title: Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942.
abstract: BACKGROUND
  Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands in the fresh water cyanobacteria Synechococcus elongatus PCC 7942 (genome size 2.7 Mb) that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival.
  
  
  RESULTS
  By using a combination of methods we identified 170 xenologs, 136 ORFans and 1401 core genes in the genome of S. elongatus PCC 7942. These represent 6.5%, 5.2% and 53.6% of the annotated genes respectively. We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage. The origin of the largest genomic island by horizontal gene transfer (HGT) could be corroborated by lack of coverage among metagenomic sequences from a fresh water microbialite. Evidence is also presented that xenologous genes tend to cluster in operons. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologs, suggesting a role for horizontal gene transfer in the evolution of Synechococcus sensory systems.
  
  
  CONCLUSIONS
  Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.
authors.affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Delaye
authors.forename: Carmen M
authors.initials: CM
authors.lastname: González-Domenech
authors.forename: María P
authors.initials: MP
authors.lastname: Garcillán-Barcia
authors.forename: Juli
authors.initials: J
authors.lastname: Peretó
authors.forename: Fernando
authors.initials: F
authors.lastname: de la Cruz
authors.forename: Andrés
authors.initials: A
authors.lastname: Moya
mesh_terms: D001426:Bacterial Proteins / Q000097:blood / Q000235:genetics*; D001482:Base Composition / Q000235:genetics; D022761:Gene Transfer, Horizontal / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D044404:Genomic Islands / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D046940:Synechococcus / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins