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Persistence drives gene clustering in bacterial genomes

Gang Fang, Eduardo PC Rocha, Antoine Danchin
2008 BMC Genomics  
Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent.  ...  Conclusion: We show that the strong selective pressure acting on the function of persistent genes, in a permanent state of flux of genes in bacterial genomes, maintaining their size fairly constant, that  ...  This clustering property has long been used to predict gene function through the annotations of its neighborhoods, with the assumption that conservation of gene proximity is coupled with their functional  ... 
doi:10.1186/1471-2164-9-4 pmid:18179692 pmcid:PMC2234087 fatcat:w7x2w3vvbfhalptptsevkajkri

Sequence and analysis of the Arabidopsis genome

M Bevan
2001 Current opinion in plant biology  
to the chromosomal location of genes, and is used as a substrate for further analyses of genome structure and protein function.  ...  This analysis is being reiterated on the complete gene set using comparisons between gene family members and other approaches to refine gene predictions.  ... 
doi:10.1016/s1369-5266(00)00144-8 pmid:11228431 fatcat:mad4pxrtpzgblnxfctmhnpotci

Comparative (Within Species) Genomics of the Vitis vinifera L. Terpene Synthase Family to Explore the Impact of Genotypic Variation Using Phased Diploid Genomes

Samuel Jacobus Smit, Melané Alethea Vivier, Philip Richard Young
2020 Frontiers in Genetics  
VviTPS gene regions were grouped to chromosomes, with the haplotig assemblies used to identify allelic variants.  ...  Functional predictions of the VviTPS subfamilies were performed using enzyme active site phylogenies resulting in the putative identification of the initial substrate and cyclization mechanism of VviTPS  ...  ., predicted to be functional).  ... 
doi:10.3389/fgene.2020.00421 pmid:32431727 pmcid:PMC7216305 fatcat:qf5e5y7przh7lj5wtlisfmjthq

nPhase: an accurate and contiguous phasing method for polyploids

Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer
2021 Genome Biology  
). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity  ...  No existing polyploid phasing method provides accurate and contiguous haplotype predictions.  ...  Acknowledgements We thank the members of the PhenoVar ANR consortium as well as the members of the Schacherer lab at the University of Strasbourg for helpful suggestions throughout the project.  ... 
doi:10.1186/s13059-021-02342-x pmid:33926549 pmcid:PMC8082856 fatcat:b6ihvxi64fglhkp44eh3t6tukm

POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat

Radosław Suchecki, Nathan S. Watson-Haigh, Ute Baumann
2017 Scientific Reports  
POTAGE aggregates those data sets and provides an intuitive interface for biologists to explore the expression of the predicted genes and their functional annotation in a chromosomal context.  ...  These include the Chromosome Survey Sequences, their order along the chromosomes determined by the population sequencing (POPSEQ) approach, the gene predictions and RNA-Seq expression data.  ...  Nick Collins for carefully reading the manuscript and for his insightful suggestions.  ... 
doi:10.1038/s41598-017-14591-7 pmid:29085014 pmcid:PMC5662734 fatcat:effhzmkn55hsdhhtu7buv5qdzy

Remodelling of a homeobox gene cluster by multiple independent gene reunions in Drosophila

Carolus Chan, Suvini Jayasekera, Bryant Kao, Moisés Páramo, Marcin von Grotthuss, José M. Ranz
2015 Nature Communications  
Here we analyse the chromosomal organization of the NK homeobox genes, presumed to be part of a single cluster in the Bilaterian ancestor, across 20 arthropods.  ...  Simulated scenarios of chromosome evolution indicate that these reunion events are unlikely unless the genome neighbourhoods harbouring the participating genes tend to colocalize in the nucleus.  ...  M.P. is grateful to the Bridges to the Baccalaureate Program supported by a National Institute of Health grant (R25-GM056647) awarded to Luís Mota-Bravo.  ... 
doi:10.1038/ncomms7509 pmid:25739651 fatcat:ctxhlb67tjenjdnqyquwktfnfq

Page 1943 of EMBO (European Molecular Biology Organization) Journal Vol. 22, Issue 9 [page]

2003 EMBO (European Molecular Biology Organization) Journal  
Integrating results from physical mapping allowed us to anchor and order contigs along the chromosome and robustly to assemble 6.5 of the 8.1 Mb chromosome.  ...  Based on InterPro results and the gene ontology (GO; terminology, 37% of the predicted proteins could be grouped into the cellular process and/or molecular function groups  ... 

Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation

P. Christoph Champ, Sandor Maurice, Jeffrey M. Vargason, Tracy Camp, P. Shing Ho
2004 Nucleic Acids Research  
An analysis of the human chromosome 22 genomic sequence shows that both Z-DNA forming regions (ZDRs) and promoter sites for nuclear factor-I (NFI) are correlated with the locations of known and predicted  ...  This suggests a distinct class of human genes that may potentially be transcriptionally regulated by a mechanism that couples Z-DNA with NFI activation, similar to the mechanism previously elucidated for  ...  This work was funded by grants from the National Institutes of Health (R1GM62957A) and the National Science Foundation (MCB0090615) to P.S.H., and by the Environmental Health Sciences Center at Oregon  ... 
doi:10.1093/nar/gkh988 pmid:15598822 pmcid:PMC545456 fatcat:f32xm2chivecljw7wpvo5cuxjq

Sensorineural deafness and male infertility: a contiguous gene deletion syndrome

Y. Zhang, M. Malekpour, N. Al-Madani, K. Kahrizi, M. Zanganeh, M. Mohseni, F. Mojahedi, A. Daneshi, H. Najmabadi, R. J H Smith
2007 Journal of Medical Genetics  
This new syndrome is caused by the deletion of contiguous genes at 15q15.3.  ...  due to a second deletion in another genomic region.  ...  ACKNOWLEDGEMENTS We wish to thank our patients and their families for their participation in this study.  ... 
doi:10.1136/jmg.2006.045765 pmid:17098888 pmcid:PMC2598039 fatcat:igdhioqoczbmfftd57y2fjf7qa

Fluorescentin situHybridization to Ascidian Chromosomes

Eiichi Shoguchi, Tetsuro Ikuta, Fumiko Yoshizaki, Yutaka Satou, Nori Satoh, Katsutoshi Asano, Hidetoshi Saiga, Takahito Nishikata
2004 Zoological Science  
Mapping of the genome sequence to the Ciona 14 haploid chromosomes is essential for future studies of the genomewide control of gene expression in this basal chordate.  ...  We also show that this method is efficient for coupling two so-far independent scaffolds into one longer scaffold when two BAC clones represent sequences located at either end of the two scaffolds.  ...  ACKNOWLEDGEMENTS We would like to express our thanks to the following colleagues who greatly helped us to establish the FISH protocol described in the present study: Drs.  ... 
doi:10.2108/zsj.21.153 pmid:14993826 fatcat:5ixlofeevzatjcp3igbhcfsqfy

Building near-complete plant genomes

Todd P Michael, Robert VanBuren
2020 Current opinion in plant biology  
Recent advances in single molecule sequencing and physical mapping technologies have enabled high-quality, chromosome scale assemblies of plant species with increasing complexity and size.  ...  to assemble.  ...  However, recent updates to the labeling techniques have enabled chromosome scale assemblies using BioNano Genomics Direct Label and Stain (DSL) coupled to ONT long reads [27, 28 ] .  ... 
doi:10.1016/j.pbi.2019.12.009 pmid:31981929 fatcat:iidgialiczer5j6mdxho3tsy2i

Back to bases in biology

Stephen Oliver
1994 Nature  
The data libraries contain a number of complete sequences of organelle genomes, but the longest contiguous sequence yet entered for a bacterial genome is 176 kb of the Escherichia coli chromosome.  ...  Only 7 per cent of the previous longest sequence-the 315 kb of Saccharomyces cerevisiae (yeast) chromosome III published in 1992 -was determined using automated methods, whereas the entire 2.1 Mb of the  ... 
doi:10.1038/368014a0 pmid:8107876 fatcat:6oa4uvkcabdy5luf4nxpug5bwa

Partial Trisomy 1q41 Syndrome Delineated by Whole Genomic Array Comparative Genome Hybridization

Yong Beom Shin, Sang Ook Nam, Eul-Ju Seo, Hyung-Hoi Kim, Chulhun L. Chang, Eun-Yup Lee, Han-Chul Son, Sang-Hyun Hwang
2008 Journal of Korean medical science  
We utilized whole genomic array comparative genome hybridization (CGH) with 4,000 selected bacterial artificial chromosomes (BACs) to define the chromosomal breakpoints and to delineate the extent of the  ...  We report on a male infant with 46,XY,der(11)t(1;11)(q41;p15.5) due to unbalanced segregation of the maternal reciprocal balanced translocation 46,XX,t(1;11)(q41;p15.5).  ...  ACKNOWLEDGMENTS We thank the proband and his family for their support of this study. We are grateful to Jeong-Yei Lee for technical support.  ... 
doi:10.3346/jkms.2008.23.6.1097 pmid:19119457 pmcid:PMC2610647 fatcat:tnwbq7qjvrad7p4jrqf467q4vm

Construction of a chromosome-scale long-read reference genome assembly for potato

Gina M Pham, John P Hamilton, Joshua C Wood, Joseph T Burke, Hainan Zhao, Brieanne Vaillancourt, Shujun Ou, Jiming Jiang, C Robin Buell
2020 GigaScience  
Here, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale  ...  The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes.  ...  The opinions in this study are those of the authors and do not necessarily represent the opinions or policies of PepsiCo, Inc.  ... 
doi:10.1093/gigascience/giaa100 pmid:32964225 pmcid:PMC7509475 fatcat:ddj7gq54izclfi2nhk27z7ccv4

An update and lessons from whole-genome sequencing projects

Steven JM Jones
1995 Current Opinion in Genetics and Development  
A number of prokaryotic and eukaryotic genomes are currently being sequenced. Already, the nucleotide sequences of four yeast chromosomes and of 2.2 Mb from Caenorhabditis elegans have been reported.  ...  Human genomic sequences have also been used in comparative studies with both mouse and Fugu rubripes.  ...  Recent advances in this system have involved the use of enzyme-linked fluorescence detection strategies coupled to direct-imaging systems [32] .  ... 
doi:10.1016/0959-437x(95)80050-6 pmid:7549430 fatcat:3fulj4vkbbhcbetkqaiazuqerq
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