Kivonat:
We present here the de novo genome assembly CerEla1.0 for the
red deer, Cervus elaphus, an emblematic member of the natural
megafauna of the Northern Hemisphere. Humans spread the species
in the South. Today, the red deer is also a farm-bred animal
and is becoming a model animal in biomedical and population
studies. Stag DNA was sequenced at 74× coverage by Illumina
technology. The ALLPATHS-LG assembly of the reads resulted in
34.7 × 103 scaffolds, 26.1 × 103 of which were utilized in
Cer.Ela1.0. The assembly spans 3.4 Gbp. For building the red
deer pseudochromosomes, a pre-established genetic map was used
for main anchor points. A nearly complete co-linearity was
found between the mapmarker sequences of the deer genetic map
and the order and orientation of the orthologous sequences in
the syntenic bovine regions. Syntenies were also conserved at
the in-scaffold level. The cM distances corresponded to 1.34
Mbp uniformly along the deer genome. Chromosomal rearrangements
between deer and cattle were demonstrated. 2.8 × 106 SNPs, 365
× 103 indels and 19368 protein-coding genes were identified in
CerEla1.0, along with positions for centromerons. CerEla1.0
demonstrates the utilization of dual references, i.e., when a
target genome (here C. elaphus) already has a pre-established
genetic map, and is combined with the well-established whole
genome sequence of a closely related species (here Bos taurus).
Genome-wide association studies (GWAS) that CerEla1.0 (NCBI,
MKHE00000000) could serve for are discussed.