Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores.

Journal of Bacteriology
G D Paul ClarkeRobert L Charlebois

Abstract

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes b...Continue Reading

References

Jun 1, 1970·Systematic Zoology·W M Fitch
Jan 1, 1994·Journal of Bacteriology·G J OlsenR Overbeek
Aug 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·S M BarnsN R Pace
Sep 17, 1996·Proceedings of the National Academy of Sciences of the United States of America·A R Mushegian, E V Koonin
Aug 1, 1996·Computer Applications in the Biosciences : CABIOS·R D Page
Apr 1, 1997·Journal of Molecular Evolution·J G Lawrence, H Ochman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 20, 1998·Current Opinion in Genetics & Development·E V Koonin, M Y Galperin
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·M A Huynen, P Bork
Nov 24, 1998·Trends in Genetics : TIG·L AravindE V Koonin
Jan 23, 1999·Nature Genetics·B SnelM A Huynen
Mar 27, 1999·Journal of Molecular Evolution·P G Foster, D A Hickey
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·R JainJ A Lake
Jun 26, 1999·Science·W F Doolittle
Aug 4, 1999·Trends in Genetics : TIG·N C Kyrpides, G J Olsen
Aug 4, 1999·Trends in Genetics : TIG·L AravindE V Koonin
Oct 16, 1999·Nucleic Acids Research·S T Fitz-Gibbon, C H House
Oct 26, 1999·Current Biology : CB·J M Logsdon, D M Faguy
Mar 11, 2000·Scientific American·W F Doolittle
Jun 1, 2000·Nature·H OchmanE A Groisman
Jul 19, 2000·Proceedings of the National Academy of Sciences of the United States of America·C R Woese
Nov 15, 2000·Genome Research·S Garcia-VallvéJ Palau
Dec 23, 2000·Nucleic Acids Research·B L MaidakJ M Tiedje
Jul 10, 2001·Journal of Molecular Evolution·L B Koski, G B Golding
Oct 30, 2001·Current Opinion in Genetics & Development·M A Ragan
Jan 5, 2002·Trends in Microbiology·Jeffrey G Lawrence, Howard Ochman
Jun 11, 2002·International Journal of Systematic and Evolutionary Microbiology·Mark A Ragan, Robert L Charlebois
Jul 1, 1985·Evolution; International Journal of Organic Evolution·Joseph Felsenstein

❮ Previous
Next ❯

Citations

Aug 26, 2006·Extremophiles : Life Under Extreme Conditions·Michael BorrissThomas Schweder
Dec 19, 2007·Theory in Biosciences = Theorie in Den Biowissenschaften·Haïtham SghaierHiroshi Mitomo
Jun 1, 2008·Indian Journal of Microbiology·Sadhana LalVipin C Kalia
Aug 15, 2002·Trends in Genetics : TIG·Yuri I WolfEugene V Koonin
Sep 3, 2003·FEMS Microbiology Letters·Robert L CharleboisAndrew St Jean
Apr 30, 2005·Nature Reviews. Genetics·Frédéric DelsucHervé Philippe
Mar 24, 2004·Nature Reviews. Microbiology·Eugene V Koonin
Dec 16, 2004·Bioinformatics·Xun GuHongmei Zhang
Mar 3, 2007·Bioinformatics·Jason S Papadopoulos, Richa Agarwala
Jun 14, 2008·Molecular Biology and Evolution·Alon Wellner, Uri Gophna
Oct 5, 2002·Nucleic Acids Research·David J LynnDonal A Hickey
Feb 1, 2005·Nucleic Acids Research·Victor KuninChristos A Ouzounis
Feb 22, 2003·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·W F DoolittleA J Roger
Jun 7, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Thomas Cavalier-Smith
Dec 3, 2004·Genome Research·Robert L Charlebois, W Ford Doolittle
Jun 21, 2005·Genome Research·Victor KuninChristos A Ouzounis
Sep 18, 2004·Journal of Bacteriology·Pavel S NovichkovEugene V Koonin
Feb 3, 2005·Journal of Bacteriology·Uri GophnaRobert L Charlebois
Aug 4, 2004·Journal of Bioinformatics and Computational Biology·Gary W Stuart, Michael W Berry
Sep 13, 2005·Annual Review of Microbiology·Berend SnelBas E Dutilh
Feb 26, 2013·BMC Bioinformatics·Jan P Meier-KolthoffMarkus Göker
May 26, 2005·BMC Evolutionary Biology·E BaptesteW F Doolittle
Jun 2, 2005·BMC Evolutionary Biology·Marshall Bern, David Goldberg
Mar 28, 2008·BMC Genomics·Javier Tamames, Andrés Moya
Jul 13, 2006·Biology Direct·Thomas Cavalier-Smith
Jul 1, 2011·Biology Direct·Robert G Beiko
Aug 14, 2003·Genome Biology·Kira S Makarova, Eugene V Koonin
Feb 6, 2007·Genome Biology·Sheila Podell, Terry Gaasterland
Aug 24, 2012·Evolutionary Bioinformatics Online·Thomas Meinel, Antje Krause
Dec 15, 2010·Proceedings of the National Academy of Sciences of the United States of America·Uri Gophna, Yanay Ofran
Jan 31, 2007·Proceedings of the National Academy of Sciences of the United States of America·W Ford Doolittle, Eric Bapteste
Jan 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·Song YangPhilip E Bourne
Apr 23, 2010·Systematic and Applied Microbiology·H-P Klenk, M Göker
May 4, 2004·Trends in Microbiology·Uri GophnaW Ford Doolittle
Oct 12, 2005·Current Opinion in Genetics & Development·Christos A Ouzounis
Sep 6, 2005·Journal of Molecular Biology·Florencio PazosMichael J E Sternberg
Jan 13, 2011·FEMS Microbiology Reviews·Elizabeth Skippington, Mark A Ragan

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.