title: Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.
abstract: Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production.
  
  
  
  In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon.
  
  
  
  Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland.
authors.forename: Philip
authors.identifier: 0000-0003-3423-7930
authors.initials: P
authors.lastname: Kelleher
authors.affiliation: Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: Francesca
authors.initials: F
authors.lastname: Bottacini
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland.|Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Mahony
authors.affiliation: Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Cork, Ireland.
authors.forename: Kieran N
authors.initials: KN
authors.lastname: Kilcawley
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland. d.vansinderen@ucc.ie.|Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland. d.vansinderen@ucc.ie.
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
mesh_terms: D026905:Amino Acid Transport Systems / Q000235:genetics; D050260:Carbohydrate Metabolism / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D013294:Lactococcus lactis / Q000145:classification / Q000235:genetics*; D050356:Lipid Metabolism / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000145:classification / Q000378:metabolism
chemical_list: D026905:Amino Acid Transport Systems; D002352:Carrier Proteins; D012336:RNA, Ribosomal, 16S; C030363:lipid transfer protein
keywords: Genomics; Lactococcus lactis; Niche adaptation; Pan-genome; SMRT sequencing