Article
Biotechnology & Applied Microbiology
Yaxian Zong, Ziyuan Hao, Zhonghua Tu, Yufang Shen, Chengge Zhang, Shaoying Wen, Lichun Yang, Jikai Ma, Huogen Li
Summary: 104 putative AP2/ERF genes were identified in Liriodendron chinense genome, grouped into four subfamilies. Three tissue-specific AP2 genes were identified as involved in early leaf development and morphogenesis, with confirmed nuclear subcellular localizations. These findings shed light on the genetic basis of leaf morphogenesis in L. chinense.
Article
Plant Sciences
Jia-li Men, Fang Li, Jin-hua Sun, Guo Wang, Huan-ling Li, Shu-jun Wang, Yun Xu, Jia-bao Wang
Summary: This study identified 202 Litchi AP2/EREBP TFs, classified into four subfamilies, and investigated their evolutionary features and tissue-specific expression patterns. The majority of litchi AP2/EREBPs showed conservative genomic organizations, with some exceptions in the AP2 subfamily. The study provides valuable information for exploring the regulatory mechanisms of AP2/EREBP TFs in litchi somatic embryogenesis and for litchi molecular breeding.
TROPICAL PLANT BIOLOGY
(2021)
Article
Plant Sciences
Hung-Chi Chen, Shi-Cheng Huang, Yen-Fu Chen, Che-Wei Kuo, Ying-Hsuan Chen, Men-Chi Chang
Summary: OsERF106MZ is an important gene expressed in germinating seeds and rice seedling roots under salinity stress. Overexpression of OsERF106MZ increases primary root length and reduces sensitivity to ABA. It promotes root growth by repressing the expression of the ABA biosynthetic gene OsAO3. These findings suggest that OsERF106MZ plays a role in maintaining root growth for resource uptake when rice seeds germinate under salinity stress by alleviating ABA-mediated root growth inhibition.
Article
Agronomy
Hung-Chi Chen, Tzu-Cheng Chien, Tsung-Yang Chen, Ming-Hau Chiang, Ming-Hsin Lai, Men-Chi Chang
Summary: This study identified a novel OsERF106MZ gene in rice with a negative regulatory role in abiotic stress responses, including growth retardation, disruption of ion homeostasis, and modulation of stress-responsive gene expression.
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
Biology
Giovanni Annona, Iori Sato, Juan Pascual-Anaya, David Osca, Ingo Braasch, Randal Voss, Jan Stundl, Vladimir Soukup, Allyse Ferrara, Quenton Fontenot, Shigeru Kuratani, John H. Postlethwait, Salvatore D'Aniello
Summary: Nitric oxide (NO) is a crucial signaling molecule in biological systems, playing important roles in cardiovascular, neurological, and immune functions. Understanding the evolution of NO synthases (Nos) genes, which produce NO in vivo, is still a puzzle, especially in fish compared to tetrapods. Recent studies have found the presence of nos3 gene, previously considered lost, in spotted gar, changing our perspective on the origin of nos genes. This study explored nos gene evolution in different vertebrate species and revealed lineage-specific gene duplications and losses, independent losses of nos3 in teleost lineages, and the expression of nos genes in the gills of certain gnathostome species. These findings provide insights into the roles and evolutionary history of nos genes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Hui Wang, Xue Li, Tezera Wolabu, Ziyao Wang, Ye Liu, Dimiru Tadesse, Naichong Chen, Aijiao Xu, Xiaojing Bi, Yunwei Zhang, Jianghua Chen, Million Tadege
Summary: The study reveals that activator WOX member NsWOX9 and repressor WOX member LAM1 regulate endogenous cytokinin balance during leaf blade outgrowth through a common target NsCKX3.
Article
Multidisciplinary Sciences
Ke Wan, Kening Lu, Mengtao Gao, Ting Zhao, Yuxin He, Dong-Lei Yang, Xiaoyuan Tao, Guosheng Xiong, Xueying Guan
Summary: The CLE gene family encodes important short peptide hormones involved in plant shoot apical meristem division and root and vascular bundle development regulation. Studies on the GhCLE gene family in cotton show functional conservation in apical shoot development regulation.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Woei-Jiun Guo, Benjamin Pommerrenig, H. Ekkehard Neuhaus, Isabel Keller
Summary: This article discusses the important role of sugar transporters in plant organ development and the integration mechanism with plant hormone responses.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Plant Sciences
Eun Kyung Yoon, Jiyeong Oh, Jun Lim
Summary: SHORT-ROOT (SHR) is a mobile transcription factor that plays important roles in ground tissue patterning, stem cell niche specification and maintenance, and vascular development in Arabidopsis roots. Recent evidence suggests that SHR may also play key roles in above-ground organs, and its novel regulatory networks have been found in shoots. Comparative research on SHR function in roots and shoots will further enhance our understanding of plant growth and development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Zejun Hu, Fuan Niu, Peiwen Yan, Kai Wang, Lixia Zhang, Ying Yan, Yu Zhu, Shiqing Dong, Fuying Ma, Dengyong Lan, Siwen Liu, Xiaoyun Xin, Ying Wang, Jinshui Yang, Liming Cao, Shujun Wu, Xiaojin Luo
Summary: Amylose content (AC) is influenced by the Waxy (Wx) gene, and OsEBP89, OsBP5, and OsSK41 play important roles in its regulation. OsSK41 phosphorylates OsEBP89, leading to its instability and reduced interaction with OsBP5, resulting in increased AC. In contrast, loss of OsEBP89 function reduces Wx expression and decreases AC. These findings provide potential targets for gene editing to regulate AC in rice grains.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Genetics & Heredity
Boling Liu, Ge Sun, Changju Liu, Shijuan Liu
Summary: Transcription factor LEC2 plays a crucial role in regulating various plant biological processes, including lateral root formation and seed development. Studies have shown that LEC2 has significant effects on plant growth and development, but further investigation is needed to understand its regulatory mechanisms.
Review
Plant Sciences
Tingwei Yan, Quancan Hou, Xun Wei, Yuchen Qi, Aqing Pu, Suowei Wu, Xueli An, Xiangyuan Wan
Summary: This review summarizes the molecular basis and emerging applications of developmental regulatory genes and nanoparticles in plant transformation, as well as discusses strategies to overcome the obstacles of genotype dependency in plant transformation.
PLANT CELL REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Hongna Zhang, Xiaolu Pan, Shenghui Liu, Wenqiu Lin, Yunhe Li, Xiumei Zhang
Summary: The study identified 97 AP2/ERF family members from the pineapple genome, revealing functional divergence of different subfamilies in biological processes, especially in ethylene response and floral organ development in pineapple. This research provides detailed information on the features of AP2/ERFs in pineapple, offering new insights into the potential functional roles of the AP2/ERF superfamily members and enhancing understanding of the molecular mechanism of flower development in pineapple.
Article
Biotechnology & Applied Microbiology
Ting Zhang, Yongheng Yang, Chunsun Gu, Xiaoyang Xu, Yuming Sun, Menglan Hou, Yinjie Wang, Yongxia Zhang, Liangqin Liu, Haiyan Yuan
Summary: This study isolated and functionally characterized a rooting-related AP2/ERF transcription factor SrERF5 in stevia. This protein may represent a candidate essential regulator of root development in stem cuttings.
PLANT CELL TISSUE AND ORGAN CULTURE
(2021)
Article
Biotechnology & Applied Microbiology
Philipp E. Bayer, Armin Scheben, Agnieszka A. Golicz, Yuxuan Yuan, Sebastien Faure, HueyTyng Lee, Harmeet Singh Chawla, Robyn Anderson, Ian Bancroft, Harsh Raman, Yong Pyo Lim, Steven Robbens, Lixi Jiang, Shengyi Liu, Michael S. Barker, M. Eric Schranz, Xiaowu Wang, Graham J. King, J. Chris Pires, Boulos Chalhoub, Rod J. Snowdon, Jacqueline Batley, David Edwards
Summary: Plant genomes show significant presence/absence variation (PAV) within a species, with different causes of gene loss between diploids and polyploids. In diploids, gene loss propensity is primarily associated with transposable elements, while in polyploids like B. napus, gene loss propensity is linked to homoeologous recombination. These findings provide insights into the underlying biological and physical factors of gene presence/absence, paving the way for the application of machine learning methods in the field.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Tao Zhao, Arthur Zwaenepoel, Jia-Yu Xue, Shu-Min Kao, Zhen Li, M. Eric Schranz, Yves Van de Peer
Summary: Plant genomes vary greatly in size, organization, and architecture, with structural differences providing valuable information for phylogenetic inference. A new method combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference has been developed to reconstruct phylogenies based on microsynteny information, showing accuracy, consistency, and wide applicability. This synteny-based approach complements traditional methods and offers insights into long-standing controversial phylogenetic relationships.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Sabrina Simon, Thijmen Breeschoten, Hans J. Jansen, Ron P. Dirks, M. Eric Schranz, Vera I. D. Ros
Summary: Researchers provided the genome assembly and developmental transcriptome data of the beet armyworm, shedding light on the biology of this devastating polyphagous insect pest. Comparative genomic analyses across Lepidoptera advanced knowledge for controlling other invasive Spodoptera species.
G3-GENES GENOMES GENETICS
(2021)
Article
Evolutionary Biology
Thijmen Breeschoten, Corne F. H. van der Linden, Vera I. D. Ros, M. Eric Schranz, Sabrina Simon
Summary: Evolutionary expansions and contractions of gene families in butterflies and moths are correlated with their feeding adaptations, specifically the expansions of detoxification gene families may facilitate a polyphagous feeding style. The gene family expansions and contractions vary across different lepidopteran families and are associated with host plant use and specialization levels.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Charles J. Underwood, Kitty Vijverberg, Diana Rigola, Shunsuke Okamoto, Carla Oplaat, Rik H. M. Op den Camp, Tatyana Radoeva, Stephen E. Schauer, Joke Fierens, Kim Jansen, Sandra Mansveld, Marco Busscher, Wei Xiong, Erwin Datema, Koen Nijbroek, Evert-Jan Blom, Ross Bicknell, Andrew Catanach, Sylvia Erasmuson, Christopher Winefield, Arjen J. van Tunen, Marcel Prins, M. Eric Schranz, Peter J. van Dijk
Summary: The PAR gene in dandelion triggers embryo development without fertilization, a rare phenomenon in flowering plants. This gene is inserted with a MITE transposon in the promoter region, and its expression is able to induce embryogenesis in the absence of fertilization.
Article
Plant Sciences
Shuang Song, Leo A. J. Willems, Ao Jiao, Tao Zhao, M. Eric Schranz, Leonie Bentsink
Summary: The NAC transcription factors ANAC040, ANAC060, and ANAC089 in Arabidopsis thaliana are highly homologous, but have distinct functions in the regulation of seed germination. Swapping experiments revealed functional redundancy between ANAC060 and ANAC040, but not between ANAC060 and ANAC089.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Yanting Wang, Janani Durairaj, Hernando G. Suarez Duran, Robin van Velzen, Kristyna Flokova, Che-Yang Liao, Aleksandra Chojnacka, Stuart MacFarlane, M. Eric Schranz, Marnix H. Medema, Aalt D. J. van Dijk, Lemeng Dong, Harro J. Bouwmeester
Summary: By using root RNA-seq data and co-expression analysis, candidate genes involved in the biosynthesis of SLs in tomato, including several cytochrome P450 genes, were discovered. Experimental results demonstrated the catalytic activity of CYP712G1 in oxidizing orobanchol to form DDH isomers, which can be further converted to solanacol, a major component of tomato root exudate.
Article
Plant Sciences
Francesco Garassino, Raul Y. Wijfjes, Rene Boesten, Francisca Reyes Marquez, Frank F. M. Becker, Vittoria Clapero, Iris van den Hatert, Rens Holmer, M. Eric Schranz, Jeremy Harbinson, Dick de Ridder, Sandra Smit, Mark G. M. Aarts
Summary: Photosynthesis is a crucial process for plant and human survival. The exceptional species Hirschfeldia incana has high photosynthetic light-use efficiency, which is also observed in closely related species Brassica rapa and Brassica nigra. The genome of H. incana has undergone extensive diversification compared to B. rapa and B. nigra, resulting in large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes involved in photosynthesis and photoprotection show a positive correlation between copy number and gene expression. This research provides valuable insights into the evolution of high photosynthetic light-use efficiency and has implications for enhancing the photosynthetic rates in crop species.
Article
Ecology
Thijmen Breeschoten, M. Eric Schranz, Erik H. Poelman, Sabrina Simon
Summary: Polyphagous insects exhibit specialization in feeding on different host plants and their transcriptional plasticity is highly species-specific. High herbivore success on specific host plants is driven by species-specific transcriptional plasticity, and more distantly related species show convergence in the expression of multiple homologous genes. Specific transcriptional responses are observed within phylogenetic lineages.
ECOLOGY AND EVOLUTION
(2022)
Article
Biology
John T. Lovell, Avinash Sreedasyam, M. Eric Schranz, Melissa Wilson, Joseph W. Carlson, Alex Harkess, David Emms, David M. Goodstein, Jeremy Schmutz
Summary: The development of multiple chromosome-scale reference genome sequences has provided a high-resolution view of molecular evolution patterns and processes. However, leveraging information across multiple genomes remains a challenge in eukaryotic systems. GENESPACE addresses these challenges by integrating conserved gene order and orthology. It offers a significant contribution to existing gene family and synteny programs, particularly in complex genomes.
Article
Biochemistry & Molecular Biology
Nam Hoang, E. O. Deedi Sogbohossou, Wei Xiong, Conor J. C. Simpson, Pallavi Singh, Nora Walden, Erik van den Bergh, Frank F. M. Becker, Zheng Li, Xin-Guang Zhu, Andrea Brautigam, Andreas P. M. Weber, Jan C. van Haarst, Elio G. W. M. Schijlen, Prasad S. Hendre, Allen Van Deynze, Enoch G. Achigan-Dako, Julian M. Hibberd, M. Eric Schranz
Summary: The genome sequence of Gynandropsis gynandra provides insights into the evolution of C-4 photosynthesis and the history of whole-genome duplication. It was found that G. gynandra and its C-3 relative Tarenaya hassleriana shared a whole-genome duplication event, but T. hassleriana experienced an additional genome addition. G. gynandra retained more duplicated copies of C-4 photosynthesis-related genes compared to T. hassleriana.
Article
Evolutionary Biology
Nora Walden, Michael Eric Schranz
Summary: Large genomic data sets pose challenges in identifying true orthologous genes and excluding problematic paralogs when using commonly used sequencing methods. In this study, we compared conventional ortholog detection with ortholog detection through genomic synteny in a data set of 11 representative diploid Brassicaceae whole-genome sequences. The use of synteny resulted in more orthologs and reliable identification of paralogs. Surprisingly, no notable differences were observed in species trees reconstructed from syntenic orthologs compared to other gene sets. However, the synteny data set provided a wide range of gene functions, making it suitable for downstream gene function analysis and network studies. Additionally, the study presents the first ancestral genome reconstruction for the Core Brassicaceae predating its lineage diversification.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Francesco Pancaldi, Michael Eric Schranz, Eibertus N. van Loo, Luisa M. Trindade
Summary: There are significant differences in the content and composition of plant cell walls between Poaceae and eudicots, but the genomic and genetic basis for these differences has not been fully understood. This research analyzed genomic properties of cell wall gene families in angiosperm genomes, revealing Divergent patterns between Poaceae and eudicots, which are associated with the distinct cell wall properties of these two plant groups.
Article
Biochemical Research Methods
Fabricio Almeida-Silva, Tao Zhao, Kristian K. Ullrich, M. Eric Schranz, Yves van de Peer
Summary: This article introduces an R package called syntenet for inferring and analyzing synteny networks from whole-genome protein sequence data. The package includes functions for data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate.
Article
Multidisciplinary Sciences
Aristide Carlos Houdegbe, Enoch G. Achigan-Dako, E. O. Deedi Sogbohossou, M. Eric Schranz, Alfred O. Odindo, Julia Sibiya
Summary: This study assessed the phenotypic variability in biomass and related traits of Gynandropsis gynandra and selected elite genotypes for improved cultivar development. Significant differences were observed among lines and genotype origins, with West African and East/Southern African genotypes showing superior biomass productivity. The results provide valuable insights for further improvement of spider plant genotypes.
