Genomes and knowledge - a questionable relationship?

被引：23

作者：

Whitworth, David E. ^{[1
]}

机构：

[1] Aberystwyth Univ, Inst Biol Environm & Rural Sci, Aberystwyth SY23 3DD, Dyfed, Wales

来源：

TRENDS IN MICROBIOLOGY | 2008年 / 16卷 / 11期

关键词：

D O I：

10.1016/j.tim.2008.08.001

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The availability of bacterial genome sequences has ushered in an era of post-genomic research - accelerating and often enabling molecular genetic analyses. For bacteriologists focussing on an individual bacterium, comparing genomes has also led to a greater understanding of their favoured organism through contextualization. But how does the value of such contextualization vary with the number of available genomes? It seems that for most genome metrics, comparison against approximately 100 genomes is sufficient, with comparison against further genomes not considerably affecting the contextual knowledge gained. It appears that quality, rather than quantity, might be the most important factor when comparing genomes.

引用

页码：512 / 519

页数：8

共 41 条

[21] Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead [J].

Konstantinidis, Konstantinos T. ;

Tiedje, James M. .

CURRENT OPINION IN MICROBIOLOGY, 2007, 10 (05) :504-509

[22] The impact of comparative genomics on our understanding of evolution [J].

Koonin, EV ;

Aravind, L ;

Kondrashov, AS .

CELL, 2000, 101 (06) :573-576

[23] A standard MIGS/MIMS compliant XML schema:: Toward the development of the Genomic Contextual Data Markup Language (GCDML) [J].

Kottmann, Renzo ;

Gray, Tanya ;

Murphy, Sean ;

Kagan, Leonid ;

Kravitz, Saul ;

Lombardot, Thierry ;

Field, Dawn ;

Gloeckner, Frank Oliver .

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 2008, 12 (02) :115-121

[24] Tracking microbial biodiversity through molecular and genomic ecology [J].

Lopez-Garcia, Purificacion ;

Moreira, David .

RESEARCH IN MICROBIOLOGY, 2008, 159 (01) :67-73

[25] Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea [J].

Makarova, Kira S. ;

Sorokin, Alexander V. ;

Novichkov, Pavel S. ;

Wolf, Yuri I. ;

Koonin, Eugene V. .

BIOLOGY DIRECT, 2007, 2 (1)

[26] The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions [J].

Markowitz, Victor M. ;

Szeto, Ernest ;

Palaniappan, Krishna ;

Grechkin, Yuri ;

Chu, Ken ;

Chen, I-Min A. ;

Dubchak, Inna ;

Anderson, Iain ;

Lykidis, Athanasios ;

Mavromatis, Konstantinos ;

Ivanova, Natalia N. ;

Kyrpides, Nikos C. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D528-D533

[27] Gene gain and gene loss in Streptococcus:: Is it driven by habitat? [J].

Marri, Pradeep Reddy ;

Hao, Weilong ;

Golding, G. Brian .

MOLECULAR BIOLOGY AND EVOLUTION, 2006, 23 (12) :2379-2391

[28] A minimal gene set for cellular life derived by comparison of complete bacterial genomes [J].

Mushegian, AR ;

Koonin, EV .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (19) :10268-10273

[29] Complete genome sequence of Caulobacter crescentus [J].

Nierman, WC ;

Feldblyum, TV ;

Laub, MT ;

Paulsen, IT ;

Nelson, KE ;

Eisen, J ;

Heidelberg, JF ;

Alley, MRK ;

Ohta, N ;

Maddock, JR ;

Potocka, I ;

Nelson, WC ;

Newton, A ;

Stephens, C ;

Phadke, ND ;

Ely, B ;

DeBoy, RT ;

Dodson, RJ ;

Durkin, AS ;

Gwinn, ML ;

Haft, DH ;

Kolonay, JF ;

Smit, J ;

Craven, MB ;

Khouri, H ;

Shetty, J ;

Berry, K ;

Utterback, T ;

Tran, K ;

Wolf, A ;

Vamathevan, J ;

Ermolaeva, M ;

White, O ;

Salzberg, SL ;

Venter, JC ;

Shapiro, L ;

Fraser, CM .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (07) :4136-4141

[30] Examining bacterial species under the specter of gene transfer and exchange [J].

Ochman, H ;

Lerat, E ;

Daubin, V .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 :6595-6599

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