461 Hits in 8.2 sec

Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics

David Sankoff, Chunfang Zheng, Yue Zhang, Joao Meidanis, Eric Lyons, Haibao Tang
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We formulate an algorithm for resolving data on local peaks in the distributions of duplicate gene similarities for a number of related genomes.  ...  We outline an integrated approach to speciation and whole genome doubling (WGD) to resolve the occurrence of these events in phylogenetic analysis.  ...  for the detailed analysis of a similarity distribution, and to 12 members of the family Brassicaceae, plus one outgroup, for the phylogenomics.  ... 
doi:10.1109/tcbb.2018.2849377 pmid:30072336 fatcat:xy6x73rcwjhg5i5tdkibiyrmma

Whole-genome microsynteny-based phylogeny of angiosperms

Tao Zhao, Arthur Zwaenepoel, Jia-Yu Xue, Shu-Min Kao, Zhen Li, M. Eric Schranz, Yves Van de Peer
2021 Nature Communications  
Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable.  ...  Indeed, microsynteny—the conservation of local gene content and order—is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited  ...  applications.  ... 
doi:10.1038/s41467-021-23665-0 pmid:34108452 fatcat:v46u7oal6jfclljpp6evmeevrm

Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

Tao Zhao, M. Eric Schranz
2019 Proceedings of the National Academy of Sciences of the United States of America  
most genes are multicopy and/or have lineage-specific distributions for angiosperms.  ...  A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across  ...  We thank Kitty Vijverberg, Klaas Bouwmeester, three anonymous reviewers, and the editor for constructive suggestions and ideas for improving the manuscript.  ... 
doi:10.1073/pnas.1801757116 pmid:30674676 pmcid:PMC6369804 fatcat:xdoo7gw4abexlokfwd7irlhcha

Comparative studies of resistin expression and phylogenomics in human and mouse

Rong-Ze Yang, Qing Huang, Aihua Xu, John C McLenithan, Jonathan A Eison, Alan R Shuldiner, Serhan Alkan, Da-Wei Gong
2003 Biochemical and Biophysical Research Communications - BBRC  
Phylogenomics revealed that the human resistin gene is the ortholog of its murine counterpart and is located in a region of chromosome 19p13.3, which is syntenic to mouse chromosome 8A1.  ...  We comparatively and quantitatively studied the tissue distributions of resistin mRNA between human and mouse.  ...  Acknowledgments We thank Toni Pollin for a critical reading of the manuscript, and Bob Stephens and Toni Harbaugh-Blackford for bioinformatics support at Advanced Biomedical Computing Center, NCI-FCRDC  ... 
doi:10.1016/j.bbrc.2003.09.093 pmid:14550293 fatcat:7gcexjivcvhvbipqflj4gy7dba

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes

Maria Waldl, Bernhard Thiel, Roman Ochsenreiter, Alexander Holzenleiter, João de Araujo Oliveira, Maria Walter, Michael Wolfinger, Peter Stadler
2018 Genes  
Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina.  ...  While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for  ...  The obvious alternative is to increase the set of known TERs by finding homologs that are sufficiently similar to one of known yeast TERs, to allow the construction of multiple alignments of phylogenetically  ... 
doi:10.3390/genes9080372 pmid:30049970 fatcat:2aihch4gm5awdkhywwvavjqmiu

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

Pierre-Marc Delaux, Kranthi Varala, Patrick P. Edger, Gloria M. Coruzzi, J. Chris Pires, Jean-Michel Ané, John M. McDowell
2014 PLoS Genetics  
Here we used the independent loss of the most widespread plantmicrobe symbiosis, arbuscular mycorrhization (AM), as a model to address this question.  ...  Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants.  ...  Ané for her help in designing the prediction model to determine the absence of symbiotic genes in transcriptome data and Dr. M. Crook for critical reading of the manuscript. We also thank Dr.  ... 
doi:10.1371/journal.pgen.1004487 pmid:25032823 pmcid:PMC4102449 fatcat:l2tnxlzfofexfp3goi2kkpodum

Applying Machine Learning to Classify the Origins of Gene Duplications [article]

Michael T.W. McKibben, Michael S. Barker
2021 bioRxiv   pre-print
Features from these genomes were used to develop simulations of syntenic blocks and paleologs to train a gradient boosted decision tree.  ...  Current methods for classifying paleologs often rely on only a subset of potential genomic features, have varying levels of accuracy, and often require significant data and/or computational time.  ...  Similar to the use of Ks plots to visualize the age distribution of paralogs in a genome, the mean synonymous divergence (Ks) of the collinear homologous gene pairs (Ks block ) in each syntenic block pair  ... 
doi:10.1101/2021.08.12.456144 fatcat:am2c2av4gfc4xnhe2j3qlsxhuu

Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting

Svetlana Romanenko, Natalya Serdyukova, Polina Perelman, Svetlana Pavlova, Nina Bulatova, Feodor Golenishchev, Roscoe Stanyon, Alexander Graphodatsky
2017 Genes  
We made a set of region specific probes by microdissection for a single syntenic region represented by the p-arm of chromosome 1 of Alexandromys oeconomus, and hybridized the probes onto the chromosomes  ...  Significant progress in the detection of intrachromosomal rearrangement is now possible, due to recent advances in molecular biology and bioinformatics.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes8090215 pmid:28867774 pmcid:PMC5615349 fatcat:nw7ki46pzzftfpwwieulnq35ou

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Johannes A Hofberger, Beifei Zhou, Haibao Tang, Jonathan DG Jones, M Schranz
2014 BMC Genomics  
In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters  ...  To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR  ...  The authors are grateful to Xinguang Zhu for his support at CAS and to Mariam Neckzei for her help with graphical editing of the figures.  ... 
doi:10.1186/1471-2164-15-966 pmid:25380807 pmcid:PMC4289383 fatcat:vndhnnbrurfuhbfng46kqgqway

Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

Maximilian Griesmann, Yue Chang, Xin Liu, Yue Song, Georg Haberer, Matthew B. Crook, Benjamin Billault-Penneteau, Dominique Lauressergues, Jean Keller, Leandro Imanishi, Yuda Purwana Roswanjaya, Wouter Kohlen (+30 others)
2018 Science  
To find all of the homologous syntenic blocks of interest, we first used Medicago genome as a reference, searching and locating the target genes along the syntenic blocks with the flanking genes surrounding  ...  from 100 to 6000 bp with ≥99% similarity.  ...  , this issue p. eaat1743; see also p. 125 Science interorganismal signaling, is susceptible to selection and prone to being lost over evolutionary time. supported nitrogen-fixing symbiosis.  ... 
doi:10.1126/science.aat1743 pmid:29794220 fatcat:75e6lev37janpcekcmkyqmc334

Novel phylogeny of angiosperms inferred from whole-genome microsynteny analysis [article]

Tao Zhao, Jiayu Xue, Shu-min Kao, Zhen Li, Arthur Zwaenepoel, Eric Schranz, Yves Van de Peer
2020 bioRxiv   pre-print
However, our results unveiled several novel relationships for some key clades, such as magnoliids sister to monocots, Vitales as sister to core-eudicots, and Saxifragales sister to Santalales, in turn  ...  Our results highlight that phylogenies based on genome structure and organization are complementary to sequence-based phylogenies and provide alternative hypotheses of angiosperm relationships to be further  ...  However, so far, application of gene order conservation for phylogenomic means has been limited (Rokas and Holland, 2000; Tang and Moret, 2003; Drillon et al., 2019) .  ... 
doi:10.1101/2020.01.15.908376 fatcat:aqyeq4n5azaptknwyqjj72sbfi

Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids

Yifei Liu, Bo Wang, Shaohua Shu, Zheng Li, Chi Song, Di Liu, Yan Niu, Jinxin Liu, Jingjing Zhang, Heping Liu, Zhigang Hu, Bisheng Huang (+14 others)
2021 Nature Communications  
Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.  ...  .), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications.  ...  Acknowledgements We thank Shuibing Wang for assistant of some bioinformatic analyses, Juan Guo for biochemical assays, and Xu Wang and Xin Hu for helping with figures.  ... 
doi:10.1038/s41467-021-23611-0 pmid:34078898 fatcat:4gkweszfijgsfkmwurdrmfypkq

Complete genome sequence of the myxobacterium Sorangium cellulosum

Susanne Schneiker, Olena Perlova, Olaf Kaiser, Klaus Gerth, Aysel Alici, Matthias O Altmeyer, Daniela Bartels, Thomas Bekel, Stefan Beyer, Edna Bode, Helge B Bode, Christoph J Bolten (+47 others)
2007 Nature Biotechnology  
Phylogenomic analysis of S. cellulosum So ce56 We attempted to use phylogenomic analysis to deduce functions for the B35% of unassigned genes in the S. cellulosum So ce56 genome.  ...  In contrast to the global pattern of gene organization, however, the overall distribution of gene functions is similar in both species (Fig. 3b) .  ... 
doi:10.1038/nbt1354 pmid:17965706 fatcat:kgdjn6hpgjdyzfzqtmemyv2xda

The opium poppy genome and morphinan production

Li Guo, Thilo Winzer, Xiaofei Yang, Yi Li, Zemin Ning, Zhesi He, Roxana Teodor, Ying Lu, Tim A. Bowser, Ian A. Graham, Kai Ye
2018 Science  
Distribution of synonymous substitutions per synonymous site (Ks) for P. somniferum paralogous genes and syntenic blocks confirmed a major WGD peak (Fig. 1C; fig.  ...  The Ks distributions of A. coerulea paralogs and syntenic genes support a WGD event in this representative of the Ranunculaceae at 111.3±35.6 MYA (Fig. 1C, table S9) .  ...  The Ks values were then fitted to a mixture model of Gaussian distribution to determine the number of components in the Ks distribution (Fig. 1C; fig.  ... 
doi:10.1126/science.aat4096 pmid:30166436 fatcat:lqv4hpvicfgujb34ueqwsnm35m

Pan-genome analyses of model fungal species

Charley G. P. McCarthy, David A. Fitzpatrick
2019 Microbial Genomics  
Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces  ...  The concept of the species 'pan-genome', the union of 'core' conserved genes and all 'accessory' non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific  ...  The authors would also like to acknowledge the DJEI/DES/ SFI/HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and support.  ... 
doi:10.1099/mgen.0.000243 pmid:30714895 pmcid:PMC6421352 fatcat:vhhoqhasird5rpk7kihpcmdz3u
« Previous Showing results 1 — 15 out of 461 results