Gene_locus Report for: cereh-a0a212dcy3

(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.)
> cellular organisms: N E > Eukaryota: N E > Opisthokonta: N E > Metazoa: N E > Eumetazoa: N E > Bilateria: N E > Deuterostomia: N E > Chordata: N E > Craniata: N E > Vertebrata: N E > Gnathostomata: N E > Teleostomi: N E > Euteleostomi: N E > Sarcopterygii: N E > Dipnotetrapodomorpha: N E > Tetrapoda: N E > Amniota: N E > Mammalia: N E > Theria: N E > Eutheria: N E > Boreoeutheria: N E > Laurasiatheria: N E > Cetartiodactyla: N E > Ruminantia: N E > Pecora: N E > Cervidae: N E > Cervinae: N E > Cervus: N E > Cervus elaphus: N E > Cervus elaphus hippelaphus: N E

Title: The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes
Bana NA, Nyiri A, Nagy J, Frank K, Nagy T, Steger V, Schiller M, Lakatos P, Sugar L and Orosz L <2 more author(s)> Bana NA, Nyiri A, Nagy J, Frank K, Nagy T, Steger V, Schiller M, Lakatos P, Sugar L, Horn P, Barta E, Orosz L (- 2)
Ref: Mol Genet Genomics, 293:665, 2018 : PubMed
Abstract


ESTHER: Bana_2018_Mol.Genet.Genomics_293_665
PubMedSearch: Bana 2018 Mol.Genet.Genomics 293 665
PubMedID: 29294181
Gene_locus related to this paper: cereh-a0a212dcm1, cereh-a0a212dcy3, cereh-a0a212c355, cereh-a0a212ci67

Abstract

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 74x coverage by Illumina technology. The ALLPATHS-LG assembly of the reads resulted in 34.7 x 10(3) scaffolds, 26.1 x 10(3) 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 x 10(6) SNPs, 365 x 10(3) 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.