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Gene Duplicates in Vibrio Genomes, Page 1 of 2
< Previous page Next page > /docserver/preview/fulltext/10.1128/9781555815714/9781555813659_Chap06-1.gif /docserver/preview/fulltext/10.1128/9781555815714/9781555813659_Chap06-2.gifAbstract:
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 Vibrionaceae genomes, i.e., Vibrio cholerae, V. vulnificus, V. parahaemolyticus, and Photobacterium profundum. 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 Vibrionaceae. The chapter provides an overview of the functional landscape of the paranome for the Vibrionaceae 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.