The sequence and analysis of Trypanosoma brucei chromosome II

Najib M A El-Sayed, Elodie Ghedin, Jinming Song, Annette MacLeod, Frederic Bringaud, Christopher Larkin, David Wanless, Jeremy Peterson, Lihua Hou, Sonya Taylor, Alison Tweedie, Nicolas Biteau, Hanif G. Khalak, Xiaoying Lin, Tanya Mason, Linda Hannick, Elisabet Caler, Gaëlle Blandin, Daniella Bartholomeu, Anjana J. SimpsonSamir Kaul, Hong Zhao, Grace Pai, Susan Van Aken, Teresa Utterback, Brian Haas, Hean L. Koo, Lowell Umayam, Bernard Suh, Caroline Gerrard, Vanessa Leech, Rong Qi, Shiguo Zhou, David Schwartz, Tamara Feldblyum, Steven Salzberg, Andrew Tait, C. Michael R Turner, Elisabetta Ullu, Owen White, Sara Melville, Mark D. Adams, Claire M. Fraser, John E. Donelson

Research output: Contribution to journalArticle

Abstract

We report here the sequence of chromosome II from Trypenosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.

Original languageEnglish (US)
Pages (from-to)4856-4863
Number of pages8
JournalNucleic Acids Research
Volume31
Issue number16
DOIs
StatePublished - Aug 15 2003

Fingerprint

Trypanosoma brucei brucei
Sequence Analysis
Chromosomes
Membrane Glycoproteins
Genes
Pseudogenes
African Trypanosomiasis
Gene Conversion
Retroelements
Centromere
DNA-Directed RNA Polymerases
Multigene Family
Gene Expression

ASJC Scopus subject areas

  • Genetics

Cite this

El-Sayed, N. M. A., Ghedin, E., Song, J., MacLeod, A., Bringaud, F., Larkin, C., ... Donelson, J. E. (2003). The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Research, 31(16), 4856-4863. https://doi.org/10.1093/nar/gkg673

The sequence and analysis of Trypanosoma brucei chromosome II. / El-Sayed, Najib M A; Ghedin, Elodie; Song, Jinming; MacLeod, Annette; Bringaud, Frederic; Larkin, Christopher; Wanless, David; Peterson, Jeremy; Hou, Lihua; Taylor, Sonya; Tweedie, Alison; Biteau, Nicolas; Khalak, Hanif G.; Lin, Xiaoying; Mason, Tanya; Hannick, Linda; Caler, Elisabet; Blandin, Gaëlle; Bartholomeu, Daniella; Simpson, Anjana J.; Kaul, Samir; Zhao, Hong; Pai, Grace; Van Aken, Susan; Utterback, Teresa; Haas, Brian; Koo, Hean L.; Umayam, Lowell; Suh, Bernard; Gerrard, Caroline; Leech, Vanessa; Qi, Rong; Zhou, Shiguo; Schwartz, David; Feldblyum, Tamara; Salzberg, Steven; Tait, Andrew; Turner, C. Michael R; Ullu, Elisabetta; White, Owen; Melville, Sara; Adams, Mark D.; Fraser, Claire M.; Donelson, John E.

In: Nucleic Acids Research, Vol. 31, No. 16, 15.08.2003, p. 4856-4863.

Research output: Contribution to journalArticle

El-Sayed, NMA, Ghedin, E, Song, J, MacLeod, A, Bringaud, F, Larkin, C, Wanless, D, Peterson, J, Hou, L, Taylor, S, Tweedie, A, Biteau, N, Khalak, HG, Lin, X, Mason, T, Hannick, L, Caler, E, Blandin, G, Bartholomeu, D, Simpson, AJ, Kaul, S, Zhao, H, Pai, G, Van Aken, S, Utterback, T, Haas, B, Koo, HL, Umayam, L, Suh, B, Gerrard, C, Leech, V, Qi, R, Zhou, S, Schwartz, D, Feldblyum, T, Salzberg, S, Tait, A, Turner, CMR, Ullu, E, White, O, Melville, S, Adams, MD, Fraser, CM & Donelson, JE 2003, 'The sequence and analysis of Trypanosoma brucei chromosome II', Nucleic Acids Research, vol. 31, no. 16, pp. 4856-4863. https://doi.org/10.1093/nar/gkg673
El-Sayed NMA, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C et al. The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Research. 2003 Aug 15;31(16):4856-4863. https://doi.org/10.1093/nar/gkg673
El-Sayed, Najib M A ; Ghedin, Elodie ; Song, Jinming ; MacLeod, Annette ; Bringaud, Frederic ; Larkin, Christopher ; Wanless, David ; Peterson, Jeremy ; Hou, Lihua ; Taylor, Sonya ; Tweedie, Alison ; Biteau, Nicolas ; Khalak, Hanif G. ; Lin, Xiaoying ; Mason, Tanya ; Hannick, Linda ; Caler, Elisabet ; Blandin, Gaëlle ; Bartholomeu, Daniella ; Simpson, Anjana J. ; Kaul, Samir ; Zhao, Hong ; Pai, Grace ; Van Aken, Susan ; Utterback, Teresa ; Haas, Brian ; Koo, Hean L. ; Umayam, Lowell ; Suh, Bernard ; Gerrard, Caroline ; Leech, Vanessa ; Qi, Rong ; Zhou, Shiguo ; Schwartz, David ; Feldblyum, Tamara ; Salzberg, Steven ; Tait, Andrew ; Turner, C. Michael R ; Ullu, Elisabetta ; White, Owen ; Melville, Sara ; Adams, Mark D. ; Fraser, Claire M. ; Donelson, John E. / The sequence and analysis of Trypanosoma brucei chromosome II. In: Nucleic Acids Research. 2003 ; Vol. 31, No. 16. pp. 4856-4863.
@article{99c92d427f33444cbdd8c49b7a2830c1,
title = "The sequence and analysis of Trypanosoma brucei chromosome II",
abstract = "We report here the sequence of chromosome II from Trypenosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.",
author = "El-Sayed, {Najib M A} and Elodie Ghedin and Jinming Song and Annette MacLeod and Frederic Bringaud and Christopher Larkin and David Wanless and Jeremy Peterson and Lihua Hou and Sonya Taylor and Alison Tweedie and Nicolas Biteau and Khalak, {Hanif G.} and Xiaoying Lin and Tanya Mason and Linda Hannick and Elisabet Caler and Ga{\"e}lle Blandin and Daniella Bartholomeu and Simpson, {Anjana J.} and Samir Kaul and Hong Zhao and Grace Pai and {Van Aken}, Susan and Teresa Utterback and Brian Haas and Koo, {Hean L.} and Lowell Umayam and Bernard Suh and Caroline Gerrard and Vanessa Leech and Rong Qi and Shiguo Zhou and David Schwartz and Tamara Feldblyum and Steven Salzberg and Andrew Tait and Turner, {C. Michael R} and Elisabetta Ullu and Owen White and Sara Melville and Adams, {Mark D.} and Fraser, {Claire M.} and Donelson, {John E.}",
year = "2003",
month = "8",
day = "15",
doi = "10.1093/nar/gkg673",
language = "English (US)",
volume = "31",
pages = "4856--4863",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "16",

}

TY - JOUR

T1 - The sequence and analysis of Trypanosoma brucei chromosome II

AU - El-Sayed, Najib M A

AU - Ghedin, Elodie

AU - Song, Jinming

AU - MacLeod, Annette

AU - Bringaud, Frederic

AU - Larkin, Christopher

AU - Wanless, David

AU - Peterson, Jeremy

AU - Hou, Lihua

AU - Taylor, Sonya

AU - Tweedie, Alison

AU - Biteau, Nicolas

AU - Khalak, Hanif G.

AU - Lin, Xiaoying

AU - Mason, Tanya

AU - Hannick, Linda

AU - Caler, Elisabet

AU - Blandin, Gaëlle

AU - Bartholomeu, Daniella

AU - Simpson, Anjana J.

AU - Kaul, Samir

AU - Zhao, Hong

AU - Pai, Grace

AU - Van Aken, Susan

AU - Utterback, Teresa

AU - Haas, Brian

AU - Koo, Hean L.

AU - Umayam, Lowell

AU - Suh, Bernard

AU - Gerrard, Caroline

AU - Leech, Vanessa

AU - Qi, Rong

AU - Zhou, Shiguo

AU - Schwartz, David

AU - Feldblyum, Tamara

AU - Salzberg, Steven

AU - Tait, Andrew

AU - Turner, C. Michael R

AU - Ullu, Elisabetta

AU - White, Owen

AU - Melville, Sara

AU - Adams, Mark D.

AU - Fraser, Claire M.

AU - Donelson, John E.

PY - 2003/8/15

Y1 - 2003/8/15

N2 - We report here the sequence of chromosome II from Trypenosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.

AB - We report here the sequence of chromosome II from Trypenosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.

UR - http://www.scopus.com/inward/record.url?scp=10744232966&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=10744232966&partnerID=8YFLogxK

U2 - 10.1093/nar/gkg673

DO - 10.1093/nar/gkg673

M3 - Article

VL - 31

SP - 4856

EP - 4863

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 16

ER -