Journal of Heredity Advance Access originally published online on June 16, 2009
Journal of Heredity 2009 100(Supplement 1):S14-S18; doi:10.1093/jhered/esp035
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This article appears in the following Journal of Heredity issue: Symposium Issue: Fourth International Conference on Advances in Canine and Feline Genomics and Inherited Diseases, Saint Malo, Brittany, France, 21-24 May 2008. [View the issue table of contents]
Original Articles |
Artifacts of the 1.9x Feline Genome Assembly Derived from the Feline-Specific Satellite Sequence
From the Laboratory of Genomic Diversity, Basic Research Program, Science Applications International Corporation-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702 (Pontius); and the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (O’Brien)
Address correspondence to Joan U. Pontius at the address above, or e-mail: pontiusj{at}ncifcrf.gov.
Two percentage of the cat genome is a repetitive, feline-specific satellite sequence (FA-SAT) of 483 bp and 65% guanine-cytosine content. Previous chromosomal localization of the satellite has demonstrated the satellite’s presence on several discrete regions of the telomeres of chromosomes, predominately on the D, E, and F chromosome groups. The recent assembly of the 1.9x whole-genome shotgun (WGS) sequence of cat illustrates the challenge of the assembly of these large numbers of relatively short, similar sequences. Clones with paired end reads that include FA-SAT sequence have a high level of assembly discrepancies compared with clones with other types of repetitive elements, such as short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs). The influence of the presence of FA-SAT but not SINEs and LINEs on genome assembly may likely reflect the evolutionary emergence of FA-SAT, which has lead to an excess of FA-SAT copies with identical sequence, which is less an issue with older, more diverse SINE and LINE sequences. The FA-SATs are restricted to a few hundred discrete regions of the cat genome, and associated errors in the assembly seem to be restricted to these loci. The findings regarding the feline-specific sequence should be considered in the pending 8x assembly of the cat genome.
Key Words: artifacts • FA-SAT • genome assembly • repetitive elements • satellite • whole-genome shotgun
Corresponding Editor: Francis Galibert
Received January 9, 2009
Revised May 8, 2009
Accepted May 8, 2009