Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T)

Cliff Han, Stefan Spring, Alla Lapidus, Tijana Glavina del Rio, Hope Tice, Alex Copeland, Jan Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam LandLoren Hauser, Yun Juan Chang, Cynthia C. Jeffries, Elizabeth Saunders, Olga Chertkov, Thomas Brettin, Markus Göker, Manfred Rohde, Jim Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans Peter Klenk, John C. Detter

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Original languageEnglish (US)
Pages (from-to)54-62
Number of pages9
JournalStandards in Genomic Sciences
Volume1
Issue number1
DOIs
StatePublished - 2009

Fingerprint

Pedobacter
Genome
Encyclopedias
Bacteroidetes
Comb and Wattles
Replicon
Archaea
Glycosaminoglycans
Heparin
Nitrogen
Soil
Carbon
RNA
Bacteria
Enzymes
Genes
Proteins

Keywords

  • Dry soil
  • Flexible rods
  • Gram-negative
  • Heparinase producer
  • Mesophile
  • Sphingobacteriaceae
  • Strictly aerobic

ASJC Scopus subject areas

  • Genetics

Cite this

Han, C., Spring, S., Lapidus, A., del Rio, T. G., Tice, H., Copeland, A., ... Detter, J. C. (2009). Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T). Standards in Genomic Sciences, 1(1), 54-62. https://doi.org/10.4056/sigs.22138

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T). / Han, Cliff; Spring, Stefan; Lapidus, Alla; del Rio, Tijana Glavina; Tice, Hope; Copeland, Alex; Cheng, Jan Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun Juan; Jeffries, Cynthia C.; Saunders, Elizabeth; Chertkov, Olga; Brettin, Thomas; Göker, Markus; Rohde, Manfred; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter; Detter, John C.

In: Standards in Genomic Sciences, Vol. 1, No. 1, 2009, p. 54-62.

Research output: Contribution to journalArticle

Han, C, Spring, S, Lapidus, A, del Rio, TG, Tice, H, Copeland, A, Cheng, JF, Lucas, S, Chen, F, Nolan, M, Bruce, D, Goodwin, L, Pitluck, S, Ivanova, N, Mavromatis, K, Mikhailova, N, Pati, A, Chen, A, Palaniappan, K, Land, M, Hauser, L, Chang, YJ, Jeffries, CC, Saunders, E, Chertkov, O, Brettin, T, Göker, M, Rohde, M, Bristow, J, Eisen, JA, Markowitz, V, Hugenholtz, P, Kyrpides, NC, Klenk, HP & Detter, JC 2009, 'Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T)', Standards in Genomic Sciences, vol. 1, no. 1, pp. 54-62. https://doi.org/10.4056/sigs.22138
Han, Cliff ; Spring, Stefan ; Lapidus, Alla ; del Rio, Tijana Glavina ; Tice, Hope ; Copeland, Alex ; Cheng, Jan Fang ; Lucas, Susan ; Chen, Feng ; Nolan, Matt ; Bruce, David ; Goodwin, Lynne ; Pitluck, Sam ; Ivanova, Natalia ; Mavromatis, Konstantinos ; Mikhailova, Natalia ; Pati, Amrita ; Chen, Amy ; Palaniappan, Krishna ; Land, Miriam ; Hauser, Loren ; Chang, Yun Juan ; Jeffries, Cynthia C. ; Saunders, Elizabeth ; Chertkov, Olga ; Brettin, Thomas ; Göker, Markus ; Rohde, Manfred ; Bristow, Jim ; Eisen, Jonathan A ; Markowitz, Victor ; Hugenholtz, Philip ; Kyrpides, Nikos C. ; Klenk, Hans Peter ; Detter, John C. / Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T). In: Standards in Genomic Sciences. 2009 ; Vol. 1, No. 1. pp. 54-62.
@article{010e6f3bfdf1493cbc992f188d1413ef,
title = "Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T)",
abstract = "Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.",
keywords = "Dry soil, Flexible rods, Gram-negative, Heparinase producer, Mesophile, Sphingobacteriaceae, Strictly aerobic",
author = "Cliff Han and Stefan Spring and Alla Lapidus and {del Rio}, {Tijana Glavina} and Hope Tice and Alex Copeland and Cheng, {Jan Fang} and Susan Lucas and Feng Chen and Matt Nolan and David Bruce and Lynne Goodwin and Sam Pitluck and Natalia Ivanova and Konstantinos Mavromatis and Natalia Mikhailova and Amrita Pati and Amy Chen and Krishna Palaniappan and Miriam Land and Loren Hauser and Chang, {Yun Juan} and Jeffries, {Cynthia C.} and Elizabeth Saunders and Olga Chertkov and Thomas Brettin and Markus G{\"o}ker and Manfred Rohde and Jim Bristow and Eisen, {Jonathan A} and Victor Markowitz and Philip Hugenholtz and Kyrpides, {Nikos C.} and Klenk, {Hans Peter} and Detter, {John C.}",
year = "2009",
doi = "10.4056/sigs.22138",
language = "English (US)",
volume = "1",
pages = "54--62",
journal = "Environmental Microbiomes",
issn = "1944-3277",
publisher = "BioMed Central Ltd.",
number = "1",

}

TY - JOUR

T1 - Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T)

AU - Han, Cliff

AU - Spring, Stefan

AU - Lapidus, Alla

AU - del Rio, Tijana Glavina

AU - Tice, Hope

AU - Copeland, Alex

AU - Cheng, Jan Fang

AU - Lucas, Susan

AU - Chen, Feng

AU - Nolan, Matt

AU - Bruce, David

AU - Goodwin, Lynne

AU - Pitluck, Sam

AU - Ivanova, Natalia

AU - Mavromatis, Konstantinos

AU - Mikhailova, Natalia

AU - Pati, Amrita

AU - Chen, Amy

AU - Palaniappan, Krishna

AU - Land, Miriam

AU - Hauser, Loren

AU - Chang, Yun Juan

AU - Jeffries, Cynthia C.

AU - Saunders, Elizabeth

AU - Chertkov, Olga

AU - Brettin, Thomas

AU - Göker, Markus

AU - Rohde, Manfred

AU - Bristow, Jim

AU - Eisen, Jonathan A

AU - Markowitz, Victor

AU - Hugenholtz, Philip

AU - Kyrpides, Nikos C.

AU - Klenk, Hans Peter

AU - Detter, John C.

PY - 2009

Y1 - 2009

N2 - Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

AB - Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

KW - Dry soil

KW - Flexible rods

KW - Gram-negative

KW - Heparinase producer

KW - Mesophile

KW - Sphingobacteriaceae

KW - Strictly aerobic

UR - http://www.scopus.com/inward/record.url?scp=77957104084&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77957104084&partnerID=8YFLogxK

U2 - 10.4056/sigs.22138

DO - 10.4056/sigs.22138

M3 - Article

C2 - 21304637

AN - SCOPUS:77957104084

VL - 1

SP - 54

EP - 62

JO - Environmental Microbiomes

JF - Environmental Microbiomes

SN - 1944-3277

IS - 1

ER -