UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

The Journal of Microbiology
Seong-In NaJongsik Chun

Abstract

Genome-based phylogeny plays a central role in the future taxonomy and phylogenetics of Bacteria and Archaea by replacing 16S rRNA gene phylogeny. The concatenated core gene alignments are frequently used for such a purpose. The bacterial core genes are defined as single-copy, homologous genes that are present in most of the known bacterial species. There have been several studies describing such a gene set, but the number of species considered was rather small. Here we present the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees. The method was successfully used to infer phylogenomic relationship of Escherichia and related taxa and can be used for the set of genomes at any taxonomic ranks of Bacteria. The UBCG pipeline and file viewer are freely available at https://www.ezbiocloud.net/tools/ubcg and https://www.ezbiocloud.net/tools/ubcg_viewer , respectively.

References

Jan 11, 1992·International Journal of Systematic Bacteriology·G E FoxP Jurtshuk
Jan 12, 2001·FEMS Microbiology Reviews·R Rosselló-Mora, R Amann
Jun 14, 2003·Science·Jonathan A Eisen, Claire M Fraser
Dec 25, 2009·Nature·Dongying WuJonathan A Eisen
Mar 10, 2010·BMC Bioinformatics·Doug HyattLoren J Hauser
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Aug 17, 2010·Bioinformatics·Robert C Edgar
Nov 1, 2011·PLoS Computational Biology·Sean R Eddy
Dec 16, 2011·The ISME Journal·Chris L DupontJ Craig Venter
Jun 1, 2012·The Journal of General Virology·Alan D RadfordNeil Hall
Dec 1, 2012·Nucleic Acids Research·Daniel H HaftErin Beck
Jan 2, 2013·Proceedings of the National Academy of Sciences of the United States of America·Patrick M ShihCheryl A Kerfeld
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Jan 16, 2014·International Journal of Systematic and Evolutionary Microbiology·Yoon-Seong JeonJongsik Chun
Feb 1, 2014·PeerJ·Aaron E DarlingJonathan A Eisen
Feb 8, 2014·International Journal of Systematic and Evolutionary Microbiology·Jongsik Chun, Fred A Rainey
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Sep 8, 2016·Genome Génome / Conseil National De Recherches Canada·Markus J Ankenbrand, Alexander Keller
Jul 1, 1985·Evolution; International Journal of Organic Evolution·Joseph Felsenstein
Jun 24, 2017·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·F Tagini, G Greub
Jan 3, 2018·International Journal of Systematic and Evolutionary Microbiology·Jongsik ChunMartha E Trujillo

❮ Previous
Next ❯

Citations

Jun 23, 2018·International Journal of Systematic and Evolutionary Microbiology·Alexandra La MuraMaría J Pujalte
Jun 27, 2018·International Journal of Systematic and Evolutionary Microbiology·David R ArahalMaría J Pujalte
Nov 22, 2018·International Journal of Systematic and Evolutionary Microbiology·Ana G AbrilTomás G Villa
Jan 22, 2019·International Journal of Systematic and Evolutionary Microbiology·Guanghua WangKefu Yu
Jan 25, 2019·International Journal of Systematic and Evolutionary Microbiology·Krishna GundawarSuresh Korpole
Feb 20, 2019·International Journal of Systematic and Evolutionary Microbiology·Mi-Jeong ParkKae Kyoung Kwon
Mar 1, 2019·International Journal of Systematic and Evolutionary Microbiology·Zeng-Hong GaoLi-Hong Qiu
Mar 26, 2019·International Journal of Systematic and Evolutionary Microbiology·Shih-Yi SheuWen-Ming Chen
Mar 29, 2019·International Journal of Systematic and Evolutionary Microbiology·Jia-Cheng FuLi-Hong Qiu
Apr 10, 2019·International Journal of Systematic and Evolutionary Microbiology·Wen-Ming ChenShih-Yi Sheu
Feb 21, 2019·International Journal of Systematic and Evolutionary Microbiology·Shuailiang XuGuanghua Wang
May 14, 2019·International Journal of Systematic and Evolutionary Microbiology·Shih-Yi SheuWen-Ming Chen
May 18, 2019·International Journal of Systematic and Evolutionary Microbiology·Boram SeoGwangPyo Ko
Apr 30, 2019·International Journal of Systematic and Evolutionary Microbiology·Wen-Ming ChenShih-Yi Sheu
Jun 4, 2019·International Journal of Systematic and Evolutionary Microbiology·Wen-Ming ChenShih-Yi Sheu
Jun 6, 2019·International Journal of Systematic and Evolutionary Microbiology·Kunal JaniAvinash Sharma
Jun 11, 2019·International Journal of Systematic and Evolutionary Microbiology·Ji-Sen PengZhi-Pei Liu
May 21, 2019·Environmental Microbiology·Lianna PoghosyanSebastian Lücker
Jul 31, 2019·International Journal of Systematic and Evolutionary Microbiology·Qing LiuYu-Hua Xin
May 29, 2019·International Journal of Systematic and Evolutionary Microbiology·Guo-Qing ZhangYu-Hua Xin
Jun 7, 2019·International Journal of Systematic and Evolutionary Microbiology·Yu Jin ParkChe Ok Jeon
May 24, 2019·International Journal of Systematic and Evolutionary Microbiology·Shih-Yi SheuWen-Ming Chen
May 24, 2019·International Journal of Systematic and Evolutionary Microbiology·Shih-Yi SheuWen-Ming Chen
Jul 17, 2019·International Journal of Systematic and Evolutionary Microbiology·Shuo WangZong-Jun Du
May 1, 2019·International Journal of Systematic and Evolutionary Microbiology·Wonduck KimKae Kyoung Kwon
May 16, 2019·International Journal of Systematic and Evolutionary Microbiology·Yunyun HuoGehong Wei
Aug 28, 2019·International Journal of Systematic and Evolutionary Microbiology·Jia-Cheng FuLi-Hong Qiu
Sep 7, 2019·International Journal of Systematic and Evolutionary Microbiology·Yu-Qi YanZong-Jun Du
Aug 30, 2019·International Journal of Systematic and Evolutionary Microbiology·Sen-Yang XiaoLi-Hong Qiu
Sep 5, 2019·International Journal of Systematic and Evolutionary Microbiology·Wen-Ming ChenShih-Yi Sheu
Jun 21, 2019·Antonie van Leeuwenhoek·Ang LiuXiu-Zhen Li
Oct 10, 2019·International Journal of Systematic and Evolutionary Microbiology·Wen-Ming ChenShih-Yi Sheu
Oct 10, 2019·International Journal of Systematic and Evolutionary Microbiology·Hyungdong KimTaegun Seo
Oct 10, 2019·International Journal of Systematic and Evolutionary Microbiology·Danqiu LinJigang Chen
Oct 16, 2019·International Journal of Systematic and Evolutionary Microbiology·Xuewen LiuZongze Shao
Oct 19, 2019·The ISME Journal·Eva SpieckJennifer Hüpeden
Oct 31, 2019·International Journal of Systematic and Evolutionary Microbiology·Min-Jung KwakJongsik Chun
Nov 2, 2019·International Journal of Systematic and Evolutionary Microbiology·Shih-Yi SheuWen-Ming Chen
Aug 20, 2019·International Journal of Systematic and Evolutionary Microbiology·Ceshing SheuWen-Ming Chen
Aug 21, 2019·International Journal of Systematic and Evolutionary Microbiology·Regina RettenmaierVladimir V Zverlov
Aug 23, 2019·International Journal of Systematic and Evolutionary Microbiology·Jungeun KimChe Ok Jeon
Aug 23, 2019·International Journal of Systematic and Evolutionary Microbiology·Haneul KimKiseong Joh
Nov 5, 2019·International Journal of Systematic and Evolutionary Microbiology·Zhaobin HuangJianjun Yuan
Aug 29, 2019·International Journal of Systematic and Evolutionary Microbiology·Rahel ParkKevin J Verstrepen

❮ Previous
Next ❯

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.