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. Simpson; Samir 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

doi:10.1093/nar/gkg673

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

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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 language	English (US)
Pages (from-to)	4856-4863
Number of pages	8
Journal	Nucleic acids research
Volume	31
Issue number	16
DOIs	https://doi.org/10.1093/nar/gkg673
State	Published - Aug 15 2003
Externally published	Yes

ASJC Scopus subject areas

Genetics

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El-Sayed, N. M. A., Ghedin, E., Song, J., MacLeod, A., Bringaud, F., Larkin, C., Wanless, D., Peterson, J., Hou, L., Taylor, S., Tweedie, A., Biteau, N., Khalak, H. G., Lin, X., Mason, T., Hannick, L., Caler, E., Blandin, G., Bartholomeu, D., ... 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

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

@article{ac8f1c93b9ac44e4b3bae2fa386efeb7,

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.}",

note = "Funding Information: We wish to acknowledge our colleagues at the Sanger Institute for useful discussions and close coordination of efforts, and Sarah McLellan for technical assistance. We are also grateful to the T.brucei research community worldwide for its continuous support of this project. In addition, we would like to thank the TIGR faculty, system administrators, sequencing facility, bioinformatics department and administrative staff. The work at the Institute for Genomic Research (TIGR) was supported by a grant from the National Institute for Allergy and Infectious Diseases, National Institutes of Health to N.E.S. (U01 AI43062). The genetic mapping studies carried out at University of Glasgow were supported by grants from The Wellcome Trust and The Sir Halley Stewart Trust.",

year = "2003",

month = aug,

day = "15",

doi = "10.1093/nar/gkg673",

language = "English (US)",

volume = "31",

pages = "4856--4863",

journal = "Nucleic acids research",

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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.

N1 - Funding Information: We wish to acknowledge our colleagues at the Sanger Institute for useful discussions and close coordination of efforts, and Sarah McLellan for technical assistance. We are also grateful to the T.brucei research community worldwide for its continuous support of this project. In addition, we would like to thank the TIGR faculty, system administrators, sequencing facility, bioinformatics department and administrative staff. The work at the Institute for Genomic Research (TIGR) was supported by a grant from the National Institute for Allergy and Infectious Diseases, National Institutes of Health to N.E.S. (U01 AI43062). The genetic mapping studies carried out at University of Glasgow were supported by grants from The Wellcome Trust and The Sir Halley Stewart Trust.

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.

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The sequence and analysis of Trypanosoma brucei chromosome II

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