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PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

Michiel Van Bel, Tim Diels, Emmelien Vancaester, Lukasz Kreft, Alexander Botzki, Yves Van de Peer, Frederik Coppens, Klaas Vandepoele
2017 Nucleic Acids Research  
PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics.  ...  A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework.  ...  ACKNOWLEDGEMENTS The authors wish to express gratitude to the various genome sequencing project managers who have graciously allowed their data to be used within the PLAZA platform, even when the genome  ... 
doi:10.1093/nar/gkx1002 pmid:29069403 pmcid:PMC5753339 fatcat:vrtlljwpwjhxrmd66va7hcp4fy

Computational Tools for Genomic Studies in Plants

Manuel Martinez
2016 Current Genomics  
In this mini-review, the databases for genome projects, the databases created to host species/clade projects and the databases developed to perform plant comparative genomics are revised.  ...  Because of their importance in modern research, an in-depth analysis of the plant comparative genomics databases has been performed.  ...  In addition, PlantsDB provides a platform for integrative and comparative plant genome research.  ... 
doi:10.2174/1389202917666160520103447 pmid:28217007 pmcid:PMC5282602 fatcat:s3hvddxlbzajtjksw5td4ucuyq

PlantOrDB: a genome-wide ortholog database for land plants and green algae

Lei Li, Guoli Ji, Congting Ye, Changlong Shu, Jie Zhang, Chun Liang
2015 BMC Plant Biology  
With the rapid increase of genomic data, identifying and distinguishing these genes among different species is becoming an important part of functional genomics research.  ...  Conclusion: PlantOrDB (http://bioinfolab.miamioh.edu/plantordb) is a genome-wide ortholog database for land plants and green algae.  ...  for functional genomics research.  ... 
doi:10.1186/s12870-015-0531-4 pmid:26112452 pmcid:PMC4481079 fatcat:ftzhstj6iffczefjylizcwvvlq

Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

Vincent J. Lynch, Mauris C. Nnamani, Aurélie Kapusta, Kathryn Brayer, Silvia L. Plaza, Erik C. Mazur, Deena Emera, Shehzad Z. Sheikh, Frank Grützner, Stefan Bauersachs, Alexander Graf, Steven L. Young (+4 others)
2015 Cell Reports  
Ober for comments on an earlier version of this manuscript and A. Smit for assistance for TE age classifications.  ...  National Institutes of Allergy and Infectious Diseases IAA-2646) and K. Smith for the generous gifts of pregnant armadillo and opossum uterus and R. Bjornson and N.  ...  Mammals are an ideal system in which to explore the molecular mechanisms that underlie the evolution of novelties because numerous genomic and experimental resources have been developed for mammals and  ... 
doi:10.1016/j.celrep.2014.12.052 pmid:25640180 pmcid:PMC4447085 fatcat:uluixpr2enddnne3y2u7uuqm2a

Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants

Pedro Humberto Castro, Grmay H. Lilay, Antonio Muñoz-Mérida, Jan K. Schjoerring, Herlânder Azevedo, Ana G. L. Assunção
2017 Scientific Reports  
Benefiting from the present abundance of plant genomic data, we performed an evolutionary and structural characterization of plant F-bZIPs.  ...  This can be partially explained by events of whole genome duplications (WGD) and small-scale genome duplications (SSD), which are more frequent in plants compared to other eukaryotes 13-15 .  ...  , Rosaceae, Benincaseae, Malvids including Brassicaceae, and Poales monocots), whose genomes have therefore been sequenced and subsequently characterized in comparative genomic resources such as the Plant  ... 
doi:10.1038/s41598-017-03903-6 pmid:28630437 pmcid:PMC5476651 fatcat:qo5bihhoyneg3pxrm5gvztm6ri

Using ARCADE (ARChaeplastida Annotation DatabasE) to understand the evolution of genome size in land plants [article]

Alison Pelri Albuquerque Menezes, Joao Victor dos Anjos Almeida, Luiz-Eduardo Del-Bem, Francisco Pereira Lobo
2022 bioRxiv   pre-print
The abundance of plant genomic information caused by the decrease of sequencing costs contrasts with the lack of databases that integrate genome annotation, taxonomy and phenotypes to produce statistically  ...  We found larger genomes to have a greater frequency of the Histone 2A superfamily, responsible for diverse functions, including the nucleosome formation and silencing of transposable elements.  ...  Leitch We used CALANGO, an in-house comparative genomics tool that integrates genotypic, phenotypic and annotation data, to build phylogeny-aware linear models and search for phenotype-genotype associations  ... 
doi:10.1101/2022.09.06.506765 fatcat:ayli2tgwu5gxvktu6bl7vvtnaq

An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals

Muzi Li, Yuwei Xiao, Steve Mount, Zhongchi Liu
2021 Frontiers in Plant Science  
This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement.  ...  With the development of high-throughput sequencing technologies and computational tools, an increasing number of high-quality genomes and transcriptomes of Rosaceae species have become available and will  ...  A pan-genome identifies genetic variations among cultivars, provides valuable resources, and supports evolutionary studies.  ... 
doi:10.3389/fpls.2021.644881 pmid:33868343 pmcid:PMC8047320 fatcat:hd2zdeh565cc3iq3czl6zywt4a

Bioinformatics: A Way Forward to Explore "Plant Omics" [chapter]

Mehboob-ur Rahman, Tayyaba Shaheen, Mahmood-ur Rahman, Muhammad Atif Iqbal, Yusuf Zafar
2016 Bioinformatics - Updated Features and Applications  
Synergism of "plant omics" and bioinformatics set a firm foundation for deducing ancestral karyotype of multiple plant families, predicting genes, etc.  ...  This science has progressed parallel to the evolution of genome-sequencing tools, for example, the next-generation sequencing technologies, that resulted in arranging and analyzing the genome-sequencing  ...  PLAZA 3.0 has been established to develop comparative genomics data of plants accessible via user-friendly web interface.  ... 
doi:10.5772/64043 fatcat:w3cwexdezvf27e5adz3gfos4v4

Transcriptome atlas of Phalaenopsis equestris [article]

Anna V Klepikova, Artem S Kasianov, Margarita A Ezhova, Aleksey A Penin, Maria D Logacheva
2020 bioRxiv   pre-print
The vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies.  ...  Here we present an RNA-seq based transcriptome map of P. equestris which covers 19 organs of the plant including leaves, roots, floral organs and shoot apical meristem.  ...  the horse phalaenopsis) (Cai et al., 2015) provided 36 novel opportunities for evolutionary and functional studies of Orchidaceae.  ... 
doi:10.1101/2020.11.03.366260 fatcat:ygakxbt5yzbx7dlteaeejchr5a

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

Daniel J Rigden, Xosé M Fernández
2017 Nucleic Acids Research  
This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE.  ...  Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families.  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva, especially, and the rest of the Oxford University Press team led by Joanna Ventikos and Elisabeth Waelkens for their help in compiling this issue.  ... 
doi:10.1093/nar/gkx1235 pmid:29316735 pmcid:PMC5753253 fatcat:ftpcgajkxbfstmn7rh37q7foyi

PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

Michiel Van Bel, Francesca Silvestri, Eric M Weitz, Lukasz Kreft, Alexander Botzki, Frederik Coppens, Klaas Vandepoele
2021
PLAZA is a platform for comparative, evolutionary, and functional plant genomics.  ...  Taken together, this new version offers extended support for plant biologists working on different families within the green plant lineage and provides an efficient and versatile toolbox for plant genomics  ...  The authors would like to thank Bj örn Usadel and Marie Bolger for generating the MapMan functional annotations.  ... 
doi:10.1093/nar/gkab1024 pmid:34747486 pmcid:PMC8728282 fatcat:7nhzy2zhtje5niabqgxbtto4ma

It's Hard to Avoid Avoidance: Uncoupling the Evolutionary Connection between Plant Growth, Productivity and Stress "Tolerance"

Albino Maggio, Ray A Bressan, Yang Zhao, Junghoon Park, Dae-Jin Yun
2018 International Journal of Molecular Sciences  
, which were originally needed for survival over long evolutionary time periods.  ...  " is fundamentally and evolutionarily based on "avoidance" of injury and death which may be referred to as evolutionary avoidance (EVOL-Avoidance).  ...  Acknowledgments: We thank Jian-Kang Zhu, José Pardo, Mike Hasegawa and Hans Bohnert for many discussions and invaluable advice over many years.  ... 
doi:10.3390/ijms19113671 pmid:30463352 fatcat:aldlpqk2wbasnjvfftsb6yxkua

PlantCAZyme: a database for plant carbohydrate-active enzymes

Alexander Ekstrom, Rahil Taujale, Nathan McGinn, Yanbin Yin
2014 Database: The Journal of Biological Databases and Curation  
PlantCAZyme: a database for plant carbohydrate-active enzymes.  ...  genomes.  ...  Acknowledgements A.E. computed most of the data and implemented the database and website. R.T. contributed to the data collection. N.M. developed an early version of the database.  ... 
doi:10.1093/database/bau079 pmid:25125445 pmcid:PMC4132414 fatcat:7n4duke7uzgqjmeerfdbfiqisu

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

Andreas D Zimmer, Daniel Lang, Karol Buchta, Stephane Rombauts, Tomoaki Nishiyama, Mitsuyasu Hasebe, Yves Van de Peer, Stefan A Rensing, Ralf Reski
2013 BMC Genomics  
We demonstrate the utility of the improved P. patens genome annotation for comparative genomics and new extensions to the cosmoss.org resource as a central repository for this plant "flagship" genome.  ...  The moss Physcomitrella patens as a model species provides an important reference for earlydiverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies.  ...  We are indebted to our collaborators at the US DoE JGI and the Moss Genome Consortium.  ... 
doi:10.1186/1471-2164-14-498 pmid:23879659 pmcid:PMC3729371 fatcat:spgnhthxanc5ppu37j7zzwxbdy

Pathogenesis-related protein 1 (PR-1) genes in soybean: genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses [article]

Fabricio Almeida-Silva, Thiago M. Venancio
2021 bioRxiv   pre-print
Plant pathogenesis-related (PR) proteins are a large group of proteins, classified in 17 families, that are induced by pathological conditions.  ...  Here, we characterized the soybean PR-1 (GmPR-1) gene repertoire at the sequence, structural and expression levels. We found 24 GmPR-1 genes, clustered in two phylogenetic groups.  ...  Vandepoele, PLAZA 4.0: An integrative resource for functional, evolutionary and comparative plant genomics, Nucleic Acids Res. 46 (2018) D1190-D1196. https://doi.org/10.1093/nar/gkx1002. [16] S.F.  ... 
doi:10.1101/2021.03.27.437342 fatcat:zfvombv5xbddhe2shsk43x5aim
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