Phylogenomic analysis of marine Roseobacters.

PloS One
Kai TangCathy H Wu

Abstract

Members of the Roseobacter clade which play a key role in the biogeochemical cycles of the ocean are diverse and abundant, comprising 10-25% of the bacterioplankton in most marine surface waters. The rapid accumulation of whole-genome sequence data for the Roseobacter clade allows us to obtain a clearer picture of its evolution. In this study about 1,200 likely orthologous protein families were identified from 17 Roseobacter bacteria genomes. Functional annotations for these genes are provided by iProClass. Phylogenetic trees were constructed for each gene using maximum likelihood (ML) and neighbor joining (NJ). Putative organismal phylogenetic trees were built with phylogenomic methods. These trees were compared and analyzed using principal coordinates analysis (PCoA), approximately unbiased (AU) and Shimodaira-Hasegawa (SH) tests. A core set of 694 genes with vertical descent signal that are resistant to horizontal gene transfer (HGT) is used to reconstruct a robust organismal phylogeny. In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC transporters and chaperones often found in the environmental metagenomic and metatranscriptomic data. These genes ...Continue Reading

References

Aug 1, 1996·Computer Applications in the Biosciences : CABIOS·R D Page
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jan 27, 1999·Bioinformatics·D Posada, K A Crandall
Dec 11, 1999·Nucleic Acids Research·R L TatusovE V Koonin
Jun 1, 2000·Nature·H OchmanE A Groisman
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Dec 26, 2001·Bioinformatics·H Shimodaira, M Hasegawa
Apr 3, 2002·Journal of Biosciences·Chitra Dutta, Archana Pan
Apr 6, 2002·Bioinformatics·Heiko A SchmidtArndt von Haeseler
Nov 26, 2002·Molecular Biology and Evolution·J Peter GogartenJeffrey G Lawrence
Jan 17, 2003·Nature·Robert L CharleboisMark A Ragan
Jun 5, 2003·Molecular Biology and Evolution·Ravi JainJames A Lake
Jun 14, 2003·Science·Jonathan A Eisen, Claire M Fraser
Sep 4, 2003·Genome Research·Li LiDavid S Roos
Sep 17, 2003·BMC Genomics·Olga Zhaxybayeva, J Peter Gogarten
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Mar 17, 2004·Computational Biology and Chemistry·Cathy H WuWinona C Barker
Apr 28, 2004·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·James R Brown, Craig Volker
Jun 9, 2004·Applied and Environmental Microbiology·Todd R Miller, Robert Belas
Sep 18, 2004·Bioinformatics·C J Creevey, J O McInerney
Jan 14, 2005·Bioinformatics·Federico AbascalDavid Posada
May 26, 2005·BMC Evolutionary Biology·E BaptesteW F Doolittle
Sep 3, 2005·Nature Reviews. Microbiology·J Peter Gogarten, Jeffrey P Townsend
Sep 3, 2005·Nature Reviews. Microbiology·Søren J SørensenStefan Wuertz
Sep 3, 2005·Nature Reviews. Microbiology·Christopher M Thomas, Kaare M Nielsen
Sep 24, 2005·Proceedings of the National Academy of Sciences of the United States of America·Robert G BeikoMark A Ragan
Oct 6, 2005·Applied and Environmental Microbiology·Alison BuchanMary Ann Moran
Feb 14, 2006·BMC Evolutionary Biology·Robert G Beiko, Nicholas Hamilton
May 25, 2006·Annual Review of Microbiology·Irene Wagner-Döbler, Hanno Biebl
Mar 16, 2007·PLoS Biology·Rekha SeshadriMarvin Frazier
Mar 23, 2007·BMC Evolutionary Biology·Maria S Poptsova, J Peter Gogarten
May 29, 2007·Applied and Environmental Microbiology·M A MoranA Buchan
Jun 15, 2007·Genome Biology·Jose Castresana
Oct 16, 2007·Nucleic Acids Research·Victor M MarkowitzNikos C Kyrpides
Feb 7, 2008·Archives of Microbiology·Thorsten BrinkhoffMeinhard Simon
Feb 13, 2008·Proceedings of the National Academy of Sciences of the United States of America·Tuo Shi, Paul G Falkowski
Sep 5, 2008·The ISME Journal·Sarah M SowellStephen J Giovanonni
Sep 17, 2008·Current Protocols in Bioinformatics·Julie D ThompsonDes G Higgins
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Nicolas Galtier, Vincent Daubin
Oct 15, 2008·Systematic Biology·Alexandros StamatakisJacques Rougemont

❮ Previous
Next ❯

Citations

Jun 28, 2014·Antonie van Leeuwenhoek·Yingfang LinNianzhi Jiao
Jun 7, 2014·Marine Genomics·Catalina Maria Alejandro-MarínBalbina Nogales
Jun 23, 2011·BMC Genomics·Daniela KalhoeferThorsten Brinkhoff
Jul 22, 2011·The ISME Journal·Joseph Alexander Christie-OlezaJean Armengaud
Oct 31, 2014·International Journal of Systematic and Evolutionary Microbiology·Shuhui LiNianzhi Jiao
Oct 7, 2017·International Journal of Systematic and Evolutionary Microbiology·Guishan ZhangUlrich Stingl
Nov 13, 2012·Journal of Bacteriology·Kai TangNianzhi Jiao
Oct 12, 2011·Nature Reviews. Microbiology·Andrew R J CursonAndrew W B Johnston
Nov 7, 2017·Microbial Biotechnology·Natascia BiondiMario R Tredici
Apr 11, 2021·Archives of Microbiology·Liuyang OuShuaiyin Chen

❮ Previous
Next ❯

Software Mentioned

Ginkgo
ProTest
Clann
Modeltest
CONSEL
MrBayes
TREEDIST
Tree
PAUP
CONSENSE

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.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Cornelia WuchterJaap S Sinninghe Damsté
© 2021 Meta ULC. All rights reserved