara A. Ambrose, James H. Leebens-Mack, Jane Grimwood, Jeremy Schmutz, Pamela S. Soltis, Douglas E. Soltis, Zhong-Hua Chen
Summary: The genome of the model fern species Ceratopteris richardii exhibits a remarkably dynamic evolution, with rapid changes in content and structure following a whole-genome duplication around 60 million years ago. These changes include gene loss, tandem duplications, multiple horizontal gene transfers, and transposable elements insertion, providing insights into defense-related gene families and the evolution of seed plants.
Article
Developmental Biology
Jessica A. Ramirez-Ramirez, Yesenia Madrigal, Juan F. Alzate, Natalia Pabon-Mora
Summary: The study highlights the diverse roles of AGL24 and SVP in the flowering transition in angiosperms, with variations in different lineages. Independent duplication events in monocots have resulted in at least three clades of AGL24/SVP homologs, some specific to Orchidaceae. The analysis suggests higher evolutionary rates and potential pleiotropic roles of these genes in maintaining the vegetative phase and promoting flowering in different plant groups.
CELLS & DEVELOPMENT
(2021)
Article
Plant Sciences
Favio Gonzalez, Vanessa Suaza-Gaviria, Natalia Pabon-Mora
Summary: Flowers in the Antidaphne genus, characterized by their small size, show distinct differences in development and morphology of staminate and carpellate inflorescences. Mechanical constraints and growth processes greatly influence the form and symmetry of these flowers.
AUSTRALIAN JOURNAL OF BOTANY
(2021)
Article
Developmental Biology
Natali Hernandez-Ciro, Natalia Pabon-Mora
Summary: This study provides insights into the anatomical and genetic basis of the independent origin of fleshy fruits in Cestrum and the reversion to dry dehiscent fruits in Brugmansia. Expression patterns of fruit development genes suggest potential controllers for homologous and homoplasious anatomical features in the fruits of both species. The fruit genetic regulatory network (GRN) in Cestrum and Brugmansia shows considerable differences compared to typical capsules and berries of Solanaceae.
INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY
(2021)