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Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)).

Anderson I, Tindall BJ, Rohde M, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Peters L, Pati A, Mikhailova N, Pagani I, Teshima H, Han C, Tapia R, Land M, Woyke T, Klenk HP, Kyrpides N, Ivanova N - Stand Genomic Sci (2012)

Bottom Line: Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth.We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids.This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.

View Article: PubMed Central - PubMed

ABSTRACT
Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree showing the relationships between haloarchaea with sequenced genomes. The sequences were aligned with the Ribosomal Database Project (RDP) aligner [3], which uses the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. The tree was generated with the Tree Builder from the RDP which uses Weighbor [4] with an alphabet size of 4 and length size of 1,000. The building of the tree also involves a bootstrapping process repeated 100 times to generate a majority consensus tree. Methanosarcina acetivorans was used as the outgroup.
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f1: Phylogenetic tree showing the relationships between haloarchaea with sequenced genomes. The sequences were aligned with the Ribosomal Database Project (RDP) aligner [3], which uses the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. The tree was generated with the Tree Builder from the RDP which uses Weighbor [4] with an alphabet size of 4 and length size of 1,000. The building of the tree also involves a bootstrapping process repeated 100 times to generate a majority consensus tree. Methanosarcina acetivorans was used as the outgroup.

Mentions: In 16S rRNA trees the Halopiger species are most closely related to Natronolimnobius species [1,2]. Currently there are fifteen complete genomes of haloarchaea in GenBank. Figure 1 shows the relationship of H. xanaduensis to other haloarchaea for which complete genomes have been sequenced. For Halobacterium salinarum and Haloquadratum walsbyi, only one sequence is included in Figure 1, although for both of these species two genomes have been sequenced.


Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)).

Anderson I, Tindall BJ, Rohde M, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Peters L, Pati A, Mikhailova N, Pagani I, Teshima H, Han C, Tapia R, Land M, Woyke T, Klenk HP, Kyrpides N, Ivanova N - Stand Genomic Sci (2012)

Phylogenetic tree showing the relationships between haloarchaea with sequenced genomes. The sequences were aligned with the Ribosomal Database Project (RDP) aligner [3], which uses the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. The tree was generated with the Tree Builder from the RDP which uses Weighbor [4] with an alphabet size of 4 and length size of 1,000. The building of the tree also involves a bootstrapping process repeated 100 times to generate a majority consensus tree. Methanosarcina acetivorans was used as the outgroup.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368405&req=5

f1: Phylogenetic tree showing the relationships between haloarchaea with sequenced genomes. The sequences were aligned with the Ribosomal Database Project (RDP) aligner [3], which uses the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. The tree was generated with the Tree Builder from the RDP which uses Weighbor [4] with an alphabet size of 4 and length size of 1,000. The building of the tree also involves a bootstrapping process repeated 100 times to generate a majority consensus tree. Methanosarcina acetivorans was used as the outgroup.
Mentions: In 16S rRNA trees the Halopiger species are most closely related to Natronolimnobius species [1,2]. Currently there are fifteen complete genomes of haloarchaea in GenBank. Figure 1 shows the relationship of H. xanaduensis to other haloarchaea for which complete genomes have been sequenced. For Halobacterium salinarum and Haloquadratum walsbyi, only one sequence is included in Figure 1, although for both of these species two genomes have been sequenced.

Bottom Line: Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth.We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids.This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.

View Article: PubMed Central - PubMed

ABSTRACT
Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.

No MeSH data available.


Related in: MedlinePlus