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The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes

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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 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.

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Acknowledgements

This work was supported by the Doctoral School of Animal Science of the Kaposvár University; by the Ministry of Agriculture, Grant No. NAIK–MBK/M71411; by the Ministry of Health, Social and Family Affairs, Grant ETT–ESKI 006/2009; by the Hungarian Academy of Sciences, Grant No. E-127/9/1/2012; by NKFP, Grant 1A/007/2004. We acknowledge NIIF for awarding us access to resources based in Hungary at Pécs, Szeged and Debrecen.

Funding

This work was supported by the Ministry of Agriculture, Grant No. NAIK–MBK/M71411; by the Ministry of Health, Social and Family Affairs, Grant ETT–ESKI 006/2009; by the Hungarian Academy of Sciences, Grant No. E-127/9/1/2012; and by NKFP, Grant 1A/007/2004.

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Authors and Affiliations

Authors

Contributions

NÁB (bioinformatics), KF (molecular genetics), JN (deer breeding) PhD students of Kaposvár University, AN (bioinformatics), TN (bioinformatics), MS (bioinformatics) research assistants of NARIC, VS (molecular genetics and genomics) supervised the laboratory work, PL (medical research, non-model animals), LS (veterinarian zoology) organized the collection of samples, EB supervised bioinformatics, PH animal geneticist, led the Doctoral School of Animal Science of the Kaposvár University, LO designed the study, analysed the data and wrote the paper. All authors contributed to revisions. Results are available online at emboss.abc.hu/wonderdeer/Jbrowse.

Corresponding author

Correspondence to László Orosz.

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Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. Blood was collected from a living animal performed by a trained veterinarian according to the standard veterinary medical practice with a permission from the Hungarian Veterinary Chamber. Sample collection was performed by a trained veterinarian according to standard veterinary medical practice with a permission from the Hungarian Veterinary Chamber [Hungarian Animal Rights Law (243/1998, XII.31)].

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

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Fig. S1

Acrocentric deer chromosome Ce15 is split to two acrocentric bovine chromosomes Bt28 and Bt26. Black dots correspond to centromerons. (TIF 64 KB)

Fig. S2

Tandem fusion of acrocentric deer chromosomes Ce28 and Ce26 in cattle acrocentric chromosome Bt9. Note, the large paracentric inversion in Ce28 overlaps the entire chromosomal segment between map markers ETH225 and CGA/OarCP021. Black dots correspond to centromerons. (TIF 151 KB)

Fig. S3

Tandem fusion of acrocentric deer chromosomes Ce3 and Ce22 in acrocentric bovine chromosome Bt5. Black dots correspond to centromerons. (TIF 108 KB)

Table S1

ALLPATH-LG report on CerEla1.0 assembly (XLSX 11 KB)

Table S2

Position (in cM and in Mbp) of the genetic map markers used along the C. elaphus linkage groups/chromosomes. The genetic map markers are aligned as is published in Slate et al. 2002a; *, centromeron–proximal marker. (XLSX 22 KB)

Table S3

Physical position (in Mbp) of the terminal genetic map markers on the C. elaphus linkage groups/chromosomes. The genetic map markers are aligned as is published in Slate et al. 2002a ; *, centromeron–proximal mapmarker. (XLSX 18 KB)

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Bana, N.Á., Nyiri, A., Nagy, J. et al. The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes. Mol Genet Genomics 293, 665–684 (2018). https://doi.org/10.1007/s00438-017-1412-3

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  • DOI: https://doi.org/10.1007/s00438-017-1412-3

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