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Journal articles on the topic 'Arabidopsis, ALOG'

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Published: 9 March 2023
Last updated: 10 March 2023

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1

Li, Na, Yang Wang, Jing Lu, and Chuan Liu. "Genome-Wide Identification and Characterization of the ALOG Domain Genes in Rice." International Journal of Genomics 2019 (February 24, 2019): 1–13. http://dx.doi.org/10.1155/2019/2146391.

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The ALOG domain genes, named after the Arabidopsis LSH1 and Oryza G1 (ALOG) proteins, have frequently been reported as key developmental regulators in rice and Arabidopsis. However, the investigation of the ALOG gene family is limited. Here, we conducted a genome-wide investigation of the ALOG gene family in rice and six other species. In total, eighty-four ALOG domain genes were identified from the seven species, of which fourteen ALOG domain genes (OsG1/G1Ls) were identified in the rice genome. The fourteen OsG1/G1Ls were unevenly distributed on eight chromosomes, and we found that eight segmental duplications contributed to the expansion of OsG1/G1Ls in the rice genome. The eighty-four ALOG family genes from seven species were classified into six clusters, and the ALOG domain-defined motifs 1, 2, and 3 were highly conserved across species according to the phylogenetic and structural analysis. However, the newly identified motifs 4 and 5 were only present in monocots, indicating a specified function in monocots. Moreover, OsG1/G1Ls exhibited tissue-specific expression patterns. Coexpression analysis suggested that OsG1 integrates OsMADS50 and the downstream MADS-box genes, such as OsMADS1, to regulate the development of rice inflorescence; OsG1L7 potentially associates with OsMADS22 and OsMADS55 to regulate stem elongation. In addition, comparative expression analysis revealed the conserved biological functions of ALOG family genes among rice, maize, and Arabidopsis. These results have shed light on the functional study of ALOG family genes in rice and other plants.
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2

He, Liang, Yawen Lei, Xin Li, Qincheng Peng, Wei Liu, Keyuan Jiao, Shihao Su, Zhubing Hu, Zhenguo Shen, and Da Luo. "SYMMETRIC PETALS 1 Encodes an ALOG Domain Protein that Controls Floral Organ Internal Asymmetry in Pea (Pisum sativum L.)." International Journal of Molecular Sciences 21, no. 11 (June 5, 2020): 4060. http://dx.doi.org/10.3390/ijms21114060.

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In contrast to typical radially symmetrical flowers, zygomorphic flowers, such as those produced by pea (Pisum sativum L.), have bilateral symmetry, manifesting dorsoventral (DV) and organ internal (IN) asymmetry. However, the molecular mechanism controlling IN asymmetry remains largely unclear. Here, we used a comparative mapping approach to clone SYMMETRIC PETALS 1 (SYP1), which encodes a key regulator of floral organ internal asymmetry. Phylogenetic analysis showed that SYP1 is an ortholog of Arabidopsis thaliana LIGHT-DEPENDENT SHORT HYPOCOTYL 3 (LSH3), an ALOG (Arabidopsis LSH1 and Oryza G1) family transcription factor. Genetic analysis and physical interaction assays showed that COCHLEATA (COCH, Arabidopsis BLADE-ON-PETIOLE ortholog), a known regulator of compound leaf and nodule identity in pea, is involved in organ internal asymmetry and interacts with SYP1. COCH and SYP1 had similar expression patterns and COCH and SYP1 target to the nucleus. Furthermore, our results suggested that COCH represses the 26S proteasome-mediated degradation of SYP1 and regulates its abundance. Our study suggested that the COCH-SYP1 module plays a pivotal role in floral organ internal asymmetry development in legumes.
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3

Nan, Wenzhi, Shandang Shi, Diddugodage Chamila Jeewani, Li Quan, Xue Shi, and Zhonghua Wang. "Genome-Wide Identification and Characterization of wALOG Family Genes Involved in Branch Meristem Development of Branching Head Wheat." Genes 9, no. 10 (October 19, 2018): 510. http://dx.doi.org/10.3390/genes9100510.

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The branched spike phenotype is an important supernumerary spikelet trait of Triticum turgidum L. associated with the production of significantly more grains per spike, thereby offering a higher potential yield. However, the genetic basis of branch meristem (BM) development remains to be fully elucidated in wheat. TAW1, an ALOG (Arabidopsis LSH1 and Oryza G1) family gene, has been shown to function as a unique regulator in promoting BM development in rice. In this study, we found that the development pattern of the BMs of the branched spike in wheat was similar to the indeterminate BMs of rice. Moreover, phylogenetic analysis classified the ALOG genes into 12 groups. This family of genes was found to have evolved independently in eudicots and monocots and was evolutionarily conserved between wheat and rice as well as during wheat polyploidization. Furthermore, experiments revealed that TtALOG2-1A, a TAW1-homologous gene, plays a significant role in regulating the transition of indeterminate BM fate. Finally, large-scale RNA-sequencing studies and quantitative real-time polymerase chain reaction (qRT-PCR) experiments revealed that members of the TtALOGs may act upstream of the TtMADS22, TtMADS47, and TtMADS55 genes to promote indeterminate BM activities. Our findings further knowledge on BM development in wheat.
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4

Hofmann, Julia, Mohamed Youssef-Banora, Janice de Almeida-Engler, and Florian M. W. Grundler. "The Role of Callose Deposition Along Plasmodesmata in Nematode Feeding Sites." Molecular Plant-Microbe Interactions® 23, no. 5 (May 2010): 549–57. http://dx.doi.org/10.1094/mpmi-23-5-0549.

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Infective second-stage juveniles of the obligate plant-parasitic root-knot and cyst nematodes invade plant roots to induce specialized feeding structures. Here, we present data on the distribution of plasmodesmata in cell walls of syncytia and giant cells induced by cyst and root-knot nematodes. An Arabidopsis and a tobacco line were used, containing viral movement proteins fused to green fluorescent protein as a localization marker for plasmodesmata. Plasmodesmata were detected in walls between giant cells but also in walls toward neighboring cells. In syncytia, plasmodesmata were mainly detected at later stages. In young syncytia, few plasmodesmata were observed and a specific temporal callose deposition along plasmodesmata indicated impaired symplasmic exchange. In order to study the relevance of callose deposition for successful cyst nematode development in Arabidopsis, two mutant lines inhibited in callose synthesis and degradation, respectively, were used in nematode infection assays. Histological analyses showed that syncytia were smaller when callose degradation was reduced, indicating a significant importance of this process to cyst nematode development.
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5

Katiyar, Arpana, and Yashwanti Mudgil. "Arabidopsis NDL-AGB1 modules Play Role in Abiotic Stress and Hormonal Responses Along with Their Specific Functions." International Journal of Molecular Sciences 20, no. 19 (September 24, 2019): 4736. http://dx.doi.org/10.3390/ijms20194736.

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Arabidopsis N-MYC Downregulated Like Proteins (NDLs) are interacting partners of G-Protein core components. Animal homologs of the gene family N-myc downstream regulated gene (NDRG) has been found to be induced during hypoxia, DNA damage, in presence of reducing agent, increased intracellular calcium level and in response to metal ions like nickel and cobalt, which indicates the involvement of the gene family during stress responses. Arabidopsis NDL gene family contains three homologs NDL1, NDL2 and NDL3 which share up to 75% identity at protein level. Previous studies on NDL proteins involved detailed characterization of the role of NDL1; roles of other two members were also established in root and shoot development using miRNA knockdown approach. Role of entire family in development has been established but specific functions of NDL2 and NDL3 if any are still unknown. Our in-silico analysis of NDLs promoters reveled that all three members share some common and some specific transcription factors (TFs) binding sites, hinting towards their common as well as specific functions. Based on promoter elements characteristics, present study was designed to carry out comparative analysis of the Arabidopsis NDL family during different stages of plant development, under various abiotic stresses and plant hormonal responses, in order to find out their specific and combined roles in plant growth and development. Developmental analysis using GUS fusion revealed specific localization/expression during different stages of development for all three family members. Stress analysis after treatment with various hormonal and abiotic stresses showed stress and tissue-specific differential expression patterns for all three NDL members. All three NDL members were collectively showed role in dehydration stress along with specific responses to various treatments. Their specific expression patterns were affected by presence of interacting partner the Arabidopsis heterotrimeric G-protein β subunit 1 (AGB1). The present study will improve our understanding of the possible molecular mechanisms of action of the independent NDL–AGB1 modules during stress and hormonal responses. These findings also suggest potential use of this knowledge for crop improvement.
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6

Fesel, Philipp H., and Alga Zuccaro. "Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis." Current Opinion in Microbiology 32 (August 2016): 103–12. http://dx.doi.org/10.1016/j.mib.2016.05.008.

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7

Foster-Hartnett, Dawn, Joann Mudge, Dana Larsen, Dariush Danesh, Huihuang Yan, Roxanne Denny, Silvia Peñuela, and Nevin D. Young. "Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G." Genome 45, no. 4 (August 1, 2002): 634–45. http://dx.doi.org/10.1139/g02-027.

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Eight DNA markers spanning an interval of approximately 10 centimorgans (cM) on soybean (Glycine max) molecular linkage group G (MLG-G) were used to identify bacterial artificial chromosome (BAC) clones. Twenty-eight BAC clones in eight distinct contiguous groups (contigs) were isolated from this genome region, along with 59 BAC clones on 17 contigs homoeologous to those on MLG-G. BAC clones in four of the MLG-G contigs were also digested to produce subclones and detailed physical maps. All of the BAC-ends were sequenced, as were the subclones, to estimate proportions in different sequence categories, compare similarities among homoeologs, and explore microsynteny with Arabidopsis. Homoeologous BAC contigs were enriched in repetitive sequences compared with those on MLG-G or the soybean genome as a whole. Fingerprint and cross-hybridization comparisons between MLG-G and homoeologous contigs revealed cases of highly similar physical organization between soybean duplicates, as did DNA sequence comparisons. Twenty-seven out of 78 total sequences on soybean MLG-G showed significant similarity to Arabidopsis. The homologs mapped to six compact genome segments in Arabidopsis, with the longest containing seven homologs spanning two million base pairs. These results extend previous observations of large-scale duplication and selective gene loss in Arabidopsis, suggesting that networks of conserved synteny between Arabidopsis and other angiosperm families can stretch over long physical distances.Key words: Arabidopsis thaliana, bacterial artificial chromosomes, Glycine max, microsynteny.
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8

Ikeuchi, Momoko, Takahiro Yamaguchi, Toshiya Kazama, Tasuku Ito, Gorou Horiguchi, and Hirokazu Tsukaya. "ROTUNDIFOLIA4 Regulates Cell Proliferation Along the Body Axis in Arabidopsis Shoot." Plant and Cell Physiology 52, no. 1 (September 8, 2010): 59–69. http://dx.doi.org/10.1093/pcp/pcq138.

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9

Paul, Abhirup, Anurag P. Srivastava, Shreya Subrahmanya, Guoxin Shen, and Neelam Mishra. "In-silico genome wide analysis of Mitogen activated protein kinase kinase kinase gene family in C. sinensis." PLOS ONE 16, no. 11 (November 4, 2021): e0258657. http://dx.doi.org/10.1371/journal.pone.0258657.

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Mitogen activated protein kinase kinase kinase (MAPKKK) form the upstream component of MAPK cascade. It is well characterized in several plants such as Arabidopsis and rice however the knowledge about MAPKKKs in tea plant is largely unknown. In the present study, MAPKKK genes of tea were obtained through a genome wide search using Arabidopsis thaliana as the reference genome. Among 59 candidate MAPKKK genes in tea, 17 genes were MEKK-like, 31 genes were Raf-like and 11 genes were ZIK- like. Additionally, phylogenetic relationships were established along with structural analysis, which includes gene structure, its location as well as conserved motifs, cis-acting regulatory elements and functional domain signatures that were systematically examined. Also, on the basis of one orthologous gene found between tea and Arabidopsis, functional interaction was carried out in C. sinensis based on an Arabidopsis association model. The expressional profiles indicated major involvement of MAPKKK genes from tea in response to various abiotic stress factors. Taken together, this study provides the targets for additional inclusive identification, functional study, and provides comprehensive knowledge for a better understanding of the MAPKKK cascade regulatory network in C. sinensis.
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10

Hardtke, Christian S., and Thomas Berleth. "Genetic and contig map of a 2200-kb region encompassing 5.5 cM on chromosome 1 of Arabidopsis thaliana." Genome 39, no. 6 (December 1, 1996): 1086–92. http://dx.doi.org/10.1139/g96-136.

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In the course of the isolation of the MONOPTEROS (MP) gene, required for primary root formation in Arabidopsis thaliana, a yeast artificial chromosome (YAC) contig encompassing approximately 2200 kilobases corresponding to 5.5 cM on the top arm of chromosome 1 was established. Forty-six YAC clones were characterized and 12 new restriction fragment length polymorphism (RFLP) markers are presented. Three new codominant amplified polymorphic sequence (CAPS) markers were generated that enabled high resolution genetic mapping and correlation of physical and genetic distances along the contig. The map contributes to the completion of a physical map of the Arabidopsis genome and should facilitate positional cloning of other genes in the region as well as studies on genome organization. We also present another set of 11 physically linked probes, as well as mapping data for additional RFLP markers within a broader interval of 10.4 cM. Key words : Arabidopsis, CAPS markers, MONOPTEROS gene, physical map, RFLP markers, YAC contig.
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11

Wang, Ting, Fanghua Li, Qingfang Liu, Po Bian, Jufang Wang, Yuejin Wu, Lijun Wu, and Wenjian Li. "Homologous recombination in Arabidopsis seeds along the track of energetic carbon ions." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 737, no. 1-2 (September 2012): 51–57. http://dx.doi.org/10.1016/j.mrfmmm.2012.05.006.

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12

Cao, Wenhan, Zhenping Li, Shuxian Huang, Yuwei Shi, Ying Zhu, Man Nga Lai, Pui Lok Lok, Xiangfeng Wang, Yong Cui, and Liwen Jiang. "Correlation of vacuole morphology with stomatal lineage development by whole-cell electron tomography." Plant Physiology 188, no. 4 (February 2, 2022): 2085–100. http://dx.doi.org/10.1093/plphys/kiac028.

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Abstract Stomatal movement is essential for plants to optimize transpiration and therefore photosynthesis. Rapid changes in the stomatal aperture are accompanied by adjustment of vacuole volume and morphology in guard cells (GCs). In Arabidopsis (Arabidopsis thaliana) leaf epidermis, stomatal development undergoes a cell-fate transition including four stomatal lineage cells: meristemoid, guard mother cell, young GC, and GC. Little is known about the mechanism underlying vacuole dynamics and vacuole formation during stomatal development. Here, we utilized whole-cell electron tomography (ET) analysis to elucidate vacuole morphology, formation, and development in different stages of stomatal lineage cells at nanometer resolution. The whole-cell ET models demonstrated that large vacuoles were generated from small vacuole stepwise fusion/maturation along stomatal development stages. Further ET analyses verified the existence of swollen intraluminal vesicles inside distinct vacuoles at certain developmental stages of stomatal lineage cells, implying a role of multivesicular body fusion in stomatal vacuole formation. Collectively, our findings demonstrate a mechanism mediating vacuole formation in Arabidopsis stomatal development and may shed light on the role of vacuoles in stomatal movement.
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13

Chan, Jordi, Adrian Sambade, Grant Calder, and Clive Lloyd. "Arabidopsis Cortical Microtubules Are Initiated along, as Well as Branching from, Existing Microtubules." Plant Cell 21, no. 8 (August 2009): 2298–306. http://dx.doi.org/10.1105/tpc.109.069716.

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14

Rao, Muhammad Junaid, Yuantao Xu, Xiaomei Tang, Yue Huang, Jihong Liu, Xiuxin Deng, and Qiang Xu. "CsCYT75B1, a Citrus CYTOCHROME P450 Gene, Is Involved in Accumulation of Antioxidant Flavonoids and Induces Drought Tolerance in Transgenic Arabidopsis." Antioxidants 9, no. 2 (February 17, 2020): 161. http://dx.doi.org/10.3390/antiox9020161.

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CYTOCHROME P450s genes are a large gene family in the plant kingdom. Our earlier transcriptome data revealed that a CYTOCHROME P450 gene of Citrus sinensis (CsCYT75B1) was associated with flavonoid metabolism and was highly induced after drought stress. Here, we characterized the function of CsCYT75B1 in drought tolerance by overexpressing it in Arabidopsis thaliana. Our results demonstrated that the overexpression of the CsCYT75B1 gene significantly enhanced the total flavonoid contents with increased antioxidant activity in transgenic Arabidopsis. The gene expression results showed that several genes that are responsible for the biosynthesis of antioxidant flavonoids were induced by 2–12 fold in transgenic Arabidopsis lines. After 14 days of drought stress, all transgenic lines displayed an enhanced tolerance to drought stress along with accumulating antioxidant flavonoids with lower superoxide radicals and reactive oxygen species (ROS) than wild type plants. In addition, drought-stressed transgenic lines possessed higher antioxidant enzymatic activities than wild type transgenic lines. Moreover, the stressed transgenic lines had significantly lower levels of electrolytic leakage than wild type transgenic lines. These results demonstrate that the CsCYT75B1 gene of sweet orange functions in the metabolism of antioxidant flavonoid and contributes to drought tolerance by elevating ROS scavenging activities.
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15

Arora, Deepanksha, and Daniёl Van Damme. "Motif-based endomembrane trafficking." Plant Physiology 186, no. 1 (February 19, 2021): 221–38. http://dx.doi.org/10.1093/plphys/kiab077.

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Abstract Endomembrane trafficking, which allows proteins and lipids to flow between the different endomembrane compartments, largely occurs by vesicle-mediated transport. Transmembrane proteins intended for transport are concentrated into a vesicle or carrier by undulation of a donor membrane. This is followed by vesicle scission, uncoating, and finally, fusion at the target membrane. Three major trafficking pathways operate inside eukaryotic cells: anterograde, retrograde, and endocytic. Each pathway involves a unique set of machinery and coat proteins that pack the transmembrane proteins, along with their associated lipids, into specific carriers. Adaptor and coatomer complexes are major facilitators that function in anterograde transport and in endocytosis. These complexes recognize the transmembrane cargoes destined for transport and recruit the coat proteins that help form the carriers. These complexes use either linear motifs or posttranslational modifications to recognize the cargoes, which are then packaged and delivered along the trafficking pathways. In this review, we focus on the different trafficking complexes that share a common evolutionary branch in Arabidopsis (Arabidopsis thaliana), and we discuss up-to-date knowledge about the cargo recognition motifs they use.
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16

Su, Shih-Heng, Alexander Moen, Rien M. Groskopf, Katherine L. Baldwin, Brian Vesperman, and Patrick H. Masson. "Low-Speed Clinorotation of Brachypodium distachyon and Arabidopsis thaliana Seedlings Triggers Root Tip Curvatures That Are Reminiscent of Gravitropism." International Journal of Molecular Sciences 24, no. 2 (January 12, 2023): 1540. http://dx.doi.org/10.3390/ijms24021540.

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Clinostats are instruments that continuously rotate biological specimens along an axis, thereby averaging their orientation relative to gravity over time. Our previous experiments indicated that low-speed clinorotation may itself trigger directional root tip curvature. In this project, we have investigated the root curvature response to low-speed clinorotation using Arabidopsis thaliana and Brachypodium distachyon seedlings as models. We show that low-speed clinorotation triggers root tip curvature in which direction is dictated by gravitropism during the first half-turn of clinorotation. We also show that the angle of root tip curvature is modulated by the speed of clinorotation. Arabidopsis mutations affecting gravity susception (pgm) or gravity signal transduction (arg1, toc132) are shown to affect the root tip curvature response to low-speed clinorotation. Furthermore, low-speed vertical clinorotation triggers relocalization of the PIN3 auxin efflux facilitator to the lateral membrane of Arabidopsis root cap statocytes, and creates a lateral gradient of auxin across the root tip. Together, these observations support a role for gravitropism in modulating root curvature responses to clinorotation. Interestingly, distinct Brachypodium distachyon accessions display different abilities to develop root tip curvature responses to low-speed vertical clinorotation, suggesting the possibility of using genome-wide association studies to further investigate this process.
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17

Wijnker, Erik, Hirofumi Harashima, Katja Müller, Pablo Parra-Nuñez, C. Bastiaan de Snoo, Jose van de Belt, Nico Dissmeyer, Martin Bayer, Monica Pradillo, and Arp Schnittger. "The Cdk1/Cdk2 homolog CDKA;1 controls the recombination landscape in Arabidopsis." Proceedings of the National Academy of Sciences 116, no. 25 (June 4, 2019): 12534–39. http://dx.doi.org/10.1073/pnas.1820753116.

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Little is known how patterns of cross-over (CO) numbers and distribution during meiosis are established. Here, we reveal that cyclin-dependent kinase A;1 (CDKA;1), the homolog of human Cdk1 and Cdk2, is a major regulator of meiotic recombination in Arabidopsis. Arabidopsis plants with reduced CDKA;1 activity experienced a decrease of class I COs, especially lowering recombination rates in centromere-proximal regions. Interestingly, this reduction of type I CO did not affect CO assurance, a mechanism by which each chromosome receives at least one CO, resulting in all chromosomes exhibiting similar genetic lengths in weak loss-of-function cdka;1 mutants. Conversely, an increase of CDKA;1 activity resulted in elevated recombination frequencies. Thus, modulation of CDKA;1 kinase activity affects the number and placement of COs along the chromosome axis in a dose-dependent manner.
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18

Giraut, Laurène, Matthieu Falque, Jan Drouaud, Lucie Pereira, Olivier C. Martin, and Christine Mézard. "Genome-Wide Crossover Distribution in Arabidopsis thaliana Meiosis Reveals Sex-Specific Patterns along Chromosomes." PLoS Genetics 7, no. 11 (November 3, 2011): e1002354. http://dx.doi.org/10.1371/journal.pgen.1002354.

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19

Drouaud, Jan, Raphaël Mercier, Liudmila Chelysheva, Aurélie Bérard, Matthieu Falque, Olivier Martin, Vanessa Zanni, Dominique Brunel, and Christine Mézard. "Sex-Specific Crossover Distributions and Variations in Interference Level along Arabidopsis thaliana Chromosome 4." PLoS Genetics 3, no. 6 (June 29, 2007): e106. http://dx.doi.org/10.1371/journal.pgen.0030106.

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20

Drouaud, Jan, Raphael Mercier, Liudmila Chelysheva, Aurélie Bérard, Matthieu Falque, Olivier Martin, Vanessa Zanni, Dominique Brunel, and Christine Mezard. "Sex-specific crossover distributions and variations in interference level along Arabidopsis thaliana chromosome 4." PLoS Genetics preprint, no. 2007 (2005): e106. http://dx.doi.org/10.1371/journal.pgen.0030106.eor.

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21

Wos, Guillaume, and Yvonne Willi. "Temperature-Stress Resistance and Tolerance along a Latitudinal Cline in North American Arabidopsis lyrata." PLOS ONE 10, no. 6 (June 25, 2015): e0131808. http://dx.doi.org/10.1371/journal.pone.0131808.

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22

O'Neal, L., L. C. Ebere, R. McIntyre, M. I. Volkova-Gugeshashvili, V. S. Markin, and A. G. Volkov. "Propagation and Collision of Nonlinear Electrical Responses in Aloe Vera L. and Arabidopsis Thaliana." ECS Transactions 50, no. 54 (April 2, 2013): 7–22. http://dx.doi.org/10.1149/05054.0007ecst.

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23

Suter, Léonie, Marlene Rüegg, Niklaus Zemp, Lars Hennig, and Alex Widmer. "Gene Regulatory Variation Mediates Flowering Responses to Vernalization along an Altitudinal Gradient in Arabidopsis." Plant Physiology 166, no. 4 (October 22, 2014): 1928–42. http://dx.doi.org/10.1104/pp.114.247346.

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24

Yan, Suli, Chunyang Jiao, Eric S. McLamore, Ningning Wang, Hongjun Yao, and Yingbai Shen. "Insect Herbivory of Leaves Affects the Auxin Flux Along Root Apices in Arabidopsis thaliana." Journal of Plant Growth Regulation 36, no. 4 (March 14, 2017): 846–54. http://dx.doi.org/10.1007/s00344-017-9688-4.

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25

Zhang, Lida, Shunwu Yu, Youfang Cao, Jiang Wang, Kaijing Zuo, Jie Qin, and Kexuan Tang. "Distributional gradient of amino acid repeats in plant proteins." Genome 49, no. 8 (August 1, 2006): 900–905. http://dx.doi.org/10.1139/g06-054.

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A computer-based analysis was conducted to assess the characteristics of amino acid repeats in Arabidopsis and rice. Our analysis showed a negative gradient in amino acid repeat distribution along the direction of translation in plants. Repeat occurrences are obviously associated with position in plant proteins but are not consistent with the corresponding amino acid contents. These repeats are encoded by the mixed synonymous codons rather than the uninterrupted reiterations of a single codon, and both Arabidopsis and rice have gradients in their distribution. Functional investigation showed that these repeat-containing proteins are preferentially involved in transcription regulation and protein ubiquitination but significantly underrepresented in the processes of DNA recombination and DNA replication. These data reveal that the direction-related mutation bias and functional selection have influenced the distribution of amino acid repeats in plants.Key words: amino acid repeats, amino acid usage, distributional gradient, regulation of transcription, protein ubiquitination.
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26

Ayaz, Asma, Haodong Huang, Minglü Zheng, Wajid Zaman, Donghai Li, Saddam Saqib, Huayan Zhao, and Shiyou Lü. "Molecular Cloning and Functional Analysis of GmLACS2-3 Reveals Its Involvement in Cutin and Suberin Biosynthesis along with Abiotic Stress Tolerance." International Journal of Molecular Sciences 22, no. 17 (August 25, 2021): 9175. http://dx.doi.org/10.3390/ijms22179175.

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Cutin and wax are the main precursors of the cuticle that covers the aerial parts of plants and provide protection against biotic and abiotic stresses. Long-chain acyl-CoA synthetases (LACSs) play diversified roles in the synthesis of cutin, wax, and triacylglycerol (TAG). Most of the information concerned with LACS functions is obtained from model plants, whereas the roles of LACS genes in Glycine max are less known. Here, we have identified 19 LACS genes in Glycine max, an important crop plant, and further focused our attention on 4 LACS2 genes (named as GmLACS2-1, 2, 3, 4, respectively). These GmLACS2 genes display different expression patterns in various organs and also show different responses to abiotic stresses, implying that these genes might play diversified functions during plant growth and against stresses. To further identify the role of GmLACS2-3, greatly induced by abiotic stresses, we transformed a construct containing its full length of coding sequence into Arabidopsis. The expression of GmLACS2-3 in an Arabidopsis atlacs2 mutant greatly suppressed its phenotype, suggesting it plays conserved roles with that of AtLACS2. The overexpression of GmLACS2-3 in wild-type plants significantly increased the amounts of cutin and suberin but had little effect on wax amounts, indicating the specific role of GmLACS2-3 in the synthesis of cutin and suberin. In addition, these GmLACS2-3 overexpressing plants showed enhanced drought tolerance. Taken together, our study deepens our understanding of the functions of LACS genes in different plants and also provides a clue for cultivating crops with strong drought resistance.
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Wang, Jiehua, Muhammad Moeen-ud-din, Rong Yin, and Shaohui Yang. "ROS Homeostasis Involved in Dose-Dependent Responses of Arabidopsis Seedlings to Copper Toxicity." Genes 14, no. 1 (December 21, 2022): 11. http://dx.doi.org/10.3390/genes14010011.

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As an essential element in plant nutrition, copper (Cu) can promote or inhibit plant growth depending on its concentration. However, the dose-dependent effects of copper, particularly on DNA damage associated with reactive oxygen species (ROS) homeostasis, are much less understood. In this work, we analyzed the dual effect of Cu (5, 20, and 60 μM) on the reproductive performance of Arabidopsis plants. Whereas Cu5 promoted inflorescence initiation and increased kilo seed weight, two higher concentrations, Cu20 and Cu60, delayed inflorescence initiation and negatively affected silique size. Excess Cu also induced changes in cellular redox homeostasis, which was examined by in situ visualization and measurements of ROS, including superoxide (O2•−), hydrogen peroxide (H2O2), malonyldialdehyde (MDA), and plasma membrane damage. The most dramatic increases in the production of O2•− and H2O2 along with increased activity of superoxide dismutase (SOD) and glutathione peroxidase (GPX) and decreased activity of catalase (CAT) and ascorbate peroxidase (APX) were observed in roots with Cu60. Oxidative stress also modulated the expression levels of a number of genes involved in the DNA damage response (DDR), particularly those related to DNA repair. The Cu-induced chlorosis of Arabidopsis seedlings could be alleviated by exogenous addition of glutathione (GSH) and ascorbate (Asc), as the chlorophyll content was significantly increased. Overall, internal homeostasis ROS and the associated DDR pathway and the corresponding scavenging mechanisms play a central role in the response of Arabidopsis to oxidative stress induced by inhibitory Cu concentrations. Our results have shown, for the first time, that the biphasic responses of Arabidopsis seedlings to increasing Cu concentrations involve different DNA damage responses and oxidative reactions. They provide the basis for elucidating the network of Cu-induced DDR-related genes and the regulatory mechanism of the complex ROS production and scavenging system.
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Hummel, Guillaume, Alexandre Berr, Stéfanie Graindorge, Valérie Cognat, Elodie Ubrig, David Pflieger, Jean Molinier, and Laurence Drouard. "Epigenetic silencing of clustered tRNA genes in Arabidopsis." Nucleic Acids Research 48, no. 18 (September 17, 2020): 10297–312. http://dx.doi.org/10.1093/nar/gkaa766.

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Abstract Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.
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Kalde, Monika, Meike Barth, Imre E. Somssich, and Bernadette Lippok. "Members of the Arabidopsis WRKY Group III Transcription Factors Are Part of Different Plant Defense Signaling Pathways." Molecular Plant-Microbe Interactions® 16, no. 4 (April 2003): 295–305. http://dx.doi.org/10.1094/mpmi.2003.16.4.295.

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WRKY proteins are a large group of transcription factors restricted to the plant kingdom. In Arabidopsis thaliana, the gene family consists of 74 members. Here, we analyzed the expression of all 13 members of one main WRKY subgroup and found that the majority are responsive both to pathogen infection and to salicylic acid. Temporal expression studies during compatible, incompatible, and nonhost interactions and employing plant defense-signaling mutants allowed us to define four distinct WRKY subsets responding to different signaling queues along defense pathways. These subsets did not reflect phylogenetic relationships. Promoter studies of one member, AtWRKY54, using a reporter gene construct in transgenic Arabidopsis plants, revealed that regulatory regions mediating pathogen and SA inducibility are clearly separable. In an AtWRKY54 knockout line, resistance to Peronospora parasitica was not compromised, but the transient expression kinetics of several WRKY genes was affected, suggesting both the existence of functional redundancy and intense cross-talk between signaling networks.
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Louveaux, Marion, Jean-Daniel Julien, Vincent Mirabet, Arezki Boudaoud, and Olivier Hamant. "Cell division plane orientation based on tensile stress in Arabidopsis thaliana." Proceedings of the National Academy of Sciences 113, no. 30 (July 19, 2016): E4294—E4303. http://dx.doi.org/10.1073/pnas.1600677113.

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Cell geometry has long been proposed to play a key role in the orientation of symmetric cell division planes. In particular, the recently proposed Besson–Dumais rule generalizes Errera’s rule and predicts that cells divide along one of the local minima of plane area. However, this rule has been tested only on tissues with rather local spherical shape and homogeneous growth. Here, we tested the application of the Besson–Dumais rule to the divisions occurring in the Arabidopsis shoot apex, which contains domains with anisotropic curvature and differential growth. We found that the Besson–Dumais rule works well in the central part of the apex, but fails to account for cell division planes in the saddle-shaped boundary region. Because curvature anisotropy and differential growth prescribe directional tensile stress in that region, we tested the putative contribution of anisotropic stress fields to cell division plane orientation at the shoot apex. To do so, we compared two division rules: geometrical (new plane along the shortest path) and mechanical (new plane along maximal tension). The mechanical division rule reproduced the enrichment of long planes observed in the boundary region. Experimental perturbation of mechanical stress pattern further supported a contribution of anisotropic tensile stress in division plane orientation. Importantly, simulations of tissues growing in an isotropic stress field, and dividing along maximal tension, provided division plane distributions comparable to those obtained with the geometrical rule. We thus propose that division plane orientation by tensile stress offers a general rule for symmetric cell division in plants.
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Rahman, Tawhidur, Mingxuan Shao, Shankar Pahari, Prakash Venglat, Raju Soolanayakanahally, Xiao Qiu, Abidur Rahman, and Karen Tanino. "Dissecting the Roles of Cuticular Wax in Plant Resistance to Shoot Dehydration and Low-Temperature Stress in Arabidopsis." International Journal of Molecular Sciences 22, no. 4 (February 4, 2021): 1554. http://dx.doi.org/10.3390/ijms22041554.

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Cuticular waxes are a mixture of hydrophobic very-long-chain fatty acids and their derivatives accumulated in the plant cuticle. Most studies define the role of cuticular wax largely based on reducing nonstomatal water loss. The present study investigated the role of cuticular wax in reducing both low-temperature and dehydration stress in plants using Arabidopsis thaliana mutants and transgenic genotypes altered in the formation of cuticular wax. cer3-6, a known Arabidopsis wax-deficient mutant (with distinct reduction in aldehydes, n-alkanes, secondary n-alcohols, and ketones compared to wild type (WT)), was most sensitive to water loss, while dewax, a known wax overproducer (greater alkanes and ketones compared to WT), was more resistant to dehydration compared to WT. Furthermore, cold-acclimated cer3-6 froze at warmer temperatures, while cold-acclimated dewax displayed freezing exotherms at colder temperatures compared to WT. Gas Chromatography-Mass Spectroscopy (GC-MS) analysis identified a characteristic decrease in the accumulation of certain waxes (e.g., alkanes, alcohols) in Arabidopsis cuticles under cold acclimation, which was additionally reduced in cer3-6. Conversely, the dewax mutant showed a greater ability to accumulate waxes under cold acclimation. Fourier Transform Infrared Spectroscopy (FTIR) also supported observations in cuticular wax deposition under cold acclimation. Our data indicate cuticular alkane waxes along with alcohols and fatty acids can facilitate avoidance of both ice formation and leaf water loss under dehydration stress and are promising genetic targets of interest.
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32

Puizina, Jasna, Hanna Weiss-Schneeweiss, Andrea Pedrosa-Harand, Juraj Kamenjarin, Ivo Trinajstic, Karel Riha, and Dieter Schweizer. "Karyotype analysis in Hyacinthella dalmatica (Hyacinthaceae) reveals vertebrate-type telomere repeats at the chromosome ends." Genome 46, no. 6 (December 1, 2003): 1070–76. http://dx.doi.org/10.1139/g03-078.

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Chromosome analysis of three different populations of Hyacinthella dalmatica (Lallem.) Trinajsti[Formula: see text] , an endemic species of the coastal region of southeastern Europe, showed a unique chromosome number, 2n = 2x = 20, and bimodal karyotype with one large and nine smaller pairs of chromosomes. Staining with fluorochromes CMA3 (chromomycin A3) and DAPI (4,6-diamidino-2-phenylindole) revealed heterochromatic regions associated with NORs, centromeres, and several interstitial heterochromatic bands on the longest chromosome pair. Double-target FISH with two ribosomal DNA probes revealed one locus of 5S rRNA genes in the pericentromeric region of chromosome pair 3 and one locus of 18S-5.8S-26S rRNA genes on the short arm of chromosome pair 4 in all plants and populations analyzed. Southern hybridization analysis and FISH experiments demonstrated that the distal ends of H. dalmatica chromosomes contain the vertebrate telomere (5'-TTAGGG-3') repeat type rather than the Arabidopsis (5'-TTTAGGG-3') heptamer, and so suggest that this Asparagales species along with Aloe and Othocallis contains the vertebrate-type telomere repeat.Key words: Hyacinthaceae, Hyacinthella, chromosomes, ribosomal genes, telomeric repeats.
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Günther, Torsten, Christian Lampei, Ivan Barilar, and Karl J. Schmid. "Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps." Molecular Ecology 25, no. 15 (July 2, 2016): 3574–92. http://dx.doi.org/10.1111/mec.13705.

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Lloyd, Andrew, and Eric Jenczewski. "Modelling Sex-Specific Crossover Patterning in Arabidopsis." Genetics 211, no. 3 (January 22, 2019): 847–59. http://dx.doi.org/10.1534/genetics.118.301838.

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“Interference” is a major force governing the patterning of meiotic crossovers. A leading model describing how interference influences crossover patterning is the beam-film model, a mechanical model based on the accumulation and redistribution of crossover-promoting “stress” along the chromosome axis. We use the beam-film model in conjunction with a large Arabidopsis reciprocal backcross data set to gain “mechanistic” insights into the differences between male and female meiosis, and crossover patterning. Beam-film modeling suggests that the underlying mechanics of crossover patterning and interference are identical in the two sexes, with the large difference in recombination rates and distributions able to be entirely explained by the shorter chromosome axes in females. The modeling supports previous indications that fewer crossovers occur via the class II pathway in female meiosis and that this could be explained by reduced DNA double-strand breaks in female meiosis, paralleling the observed reduction in synaptonemal complex length between the two sexes. We also demonstrate that changes in the strength of suppression of neighboring class I crossovers can have opposite effects on “effective” interference depending on the distance between two genetic intervals.
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Balasubramanian, Sureshkumar, and Kay Schneitz. "NOZZLE links proximal-distal and adaxial-abaxial pattern formation during ovule development in Arabidopsis thaliana." Development 129, no. 18 (September 15, 2002): 4291–300. http://dx.doi.org/10.1242/dev.129.18.4291.

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The ovules of Arabidopsis show polarity along the proximal-distal and the adaxial-abaxial axis. NOZZLE, a gene that encodes a novel protein and BELL1, encoding a homeodomain protein, play a vital role in pattern formation along the proximal-distal axis. INNER NO OUTER, which encodes a member of the YABBY family of transcription factors and SUPERMAN, encoding a zinc finger transcription factor, are essential for the establishment and maintenance of adaxial-abaxial polarity. To date, the co-ordination of patterning along these two axes is unclear. Here we show that NOZZLE plays a vital role in pattern formation along the adaxial-abaxial axis as well. We investigated the expression of INNER NO OUTER in various mutant backgrounds and have identified ABERRANT TESTA SHAPE and NOZZLE as spatial regulators of INNER NO OUTER expression. In addition, we show that NOZZLE and AINTEGUMENTA, which encodes an AP2 domain transcription factor, regulate the temporal expression of INNER NO OUTER and that BELL1 is essential for INNER NO OUTER expression. We further analysed the expression of BELL1 and AINTEGUMENTA in inner no outer mutants and show that the positive auto-regulatory control of INNER NO OUTER expression involves AINTEGUMENTA. Based on our results we propose a model for adaxial-abaxial pattern formation during ovule development. Our results indicate that NOZZLE plays a central role in patterning both the proximal-distal and the adaxial-abaxial axes. Furthermore, negatively regulating INO expression in a temporal manner, ensures that the adaxial-abaxial polarity is established after the specification of the chalaza, a proximal-distal axis pattern element. It therefore serves as a molecular link between these processes during ovule development in Arabidopsis thaliana.
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36

Naz, Ruphi, Andleeb Khan, Badrah S. Alghamdi, Ghulam Md Ashraf, Maimonah Alghanmi, Altaf Ahmad, Sheikh Shanawaz Bashir, and Qazi Mohd Rizwanul Haq. "An Insight into Animal Glutamate Receptors Homolog of Arabidopsis thaliana and Their Potential Applications—A Review." Plants 11, no. 19 (September 30, 2022): 2580. http://dx.doi.org/10.3390/plants11192580.

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Most excitatory impulses received by neurons are mediated by ionotropic glutamate receptors (iGluRs). These receptors are located at the apex and play an important role in memory, neuronal development, and synaptic plasticity. These receptors are ligand-dependent ion channels that allow a wide range of cations to pass through. Glutamate, a neurotransmitter, activates three central ionotropic receptors: N-methyl-D-aspartic acid (NMDA), -amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA), and kainic acid (KA). According to the available research, excessive glutamate release causes neuronal cell death and promotes neurodegenerative disorders. Arabidopsis thaliana contains 20 glutamate receptor genes (AtGluR) comparable to the human ionotropic glutamate (iGluRs) receptor. Many studies have proved that AtGL-rec genes are involved in a number of plant growth and physiological activities, such as in the germination of seeds, roots, abiotic and biotic stress, and cell signaling, which clarify the place of these genes in plant biology. In spite of these, the iGluRs, Arabidopsis glutamate receptors (AtGluR), is associated with the ligand binding activity, which confirms the evolutionary relationship between animal and plant glutamate receptors. Along with the above activities, the impact of mammalian agonists and antagonists on Arabidopsis suggests a correlation between plant and animal glutamate receptors. In addition, these glutamate receptors (plant/animal) are being utilized for the early detection of neurogenerative diseases using the fluorescence resonance energy transfer (FRET) approach. However, a number of scientific laboratories and institutes are consistently working on glutamate receptors with different aspects. Currently, we are also focusing on Arabidopsis glutamate receptors. The current review is focused on updating knowledge on AtGluR genes, their evolution, functions, and expression, and as well as in comparison with iGluRs. Furthermore, a high throughput approach based on FRET nanosensors developed for understanding neurotransmitter signaling in animals and plants via glutamate receptors has been discussed. The updated information will aid in the future comprehension of the complex molecular dynamics of glutamate receptors and the exploration of new facts in plant/animal biology.
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37

Aslam, Muhammad Zeshan, Xiang Lin, Xiang Li, Nan Yang, and Longqing Chen. "Molecular Cloning and Functional Characterization of CpMYC2 and CpBHLH13 Transcription Factors from Wintersweet (Chimonanthus praecox L.)." Plants 9, no. 6 (June 23, 2020): 785. http://dx.doi.org/10.3390/plants9060785.

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Wintersweet (Chimonanthus praecox L.) is an ornamental and economically significant shrub known for its unique flowering characteristics, especially the emission of abundant floral volatile organic compounds. Thus, an understanding of the molecular mechanism of the production of these compounds is necessary to create new breeds with high volatile production. In this study, two bHLH transcription factors (CpMYC2 and CpbHLH13) of Wintersweet H29 were functionally characterized to illustrate their possible role in the production of volatile compounds. The qRT-PCR results showed that the expression of CpMYC2 and CpbHLH13 increased from the flower budding to full bloom stage, indicating that these two genes may play an essential role in blooming and aroma production in wintersweet. Gas chromatography-mass spectroscopy (GC-MS) analysis revealed that the overexpression of CpMYC2 in arabidopsis (Arabidopsis thaliana) AtMYC2-2 mutant (Salk_083483) and tobacco (Nicotiana tabaccum) genotype Petit Havana SR1 significantly increased floral volatile monoterpene, especially linalool, while the overexpression of CpbHLH13 in Arabidopsis thaliana ecotype Columbia-0 (Col-0) and tobacco genotype SR1 increased floral sesquiterpene β-caryophyllene production in both types of transgenic plants respectively. High expression of terpene synthase (TPS) genes in transgenic A. thaliana along with high expression of CpMYC2 and CpbHLH13 in transgenic plants was also observed. The application of a combination of methyl jasmonic acid (MeJA) and gibberellic acid (GA3) showed an increment in linalool production in CpMYC2-overexpressing arabidopsis plants, and the high transcript level of TPS genes also suggested the involvement of CpMYC2 in the jasmonic acid (JA) signaling pathway. These results indicate that both the CpMYC2 and CpbHLH13 transcription factors of wintersweet are possibly involved in the positive regulation and biosynthesis of monoterpene (linalool) and sesquiterpene (β-caryophyllene) in transgenic plants. This study also indicates the potential application of wintersweet as a valuable genomic material for the genetic modification of floral scent in other flowering plants that produce less volatile compounds.
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38

Zhang, Liquan, Xuhui Jia, Jingwei Zhao, Agula Hasi, and Yiding Niu. "Molecular characterisation and expression analysis of NAC transcription factor genes in wild Medicago falcata under abiotic stresses." Functional Plant Biology 47, no. 4 (2020): 327. http://dx.doi.org/10.1071/fp19199.

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The No apical meristem–Arabidopsis transcription activation factor–Cup-shaped cotyledon (NAC) proteins play vital roles in plant development processes and responses to abiotic stress. In this study, 146 unigenes were identified as NAC genes from wild Medicago falcata L. by RNA sequencing. Among these were 30 full-length NACs, which, except for MfNAC63, MfNAC64 and MfNAC91, contained a complete DNA-binding domain and a variable transcriptional activation region. Sequence analyses of MfNACs along with their Arabidopsis thaliana (L.) Heynh. counterparts allowed these proteins to be phylogenetically classified into nine groups. MfNAC35, MfNAC88, MfNAC79, MfNAC26 and MfNAC95 were found to be stress-responsive genes. The eight MfNAC genes that were chosen for further analysis had different expression abilities in the leaves, stems and roots of M. falcata. Additionally, their expression levels were regulated by salinity, drought and cold stress, and ABA. This study will be useful for understanding the roles of MfNACs in wild M. falcata and could provide important information for the selection of candidate genes associated with stress tolerance.
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39

Sessions, R. A., and P. C. Zambryski. "Arabidopsis gynoecium structure in the wild and in ettin mutants." Development 121, no. 5 (May 1, 1995): 1519–32. http://dx.doi.org/10.1242/dev.121.5.1519.

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The gynoecium is the female reproductive structure of flowering plants. Here we present a description of the Arabidopsis thaliana gynoecium at anthesis. The cylindrical organ can be broken down into three longitudinal regions arranged in an apical-basal order: stigma, style, and ovary. Each region can be distinguished histologically and morphologically. The transmitting (pollination) tract is axially positioned along the center of the gynoecium and spans stigma, style and ovary. Histochemistry, scanning electron microscopy and a style-specific reporter gene are used to compare the wild-type pattern of gynoecium cell types and regions, with patterns formed in gynoecia of individuals homozygous for a series of allelic mutations at the ETTIN locus. ettin gynoecia show morphological and histological alterations that appear to result from the merging of apical and basal regions and the development of abaxial into adaxial tissues. These developmental abnormalities result in a reduction of the ovary region, an expansion of the stylar and stigmatic regions, and the abaxial (outward) proliferation of transmitting tract tissue. The alterations in the mutants can be interpreted as resulting from misspecifications of position along the longitudinal and transverse axes during gynoecium development. The results suggest that early patterning events underlie wild-type gynoecium development, and that ETT functions during this early programming.
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40

Yuan, Benqi, Minghao Chen, and Shaoshan Li. "Isolation and Identification of Ipomoea cairica (L.) Sweet Gene IcSRO1 Encoding a SIMILAR TO RCD-ONE Protein, Which Improves Salt and Drought Tolerance in Transgenic Arabidopsis." International Journal of Molecular Sciences 21, no. 3 (February 4, 2020): 1017. http://dx.doi.org/10.3390/ijms21031017.

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Ipomoea cairica is a tropical plant and a wild relative of the food plant sweet potato (Ipomoea batatas), listed as one of the most invasive alien species in China. Recently, it has been reported that I. cairica had successfully invaded mangrove wetlands, indicating its high salt tolerance. Based on previous genetic studies, I. cairica offers a good model for characterizing stress-resistant genes. It has recently been identified that the SRO proteins (SIMILAR TO RCD-ONE) play important roles in a variety of stress and developmental responses. Radical-Induced Cell Death1 (RCD1) was the first identified plant SRO protein from Arabidopsis thaliana. As a typical SRO protein, IcSRO1 had a highly conservative WWE domain, a conserved PARP fold and protein C in the RST function area. The expression of IcSRO1 was induced by salt, drought, and the plant hormone ABA. The transgenic Arabidopsis overexpressing IcSRO1 showed higher tolerance against salt and drought stress along with lower accumulation of hydrogen peroxide (H2O2) and superoxide (O2−) than the wild type. The IcSRO1 protein was localized in the nucleus after cultivation in the buffer. Our results indicated it could interact with Arabidopsis SALT OVERLY SENSITIVE 1 (AtSOS1), suggesting IcSRO1 may have similar functions. The pleiotropic effect of IcSRO1 on physiological processes contributes to the improvement of plant tolerance against diverse abiotic stresses, and may be associated with the adaptation of I. cairica to those environments with extreme saline and drought conditions. It therefore provides valuable gene resources for crop breeding enhancement.
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Hua, Zhihua. "Diverse Evolution in 111 Plant Genomes Reveals Purifying and Dosage Balancing Selection Models for F-Box Genes." International Journal of Molecular Sciences 22, no. 2 (January 16, 2021): 871. http://dx.doi.org/10.3390/ijms22020871.

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The F-box proteins function as substrate receptors to determine the specificity of Skp1-Cul1-F-box ubiquitin ligases. Genomic studies revealed large and diverse sizes of the F-box gene superfamily across plant species. Our previous studies suggested that the plant F-box gene superfamily is under genomic drift evolution promoted by epigenomic programming. However, how the size of the superfamily drifts across plant genomes is currently unknown. Through a large-scale genomic and phylogenetic comparison of the F-box gene superfamily covering 110 green plants and one red algal species, I discovered four distinct groups of plant F-box genes with diverse evolutionary processes. While the members in Clusters 1 and 2 are species/lineage-specific, those in Clusters 3 and 4 are present in over 46 plant genomes. Statistical modeling suggests that F-box genes from the former two groups are skewed toward fewer species and more paralogs compared to those of the latter two groups whose presence frequency and sizes in plant genomes follow a random statistical model. The enrichment of known Arabidopsis F-box genes in Clusters 3 and 4, along with comprehensive biochemical evidence showing that Arabidopsis members in Cluster 4 interact with the Arabidopsis Skp1-like 1 (ASK1), demonstrates over-representation of active F-box genes in these two groups. Collectively, I propose purifying and dosage balancing selection models to explain the lineage/species-specific duplications and expansions of F-box genes in plant genomes. The purifying selection model suggests that most, if not all, lineage/species-specific F-box genes are detrimental and are thus kept at low frequencies in plant genomes.
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Schneitz, K., S. C. Baker, C. S. Gasser, and A. Redweik. "Pattern formation and growth during floral organogenesis: HUELLENLOS and AINTEGUMENTA are required for the formation of the proximal region of the ovule primordium in Arabidopsis thaliana." Development 125, no. 14 (July 15, 1998): 2555–63. http://dx.doi.org/10.1242/dev.125.14.2555.

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Our understanding of the molecular mechanisms that regulate and integrate the temporal and spatial control of cell proliferation during organ ontogenesis, particularly of floral organs, continues to be primitive. The ovule, the progenitor of the seed, of Arabidopsis thaliana has been used to develop an effective model system for the analysis of plant organogenesis. A typical feature of a generalized ovule is the linear arrangement of at least three distinct elements, the funiculus, chalaza and nucellus, along a proximal-distal axis. This pattern is supposed to be established during the early proliferative phase of ovule development. We provide genetic evidence that the young ovule primordium indeed is a composite structure. Two genes, HUELLENLOS and AINTEGUMENTA have overlapping functions in the ovule and differentially control the formation of the central and proximal elements of the primordium. The results indicate that proximal-distal pattern formation in the Arabidopsis ovule takes place in a sequential fashion, starting from the distal end. Furthermore, we show that HUELLENLOS also regulates the initiation and/or maintenance of integument and embryo sac ontogenesis and interestingly prevents inappropriate cell death in the young ovule.
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43

Pick, Elah, On-Sun Lau, Tomohiko Tsuge, Suchithra Menon, Yingchun Tong, Naoshi Dohmae, Scott M. Plafker, Xing Wang Deng, and Ning Wei. "Mammalian DET1 Regulates Cul4A Activity and Forms Stable Complexes with E2 Ubiquitin-Conjugating Enzymes." Molecular and Cellular Biology 27, no. 13 (April 23, 2007): 4708–19. http://dx.doi.org/10.1128/mcb.02432-06.

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ABSTRACT DET1 (de-etiolated 1) is an essential negative regulator of plant light responses, and it is a component of the Arabidopsis thaliana CDD complex containing DDB1 and COP10 ubiquitin E2 variant. Human DET1 has recently been isolated as one of the DDB1- and Cul4A-associated factors, along with an array of WD40-containing substrate receptors of the Cul4A-DDB1 ubiquitin ligase. However, DET1 differs from conventional substrate receptors of cullin E3 ligases in both biochemical behavior and activity. Here we report that mammalian DET1 forms stable DDD-E2 complexes, consisting of DDB1, DDA1 (DET1, DDB1 associated 1), and a member of the UBE2E group of canonical ubiquitin-conjugating enzymes. DDD-E2 complexes interact with multiple ubiquitin E3 ligases. We show that the E2 component cannot maintain the ubiquitin thioester linkage once bound to the DDD core, rendering mammalian DDD-E2 equivalent to the Arabidopsis CDD complex. While free UBE2E-3 is active and able to enhance UbcH5/Cul4A activity, the DDD core specifically inhibits Cul4A-dependent polyubiquitin chain assembly in vitro. Overexpression of DET1 inhibits UV-induced CDT1 degradation in cultured cells. These findings demonstrate that the conserved DET1 complex modulates Cul4A functions by a novel mechanism.
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44

Viñegra de la Torre, Natanael, Farnusch Kaschani, Markus Kaiser, Renier A. L. van der Hoorn, Wim J. J. Soppe, and Johana C. Misas Villamil. "Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds." Biochemical Journal 476, no. 5 (March 12, 2019): 843–57. http://dx.doi.org/10.1042/bcj20180911.

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Abstract Seed quality is affected by different constituents of the seed. In general, seed lots are considered to be of high quality when they exhibit fast and homogeneous germination. When seeds are stored, they undergo different degrees of damage that have detrimental effects on their quality. Therefore, accurate prediction of the seed quality and viability levels of a seed lot is of high importance in the seed-producing industry. Here, we describe the use of activity-based protein profiling of proteases to evaluate the quality of artificially and naturally aged seeds of Arabidopsis thaliana. Using this approach, we have identified two protease activities with opposite behaviours in aged seeds of Arabidopsis that correlate with the quality status of the seeds. We show that vacuolar processing enzymes (VPEs) become more active during the ageing process, in both artificial and natural ageing treatments. Secondly, we demonstrate that serine hydrolases are active at the beginning of our artificial ageing treatment, but their labelling decreases along with seed viability. We present a list of candidate hydrolases active during seed germination and propose that these protease activities can be used in combination with VPEs to develop novel markers of seed quality.
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Wang, Feng, Dong Ding, Jiaxin Li, Lin He, Xiaoxuan Xu, Ying Zhao, Bowei Yan, Zuotong Li, and Jingyu Xu. "Characterisation of genes involved in galactolipids and sulfolipids metabolism in maize and Arabidopsis and their differential responses to phosphate deficiency." Functional Plant Biology 47, no. 4 (2020): 279. http://dx.doi.org/10.1071/fp19082.

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Galactolipids (MGDG and DGDG) and sulfolipids (SQDG) are key components of plastidic membranes, and play important roles in plant development and photosynthesis. In this study, the whole families of MGD, DGD and SQD were identified in maize genome, and were designated as ZmMGD1-3, ZmDGD1-5 and ZmSQD1-5 respectively. Based on the phylogenetic analyses, maize and Arabidopsis MGDs, DGDs and SQDs were clearly divided into two major categories (Type A and Type B) along with their orthologous genes from other plant species. Under low-phosphorus condition, the expression of Type B MGD, DGD and SQD genes of maize and Arabidopsis were significantly elevated in both leaf and root tissues. The lipid analysis was also conducted, and an overall increase in non-phosphorus lipids (MGDG, DGDG and SQDG), and a decrease in phosphorus lipids (PC, PE and PA) were observed in maize leaves and roots under phosphate deficiency. Several maize MGD and SQD genes were found involved in various abiotic stress responses. These findings will help for better understanding the specific functions of MGDs, DGDs and SQDs in 18:3 plants and for the generation of improved crops adapted to phosphate starvation and other abiotic stresses.
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Li, Chunyang, Ke Zhang, Xianwu Zeng, Stephen Jackson, Yu Zhou, and Yiguo Hong. "A cis Element within Flowering Locus T mRNA Determines Its Mobility and Facilitates Trafficking of Heterologous Viral RNA." Journal of Virology 83, no. 8 (February 4, 2009): 3540–48. http://dx.doi.org/10.1128/jvi.02346-08.

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ABSTRACT The Arabidopsis flowering locus T (FT) gene encodes the mobile florigen essential for floral induction. While movement of the FT protein has been shown to occur within plants, systemic spread of FT mRNA remains to be unequivocally demonstrated. Utilizing novel RNA mobility assay vectors based on two distinct movement-defective viruses, Potato virus X and Turnip crinkle virus, and an agroinfiltration assay, we demonstrate that nontranslatable FT mRNA, independent of the FT protein, moves throughout Nicotiana benthamiana and mutant Arabidopsis plants and promotes systemic trafficking of viral and green fluorescence protein RNAs. Viral ectopic expression of FT induced flowering in the short-day N. tabacum Maryland Mammoth tobacco under long-day conditions. Recombinant Potato virus X bearing FT RNA spread and established systemic infection more quickly than the parental virus. The cis-acting element essential for RNA movement was mapped to the nucleotides 1 to 102 of the FT mRNA coding sequence. These data demonstrate that a plant self-mobile RNA molecule can mediate long-distance trafficking of heterologous RNAs and raise the possibility that FT RNA, along with the FT protein, may be involved in the spread of the floral stimulus throughout the plant.
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47

Moreno-Risueno, Miguel A., Jaimie M. Van Norman, Antonio Moreno, Jingyuan Zhang, Sebastian E. Ahnert, and Philip N. Benfey. "Oscillating Gene Expression Determines Competence for Periodic Arabidopsis Root Branching." Science 329, no. 5997 (September 9, 2010): 1306–11. http://dx.doi.org/10.1126/science.1191937.

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Plants and animals produce modular developmental units in a periodic fashion. In plants, lateral roots form as repeating units along the root primary axis; however, the developmental mechanism regulating this process is unknown. We found that cyclic expression pulses of a reporter gene mark the position of future lateral roots by establishing prebranch sites and that prebranch site production and root bending are periodic. Microarray and promoter-luciferase studies revealed two sets of genes oscillating in opposite phases at the root tip. Genetic studies show that some oscillating transcriptional regulators are required for periodicity in one or both developmental processes. This molecular mechanism has characteristics that resemble molecular clock–driven activities in animal species.
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48

Kim, Mangi, Hong Xi, and Jongsun Park. "Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors." PLOS ONE 16, no. 5 (May 26, 2021): e0252181. http://dx.doi.org/10.1371/journal.pone.0252181.

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GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
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49

Ye, Tao, Wang Dan, Liu Tong, Jiang Chengguo, Zhai Wei, Li Yongguan, and Tang Cheng. "Community characteristics of Arabidopsis thaliana natural populations in the northern Tianshan Mountains along with relevant environmental factors." Biodiversity Science 17, no. 1 (2009): 51. http://dx.doi.org/10.3724/sp.j.1003.2009.08169.

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50

Toyokura, Koichi, Keiro Watanabe, Akira Oiwaka, Miyako Kusano, Toshiaki Tameshige, Kiyoshi Tatematsu, Noritaka Matsumoto, Ryuji Tsugeki, Kazuki Saito, and Kiyotaka Okada. "Succinic Semialdehyde Dehydrogenase is Involved in the Robust Patterning of Arabidopsis Leaves along the Adaxial–Abaxial Axis." Plant and Cell Physiology 52, no. 8 (June 20, 2011): 1340–53. http://dx.doi.org/10.1093/pcp/pcr079.

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