The Genome of the Iberian Lynx

The Iberian lynx (Lynx pardinus) is considered to be the most endangered felid in the world. The only two known breeding populations, one in the Sierra Morena mountains and the other in Doñana National Park, host less than 200 and 90 individuals, respectively. As part of the Iberian Lynx Genome Project (www.lynxgenomics.es), the 2.5 Gb genome of one individual, Candiles, was sequenced to high coverage and assembled de novo. Ten additional Iberian and one Eurasian male lynx (Lynx lynx) were sequenced to medium coverage (~26X). We used primarily the Illumina GAIIx to produce whole genome shotgun sequence (>130x coverage in paired-end libraries plus 35x in mate pair libraries) and shotgun sequence of 90 fosmid pools of 1200 clones each. Additional data included fosmid end sequences and a 454 paired-end library. We also used RNAseq from 10 different tissues. Our assembly procedures resulted in contig and scaffold N50s of 68 kb and 1.52 Mb, respectively. The completeness of the genome with respect to the gene space as reported by CEGMA was 95% (98% including partial genes). We provide an overview of our bag of assembly tricks for producing high quality draft genome sequences, including software to merge fosmid pool assemblies, detect and repair misassemblies, and perform scaffolding using RNAseq data. When appropriate, we use examples from some of our other genome projects, which include fish, mammals, mollusks, insects and their endosymbionts, fungi and plants.