The sequence and analysis of Trypanosoma brucei chromosome II.
We report here the sequence of chromosome II from Trypanosoma 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.
El-Sayed
Najib M A
NM
The Institute for Genomic Research, Rockville, MD 20850, USA. nelsayed@tigr.org
Ghedin
Elodie
E
Song
Jinming
J
MacLeod
Annette
A
Bringaud
Frederic
F
Larkin
Christopher
C
Wanless
David
D
Peterson
Jeremy
J
Hou
Lihua
L
Taylor
Sonya
S
Tweedie
Alison
A
Biteau
Nicolas
N
Khalak
Hanif G
HG
Lin
Xiaoying
X
Mason
Tanya
T
Hannick
Linda
L
Caler
Elisabet
E
Blandin
Gaëlle
G
Bartholomeu
Daniella
D
Simpson
Anjana J
AJ
Kaul
Samir
S
Zhao
Hong
H
Pai
Grace
G
Van Aken
Susan
S
Utterback
Teresa
T
Haas
Brian
B
Koo
Hean L
HL
Umayam
Lowell
L
Suh
Bernard
B
Gerrard
Caroline
C
Leech
Vanessa
V
Qi
Rong
R
Zhou
Shiguo
S
Schwartz
David
D
Feldblyum
Tamara
T
Salzberg
Steven
S
Tait
Andrew
A
Turner
C Michael R
CM
Ullu
Elisabetta
E
White
Owen
O
Melville
Sara
S
Adams
Mark D
MD
Fraser
Claire M
CM
Donelson
John E
JE
D000818:Animals; D000953:Antigens, Protozoan / Q000235:genetics; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics*; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics*; D020440:Gene Duplication; D017125:Genes, Protozoan / Q000235:genetics; D008969:Molecular Sequence Data; D011544:Pseudogenes / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014346:Trypanosoma brucei brucei / Q000235:genetics*
D000953:Antigens, Protozoan; D016054:DNA, Protozoan