10.5061/DRYAD.89V53
Lynch, Erin A.
University of California, Davis
Langille, Morgan G. I.
Dalhousie University
Darling, Aaron
University of California, Davis
Wilbanks, Elizabeth G.
University of California, Davis
Haltiner, Caitlin
University of California, Davis
Shao, Katie S. Y.
Davis Senior High School, Davis, California, United States of America
Starr, Michael O.
University of California, Davis
Teiling, Clotilde
454 Life Sciences, a Roche Company, Branford, Connecticut, United States
of America
Harkins, Timothy T.
Life Technologies, Beverly, Massachusetts, United States of America
Edwards, Robert A.
San Diego State University
Argonne National Laboratory
Eisen, Jonathan A.
University of California, Davis
Facciotti, Marc T.
University of California, Davis
Data from: Sequencing of seven haloarchaeal genomes reveals patterns of
genomic flux
Dryad
dataset
2012
Microbes
halophiles
Haloferax
Haloarcula
Haloarchaea
Haloarchaea
Archaea
2012-08-30T20:21:01Z
2012-08-30T20:21:01Z
en
https://doi.org/10.1371/journal.pone.0041389
472017300 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
We report the sequencing of seven genomes from two haloarchaeal genera,
Haloferax and Haloarcula. Ease of cultivation and the existence of
well-developed genetic and biochemical tools for several diverse
haloarchaeal species make haloarchaea a model group for the study of
archaeal biology. The unique physiological properties of these organisms
also make them good candidates for novel enzyme discovery for
biotechnological applications. Seven genomes were sequenced to
~20×coverage and assembled to an average of 50 contigs (range 5 scaffolds
- 168 contigs). Comparisons of protein-coding gene compliments revealed
large-scale differences in COG functional group enrichment between these
genera. Analysis of genes encoding machinery for DNA metabolism reveals
genera-specific expansions of the general transcription factor TATA
binding protein as well as a history of extensive duplication and
horizontal transfer of the proliferating cell nuclear antigen. Insights
gained from this study emphasize the importance of haloarchaea for
investigation of archaeal biology.
RAST_AnnotationsRAST-generated annotations for all genomes included in the
analyses in this manuscript.Raw_sequence_readsFragment libraries were
constructed for eight species of the family Halobacteriacea, three from
the genus Haloarcula (Har. californiae, Har. sinaiiensis, Har.
vallismortis) and five from the genus Haloferax (Hfx. denitrificans, Hfx.
mediterranei, Hfx. mucosum, Hfx. sulfurifontis, and Hfx. volcanii), and
sequenced on a single GS FLX Titanium run following standard protocols
(454 Life Sciences - http://454.com/). Hfx. volcanii was included as a
sequencing control, as its genome had been completed previously [19].
Additionally, for Har. sinaiiensis and Hfx. mediterranei, 8 Kb pair-end
libraries were constructed and the terminal 100 bp of each end was
sequenced, according to standard protocols. The paired-end information and
any trimming information are specified using annotation strings on the
description line of the reads. Reads were assembled using the Genome
Sequencer De Novo assembler (454 Life Sciences - http://www.my454.com/).