Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation

Kelleher, Philip; Bottacini, Francesca; Mahony, Jennifer; Kilcawley, Kieran N.; van Sinderen, Douwe

Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation

dc.contributor.author	Kelleher, Philip
dc.contributor.author	Bottacini, Francesca
dc.contributor.author	Mahony, Jennifer
dc.contributor.author	Kilcawley, Kieran N.
dc.contributor.author	van Sinderen, Douwe
dc.contributor.funder	Department of Agriculture, Food and the Marine	en
dc.contributor.funder	Science Foundation Ireland	en
dc.date.accessioned	2017-05-03T11:19:55Z
dc.date.available	2017-05-03T11:19:55Z
dc.date.issued	2017-03-29
dc.date.updated	2017-05-03T11:07:56Z
dc.description.abstract	Background: 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. Results: 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. Conclusions: 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.	en
dc.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	267
dc.identifier.citation	Kelleher, P., Bottacini, F., Mahony, J., Kilcawley, K. N. and van Sinderen, D. (2017) 'Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation', BMC Genomics, 18, 267 (20pp). doi: 10.1186/s12864-017-3650-5	en
dc.identifier.doi	10.1186/s12864-017-3650-5
dc.identifier.endpage	20	en
dc.identifier.issn	1471-2164
dc.identifier.journaltitle	BMC Genomics	en
dc.identifier.startpage	1	en
dc.identifier.uri	https://hdl.handle.net/10468/3911
dc.identifier.volume	18	en
dc.language.iso	en	en
dc.publisher	BioMed Central	en
dc.relation.project	Department of Agriculture, Food and the Marine (FIRM Ref: 10/RD/TMFRC/704–‘CheeseBoard 2015’ project); Science Foundation Ireland (Principal Investigator Award Ref. No. 13/IA/1953; TIDA Ref. No. 14/TIDA/2287; Starting Investigator Research Grant 15/SIRG/3430)	en
dc.rights	© 2017, the Authors. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.subject	Lactococcus lactis	en
dc.subject	Genomics	en
dc.subject	SMRT sequencing	en
dc.subject	Pan-genome	en
dc.subject	Niche adaptation	en
dc.title	Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation	en
dc.type	Article (peer-reviewed)	en