Artifacts of the 1.9x feline genome assembly derived from the feline-specific satellite sequence.
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.
Pontius
Joan U
JU
Laboratory of Genomic Diversity, Basic Research Program, Science Applications International Corporation-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA. pontiusj@ncifcrf.gov
O'Brien
Stephen J
SJ
D000818:Animals; D016477:Artifacts; D002415:Cats / Q000235:genetics*; D033481:Chromosomes, Mammalian / Q000235:genetics*; D018899:CpG Islands; D004276:DNA, Satellite / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D020086:Short Interspersed Nucleotide Elements
D004276:DNA, Satellite