Sequence map of the 3-Mb Giardia duodenalis assemblage A chromosome.
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromosome, a library of probes specific for this chromosome was constructed. The probes were hybridised to NotI-cleaved whole chromosomes, and the combined size of different NotI segments identified by the probes was 2,225 kb indicating the probes were well distributed along the 3-Mb chromosome. Six scaffolds (CH991814, CH991779, CH991793, CH991763, CH991764, and CH991761) were identified as belonging to the 3-Mb chromosome, and these scaffolds were ordered and oriented according to scaffold features including I-PpoI sites and hybridisation pattern. However, the combined size of scaffolds was more than 4 Mb. Approximately, 1 Mb of scaffold CH991763 carrying previously identified sequences specific for the 1.5-Mb chromosome(s) including subtelomeric sequence was reassigned, and several other anomalies were addressed such that the final size of the apparently 3-Mb chromosome is estimated to be 2,885 kb. This work addresses erroneous computer-based assignment of a number of contigs and emphasises the need for alternative and confirmatory methods of scaffold construction.
Queensland Institute of Medical Research, Brisbane, QLD, 4006, Australia. Jacqui.Upcroft@qimr.edu.au
Jacqueline A
JA
Upcroft
Kenia G
KG
Krauer
Anita G
AG
Burgess
Linda A
LA
Dunn
Nanhua
N
Chen
Peter
P
Upcroft
D002875:Chromosomes; D020451:Contig Mapping; D015342:DNA Probes; D015252:Deoxyribonucleases, Type II Site-Specific; D017125:Genes, Protozoan; D005872:Giardia / Q000235:genetics*
D015342:DNA Probes; D015252:Deoxyribonucleases, Type II Site-Specific; C038565:GCGGCCGC-specific type II deoxyribonucleases