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Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs

Xiangqun H. Zheng, Fu Lu, Zhen-Yuan Wang, Fei Zhong, Jeffrey Hoover, Richard Mural
2004 Computer applications in the biosciences : CABIOS  
ACKNOWLEDGEMENT We would like to thank Dr. Graziella Piras for providing a graphic representation of the process to generate syntenic blocks (figure 1); Dr. Peter Roberts, Dr. Peter Li and Dr.  ...  Xiaoying Lin for critical readings of the manuscript.  ...  To overcome these shortcomings, we have developed a pipeline that uses conserved synteny and protein functions, as well as sequence similarity, to identify orthologous pairs of genes.  ... 
doi:10.1093/bioinformatics/bti045 pmid:15458983 fatcat:5222kkfpcjbinidkwk7drjjpaq

Vertebrate Paralogous Conserved Noncoding Sequences May Be Related to Gene Expressions in Brain

Masatoshi Matsunami, Naruya Saitou
2012 Genome Biology and Evolution  
The two-round whole-genome duplications (2R WGDs), which most probably occurred in the vertebrate common ancestors, generated large numbers of paralogous protein-coding genes and their regulatory elements  ...  Region-focused Basic Local Alignment Search Tool (BLAST) search of each synteny block revealed 7,924 orthologous CNSs and 309 paralogous CNSs conserved among eight high-quality vertebrate genomes.  ...  of Education, Culture, Sports, Science, and Technology of Japan to M.M. and N.S.  ... 
doi:10.1093/gbe/evs128 pmid:23267051 pmcid:PMC3595034 fatcat:62vidmly3nc6dken5ljmgdjntq

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes

Param Priya Singh, Jatin Arora, Hervé Isambert, A. Christos
2015 PLoS Computational Biology  
Such a synteny comparison across multiple genomes is shown to enhance the statistical power of ohnolog identification in vertebrates compared to earlier approaches, by overcoming lineage specific genome  ...  Ohnologs, which amount to about 20 to 35% of genes in the human genome, have also been shown to be prone to dominant deleterious mutations and frequently implicated in cancer and genetic diseases.  ...  Acknowledgments We thank Hugues Roest-Crollius and Pierre Pontarotti for discussion and acknowledge technical support from the service informatique of Institut Curie.  ... 
doi:10.1371/journal.pcbi.1004394 pmid:26181593 pmcid:PMC4504502 fatcat:qargr5kvpreepjxckz7nhlvktm

Inferring Orthologs: Open Questions and Perspectives

Fredj Tekaia
2016 Genomics Insights  
With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species.  ...  Moreover, the lack of direct functional evidence and the questionable quality of some available genome sequences and annotations present additional difficulties to assess orthology.  ...  Acknowledgments I thank Bernard Dujon for constant support, Pedro Alzari for his careful reading of the manuscript and his suggestions, and Thomas Rolland for constructive discussions.  ... 
doi:10.4137/gei.s37925 pmid:26966373 pmcid:PMC4778853 fatcat:eo36owlqzvcnhjvsfwwwzicxei

Evolutionary divergence of the vertebrate TNFAIP8 gene family: Applying the spotted gar orthology bridge to understand ohnolog loss in teleosts

Con Sullivan, Christopher R. Lage, Jeffrey A. Yoder, John H. Postlethwait, Carol H. Kim, Pierre Boudinot
2017 PLoS ONE  
Comparative functional genomic studies require the proper identification of gene orthologs to properly exploit animal biomedical research models.  ...  of teleost orthologs to human genes and to enhance the power of teleosts as biomedical models.  ...  Acknowledgments This work was supported by National Institutes of Health ( grants to C.S.  ... 
doi:10.1371/journal.pone.0179517 pmid:28658311 pmcid:PMC5489176 fatcat:o7h36m4y2bcstjcyle2b46moty

Evolutionary expansion of nematode-specific glycine-rich secreted peptides

Muying Ying, Yangyang Qiao, Lehan Yu
2016 Gene  
The conserved synteny blocks of GRSP clusters between their genomes, the co-expressed GRSPs clusters after C. elegans infections, and a strong purifying selection of protein-coding sequences suggested  ...  evolutionary constraint acting on C. elegans to ensure that C. elegans could rapidly launch and fulfill systematic responses against infections by co-expression, co-regulation, and co-functionality of  ...  Acknowledgements This work was supported by grants from the National Nature Science Foundation of China (31160233), the Science and Technology Foundation of Jiangxi Province (20142BAB204013).  ... 
doi:10.1016/j.gene.2016.04.049 pmid:27129940 fatcat:3qppp7ybanee7bbqikchqmlple

OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates

2019 Nucleic Acids Research  
However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD.  ...  The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases.  ...  ACKNOWLEDGEMENTS We acknowledge technical support from the service informatique of Institut Curie for hosting and maintaining the  ... 
doi:10.1093/nar/gkz909 pmid:31612943 pmcid:PMC7145513 fatcat:4cqfeslq25b27bei45m3hbwasu

A Comparative Map of the Zebrafish Genome

I. G. Woods
2000 Genome Research  
Zebrafish mutations define the functions of hundreds of essential genes in the vertebrate genome.  ...  To accelerate the molecular analysis of zebrafish mutations and to facilitate comparisons among the genomes of zebrafish and other vertebrates, we used a homozygous diploid meiotic mapping panel to localize  ...  assistance, and the Stanford Genome Technology Center for oligonucleotide synthesis.  ... 
doi:10.1101/gr.10.12.1903 pmid:11116086 pmcid:PMC313070 fatcat:cufxfxeeu5cn7djk3hho6kzgqi

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Ingo Braasch, Andrew R Gehrke, Jeramiah J Smith, Kazuhiko Kawasaki, Tereza Manousaki, Jeremy Pasquier, Angel Amores, Thomas Desvignes, Peter Batzel, Julian Catchen, Aaron M Berlin, Michael S Campbell (+49 others)
2016 Nature Genetics  
genes 15,16 ; and (iii) rapid teleost sequence evolution 17,18 , often due to asymmetric rates of ohnolog evolution, that frustrates ortholog identification.  ...  Gar informs the evolution of vertebrate genomes and gene functions after genome duplication and illuminates evolutionary mechanisms leading to teleost biodiversity.  ...  ACKNOWLEDGMENTS We thank the Broad Institute Genomics Platform for constructing and sequencing gar DNA and RNA libraries and J. TurnerMaier for the gar transcriptome assembly.  ... 
doi:10.1038/ng.3526 pmid:26950095 pmcid:PMC4817229 fatcat:oqldvyvguveell3dxg6ftsjleu

CYNTENATOR: Progressive Gene Order Alignment of 17 Vertebrate Genomes

Christian Rödelsperger, Christoph Dieterich, Sridhar Hannenhalli
2010 PLoS ONE  
Gene order conservation or conserved synteny was seen as a feature of common descent and did not imply the existence of functional constraints.  ...  Lineage-specific characterization of gene order across 17 vertebrate genomes revealed mechanisms for maintaining conserved synteny such as enhancers and coregulation by bidirectional promoters.  ...  Acknowledgments The authors appreciate numerous discussions with other members of the Berlin Institute for Medical Systems Biology. Author Contributions Conceived and designed the experiments: CD.  ... 
doi:10.1371/journal.pone.0008861 pmid:20126624 pmcid:PMC2812507 fatcat:taeyroth3rdfvna652aqf33oqi

The zebrafish gene map defines ancestral vertebrate chromosomes

I. G. Woods
2005 Genome Research  
Acknowledgments We thank members of our laboratories for helpful discussions, Tom Conlin for expert help with bioinformatics, Greg Cooper and Jon Binkley for assistance with phylogenetic analyses, and  ...  Alex Schier for critical comments on the manuscript.  ...  Map locations of orthologous gene pairs can be used to define regions of conserved synteny between species.  ... 
doi:10.1101/gr.4134305 pmid:16109975 pmcid:PMC1199546 fatcat:p65qnne3xbchxjxf2n33llnpze


2007 Genome Informatics Series  
By comparing orthologs in multiple species, we found that the breakpoint of chromosomal rearrangements could have had an impact on regulatory changes of genes next to it with respect to the gene function  ...  This has made use of the wealth of synteny information among these species.  ...  Acknowledgments We thank AAA site [12] for genome assemblies. We also thank Douglas Smith for permission of using sequence data and Venky Iyer at Eisen Lab UC Berkeley for ortholog model.  ... 
doi:10.11234/gi1990.18.12 fatcat:77ckxg7zgzcafacib34yr3e4mu

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

A. L. Hufton, S. Mathia, H. Braun, U. Georgi, H. Lehrach, M. Vingron, A. J. Poustka, G. Panopoulou
2009 Genome Research  
Next, we classify mouse and zebrafish genes according to association with PCNEs, synteny conservation, duplication history, and presence in bidirectional promoter pairs, and use these data to cluster gene  ...  We test 42 of our PCNEs in transgenic zebrafish assays-including examples from vertebrates and amphioxus-and find that the majority are functional enhancers.  ...  Cusack for helpful advice and code related to the handling and processing of genome annotation data.  ... 
doi:10.1101/gr.093237.109 pmid:19704032 pmcid:PMC2775584 fatcat:csbcml5v3ff2boe646e45l5xby

Automated identification of conserved synteny after whole-genome duplication

J. M. Catchen, J. S. Conery, J. H. Postlethwait
2009 Genome Research  
The contents of this paper are solely the responsibility of the investigators and do not necessarily represent the official views of NCRR or NIH.  ...  Acknowledgments J.C. was supported in part by an IGERT grant from NSF in Evolution, Development, and Genomics (DGE 9972830).  ...  Automated identification of conserved synteny Genome Research 1499 While dotplots enhance visualization of data across the entire genome, a gene trace provides a more detailed view of a  ... 
doi:10.1101/gr.090480.108 pmid:19465509 pmcid:PMC2720179 fatcat:a5udai5pvfftrfm5ecydezncie

Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum

Nida Mushtaq, Faiza Munir, Alvina Gul, Rabia Amir, Rehan Zafar Paracha
2021 PeerJ  
The Ka/Ks ratios of the orthologous pairs also demonstrated the StDREB genes were under strong purification selection in the course of evolution.  ...  Interspecies synteny analysis revealed 45 and 36 StDREB genes were orthologous to Arabidopsis and Solanum lycopersicum, respectively.  ...  According to gene duplication analysis, it was Synteny relationship of StDREB genes To further infer the evolutionary relationship, DREB genes were compared to identify orthologous StDREB gene pairs  ... 
doi:10.7717/peerj.11647 pmid:34221730 pmcid:PMC8236231 fatcat:f72ualcrangwtp7fqhdsnk5g2e
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