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Chapter 6 : Gene Duplicates in Vibrio Genomes

Authors: Dirk Gevers1, Yves Van de Peer2
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Affiliations: 1: Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium; 2: BioInformatics and Evolutionary Genomics, Ghent University/VIB Technologiepark 927, B-9052 Ghent, Belgium
Content Type: Monograph
Publication Year: 2006

Category: Environmental Microbiology

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Abstract:

This chapter discusses the collection of gene duplicates (the paranome) in relation to the whole proteome, the functional composition, and organization for all currently available genomes, i.e., , , , and . The vibrio genomes are organized into two replicons, a main chromosome and an auxiliary chromosome, the latter characterized by less gene synteny than the former. The majority (>77%) of the strain-specific expansion (SSEs) consist of hypothetical proteins or proteins with unknown functions, of which most have no homologous genes outside the . The chapter provides an overview of the functional landscape of the paranome for the is presented, which allows to determine whether duplicate retention is biased toward specific functional classes for each of the bacterial strains. It appears that the preferentially retained duplicated genes mainly belong to the functional classes that are associated with amino acid metabolism (class E) and transcription (class K). Such genes are directly or indirectly (via regulation) involved in adapting to a constantly changing environment, showing the importance of gene duplicates for biological evolution. Gene duplications can occur on a gene-by-gene basis, resulting in tandem duplicates, or they can result from the duplication of larger regions. Rearrangements after duplication and acquisition of homologs via horizontal gene transfer (HGT) result in duplicates’ being dispersed over the genome.

Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6
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Gene Duplicates in Vibrio Genomes
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Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6
/content/10.1128/9781555815714.ch06.ch06fig01
FIGURE 1
Parsimonious evolutionary scenario for vibrio proteomes. A reconstruction of acquisition, loss, and gene genesis events was based on the species tree (constructed from 16S rRNA gene sequence) and on protein families as described in the introduction. Numbers along the branches refer to the number of acquisitions, losses, and genesis, respectively. Each node has a number that refers to data in Table 2 . The number between brackets is the total number of genes for that particular genome. Inference of ancestral gene contents was made by parsimony analysis in PAUP with penalties for acquisition, deletion, and gene genesis set to 1, 1, and 5, respectively.
10.1128/9781555815714/f0078-01_thmb.gif
10.1128/9781555815714/f0078-01.gif
Image of FIGURE 1
FIGURE 1

Parsimonious evolutionary scenario for vibrio proteomes. A reconstruction of acquisition, loss, and gene genesis events was based on the species tree (constructed from 16S rRNA gene sequence) and on protein families as described in the introduction. Numbers along the branches refer to the number of acquisitions, losses, and genesis, respectively. Each node has a number that refers to data in Table 2 . The number between brackets is the total number of genes for that particular genome. Inference of ancestral gene contents was made by parsimony analysis in PAUP with penalties for acquisition, deletion, and gene genesis set to 1, 1, and 5, respectively.

Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6
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/content/10.1128/9781555815714.ch06.ch06fig02
FIGURE 2
Sequence divergence within families versus family size. For each family of the CMCP6 proteome, the average amino acid sequence identity of pairwise comparisons among the members of the family is determined and plotted against the family size.
10.1128/9781555815714/f0079-01_thmb.gif
10.1128/9781555815714/f0079-01.gif
Image of FIGURE 2
FIGURE 2

Sequence divergence within families versus family size. For each family of the CMCP6 proteome, the average amino acid sequence identity of pairwise comparisons among the members of the family is determined and plotted against the family size.

Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6
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Tables

Gene Duplicates in Vibrio Genomes
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Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6
/content/10.1128/9781555815714.ch06.ch06tab01
TABLE 1
Properties of the vibrio genomes
Generic image for table
TABLE 1

Properties of the vibrio genomes

Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6
/content/10.1128/9781555815714.ch06.ch06tab02
TABLE 2
Properties of the vibrio ancestral nodes
Generic image for table
TABLE 2

Properties of the vibrio ancestral nodes

Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6
/content/10.1128/9781555815714.ch06.ch06tab03
TABLE 3
Examples of strain-specific expansions
Generic image for table
TABLE 3

Examples of strain-specific expansions

Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6
/content/10.1128/9781555815714.ch06.ch06tab04
TABLE 4
Organization of the paranome
Generic image for table
TABLE 4

Organization of the paranome

Citation: Gevers D, Peer Y. 2006. Gene Duplicates in Vibrio Genomes, p 76-83. In Thompson F, Austin B, Swings J (ed), The Biology of Vibrios. ASM Press, Washington, DC. doi: 10.1128/9781555815714.ch6

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