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DeOri: a database of eukaryotic DNA replication origins

F. Gao, H. Luo, C.-T. Zhang
2012 Bioinformatics  
However, only few eukaryotic replication origins were characterized not long ago; nevertheless, recent genome-wide approaches have boosted the number of mapped replication origins.  ...  148, 348 and 6184 for humans, mice, Arabidopsis thaliana, Kluyveromyces lactis, Schizosaccharomyces pombe and Drosophila melanogaster, respectively.  ...  Dutta and Dr Kumar for providing the positions of 150 replication origins in human. We would also like to thank Prof. Masukata and Prof.  ... 
doi:10.1093/bioinformatics/bts151 pmid:22467915 fatcat:juh4ofkaijcmrn3z4rpwfianbe

G4 Structures in Control of Replication and Transcription of rRNA Genes

Kateřina Havlová, Jiří Fajkus
2020 Frontiers in Plant Science  
Here, we present examples of rDNA promoter regions with extremely high potential to form G4 in two model plants, Arabidopsis thaliana and Physcomitrella patens.  ...  ancient origin of G4 as a regulatory module.  ...  RTEL1 also promotes genome-wide replication through its interaction with PCNA, increasing replication fork stability, extension rates, and origin usage (Vannier et al., 2013) .  ... 
doi:10.3389/fpls.2020.593692 pmid:33133121 pmcid:PMC7579416 fatcat:ptsx2pd4hvb3tnlzjdl66pfdva

Comparative Genomics of Brassica oleracea and Arabidopsis thaliana Reveal Gene Loss, Fragmentation, and Dispersal after Polyploidy

C. D. Town
2006 The Plant Cell  
We found evidence for the frequent insertion of gene fragments of nuclear genomic origin and identified four apparently intact genes in noncollinear positions in the B. oleracea and A. thaliana genomes  ...  We sequenced 2.2 Mb representing triplicated genome segments of Brassica oleracea, which are each paralogous with one another and homologous with a segmentally duplicated region of the Arabidopsis thaliana  ...  Biotechnology and Biological Sciences Research Council competitive support grant to I.B. and M.T. and by U.S. National Science Foundation Cooperative Agreement DBI-9813586 to TIGR.  ... 
doi:10.1105/tpc.106.041665 pmid:16632643 pmcid:PMC1475499 fatcat:ntwrlwkkf5dbzjt74fkrqadbq4

Codon usage pattern and predicted gene expression in Arabidopsis thaliana

Satyabrata Sahoo, Shib Sankar Das, Ria Rakshit
2019 Gene: X  
The codon usage pattern of genes in Arabidopsis thaliana genome is a classical topic for plant biologists for its significance in the understanding of molecular plant biology.  ...  In this study, a critical analysis of predicted highly expressed (PHE) genes in Arabidopsis thaliana has been performed using MRCBS as a numerical estimator of gene expression level.  ...  Declaration of interests We, the authors declare that we have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.  ... 
doi:10.1016/j.gene.2019.100012 pmid:32550546 pmcid:PMC7286098 fatcat:24azyha5rradjbd4lpgfkttzde

Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases

J. Alberto Romero Navarro, Wilbert Phillips-Mora, Adriana Arciniegas-Leal, Allan Mata-Quirós, Niina Haiminen, Guiliana Mustiga, Donald Livingstone III, Harm van Bakel, David N. Kuhn, Laxmi Parida, Andrew Kasarskis, Juan C. Motamayor
2017 Frontiers in Plant Science  
Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance.  ...  A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years.  ...  ACKNOWLEDGMENTS We would like to thank José Castillo and field workers at the trial locations for their contributions to data collection and maintenance of the plants in the field.  ... 
doi:10.3389/fpls.2017.01905 pmid:29184558 pmcid:PMC5694496 fatcat:omjn5n2vcbf5xbetkjxmk24a2i

Diversity and evolution of transposable elements in Arabidopsis

Zoé Joly-Lopez, Thomas E. Bureau
2014 Chromosome Research  
Although first viewed solely as selfish, transposable elements are now known as important vectors to drive the adaptation and evolution of their host genome.  ...  In plants, the need to adapt rapidly to changing environmental conditions is essential and is reflected, as will be discussed, by genome plasticity and an abundance of diverse, active transposon families  ...  the new mil- lennium: the publication of the first plant genome sequence, Arabidopsis thaliana (Arabidopsis Genome  ... 
doi:10.1007/s10577-014-9418-8 pmid:24801342 fatcat:tn7ltrruajeafgfahinsymw6cy

Chloroplast research in the genomic age

Dario Leister
2003 Trends in Genetics  
In A. thaliana, the protein content of the thylakoid lumen has been characterized by two-dimensional electrophoresis and mass spectrometry, as well as by genome-wide searches for the TAT motif.  ...  These estimates are based on the computational identification of cTPs in the predicted protein-coding regions of the Arabidopsis genome.  ...  Work in my laboratory is supported by grants of the Deutsche Forschungsgemeinschaft, the Bundesministerium fü r Bildung and Forschung, and the European Community.  ... 
doi:10.1016/s0168-9525(02)00003-3 pmid:12493248 fatcat:la3inpesgjb6xdy2atojdh63ge

Genomic Survey and Cold-Induced Expression Patterns of bHLH Transcription Factors in Liriodendron chinense (Hemsl) Sarg

Rongxue Li, Baseer Ahmad, Delight Hwarari, Dong'ao Li, Ye Lu, Min Gao, Jinhui Chen, Liming Yang
2022 Forests  
In this current study, we conducted, the genome-wide survey of bHLH transcription factors in Liriodendron chinense (Hemsl) Sarg., 91 LcbHLH family members were identified.  ...  RNA-seq and real-time quantitative PCR analysis of LcbHLH members showed that the expression of LcbHLH35, 55, and 86 are up-regulated, and the expression of LcbHLH9, 20, 39, 54, 56, and 69 is down-regulated  ...  The analysis of genome-wide replication, fragment replication, and tandem replication of gene family has a significant role in explaining the process of gene family expansion.  ... 
doi:10.3390/f13040518 fatcat:yej5azgyi5cspiri4h4jojiy74

Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)

Yong Xiao, Wei Xia, Yaodong Yang, Annaliese S. Mason, Xintao Lei, Zilong Ma, Marc Robinson-Rechavi
2013 PLoS ONE  
influenced by and diverged as a result of genomic duplication events.  ...  MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species.  ...  Acknowledgments We thank Qixing Huang in the Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science for the suggestions in date palm miRNA analysis.  ... 
doi:10.1371/journal.pone.0071435 pmid:23951162 pmcid:PMC3738527 fatcat:qup3i2hhibbgpnkmkpnwodqnqi

A genome‐wide association study approach to the identification of candidate genes underlying agronomic traits in alfalfa ( Medicago sativa L.)

Zan Wang, Xuemin Wang, Han Zhang, Lin Ma, Haiming Zhao, Chris Stephen Jones, Jin Chen, Guibo Liu
2019 Plant Biotechnology Journal  
In the present study, we applied the GWAS approach to a collection of 322 alfalfa genotypes of diverse geographic origin to investigate marker-trait associations for nine agronomic traits characterized  ...  reference genome sequences (Mt4.0 V1) and NCBI nucleotide acid databases.  ...  and Technology Innovation Program of Chinese Academy of Agricultural Sciences (CAAS-XTCX2018020).  ... 
doi:10.1111/pbi.13251 pmid:31487419 fatcat:h5attqcenja6nehoqssojxothy

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

Mark TA Donoghue, Channa Keshavaiah, Sandesh H Swamidatta, Charles Spillane
2011 BMC Evolutionary Biology  
The evolutionary origins of two thirds of the lineagespecific genes within the Arabidopsis thaliana genome are also identified.  ...  origin in Arabidopsis thaliana.  ...  The authors are thankful for reviewer comments on an earlier version of this manuscript and for advice offered by Dr Mary O'Connell, Dr Rachel Clifton and Prof. Cathal Seoighe.  ... 
doi:10.1186/1471-2148-11-47 pmid:21332978 pmcid:PMC3049755 fatcat:zxxbpbjo3vblhmlxxzhy4gkaly

Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana

Athanasios Theologis, Joseph R. Ecker, Curtis J. Palm, Nancy A. Federspiel, Samir Kaul, Owen White, Jose Alonso, Hootan Altafi, Rina Araujo, Cheryl L. Bowman, Shelise Y. Brooks, Eugen Buehler (+77 others)
2000 Nature  
This work was supported by the National Science Foundation, the Department of Energy and the US Department of Agriculture.  ...  Richards and S. Tabata for helpful contributions in completing the chromosome.  ...  By contrast, the genomic organization of A. thaliana centromeres is not well characterized.  ... 
doi:10.1038/35048500 pmid:11130712 fatcat:dto43odkfrgepmdfxxx2xbnfky

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Xiaoying Lin, Samir Kaul, Steve Rounsley, Terrance P. Shea, Maria-Ines Benito, Christopher D. Town, Claire Y. Fujii, Tanya Mason, Cheryl L. Bowman, Mary Barnstead, Tamara V. Feldblyum, C. Robin Buell (+25 others)
1999 Nature  
This work was supported by the National Science Foundation, the Department of Energy and the US Department of Agriculture.  ...  Richards and S. Tabata for helpful contributions in completing the chromosome.  ...  By contrast, the genomic organization of A. thaliana centromeres is not well characterized.  ... 
doi:10.1038/45471 pmid:10617197 fatcat:kanpi6tpuveh3d5b34h67igl7q

Novel Genes Affecting the Interaction between the Cabbage Whitefly and Arabidopsis Uncovered by Genome-Wide Association Mapping

Colette Broekgaarden, Johan Bucher, Johanna Bac-Molenaar, Joost J. B. Keurentjes, Willem Kruijer, Roeland E. Voorrips, Ben Vosman, Swarup Kumar Parida
2015 PLoS ONE  
Genome-wide association (GWA) mapping is a useful tool to study the genetic architecture of traits, but has so far only had limited exploitation in studies of plant defense.  ...  Here, we study the genetic architecture of defense against the phloem-feeding insect cabbage whitefly (Aleyrodes proletella) in Arabidopsis thaliana.  ...  Acknowledgments We thank Richard Visser for advice on experimental design and GWA mapping and for valuable comments on an earlier version of the manuscript; Frank Becker for generation of seeds; Unifarm  ... 
doi:10.1371/journal.pone.0145124 pmid:26699853 pmcid:PMC4689410 fatcat:4b3hi2zzdrey5eilqekxpsztwe

Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand's high ultraviolet B radiation environment

Yanni Dong, Saurabh Gupta, Rixta Sievers, Jason J. Wargent, David Wheeler, Joanna Putterill, Richard Macknight, Tsanko Gechev, Bernd Mueller-Roeber, Paul P. Dijkwel
2019 BMC Genomics  
Pachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand.  ...  To gain first insights into how Pachycladon copes with UV-B stress, we sequenced its genome and compared the UV-B tolerance of two Pachycladon accessions with those of two A. thaliana accessions from different  ...  Christian Kappel (University of Potsdam, Potsdam, Germany) for providing infrastructure for bioinformatics analysis, Dr. Claudia Voelckel (MPI for Chemical Eology, Jena, Germany) and Dr.  ... 
doi:10.1186/s12864-019-6084-4 pmid:31718535 pmcid:PMC6849220 fatcat:helytwfhdvbqpcxcuupqsu6rua
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