The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes
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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.
KeywordsCervus elaphus genome Deer genome Bos taurus genome Cattle genome Next-generation sequencing De novo assembly
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.
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.
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.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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)].
- Balla B, Kósa J, Kiss J, Borsy A, Podani J, Takács I, Lazáry Á, Nagy Z, Bácsi K, Speer G, Orosz L, Lakatos P (2008) Different gene expression patterns in the bone tissue of aging postmenopausal osteoporotic women. Calcif Tissue Int 82(1):12–26. https://doi.org/10.1007/s00223-007-9092-3 CrossRefPubMedGoogle Scholar
- Bán I (1998) The Hungarian wonder deer. EP Systema, Debrecen (ISBN:963-03-4955-8) Google Scholar
- Barta E, Bánfalvi Z, Havelda Z, Hiripi L, Jeney Z, Kiss J, Kolics B, Marincs F, Silhavy D, Stéger V, Várallyay É (2016) Agricultural genomics: an overview of the next generation sequencing projects at the NARIC-Agricultural Biotechnology Institute in Gödöllő. Hung Agric Res 25:10–21Google Scholar
- Borsy A, Podani J, Stéger V, Balla B, Horváth A, Kósa J, Gyurján I, Molnár A, Szabolcsi Z, Szabó L, Jakó E, Zomborszky Z, Nagy J, Semsey S, Vellai T, Lakatos P, Orosz L (2009) Identifying novel genes involved in both deer physiological and human pathological osteoporosis. Mol Genet Genom 281:301–313. https://doi.org/10.1007/s00438-008-0413-7 CrossRefGoogle Scholar
- Brauning R, Fisher PJ, McCulloch AF, Smithies RJ, Ward JF, Bixley MJ, Lawley CT, Rowe SJ, McEwan JC (2015) Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk. bioRxiv. https://doi.org/10.1101/027318 Google Scholar
- Everts-van der Wind A, Kata SR, Band MR, Rebeiz M, Larkin DM, Everts RE, Green CA, Liu L, Natarjan S, Goldammer T, Lee JH, McKay S, Womack JE, Lewin HA (2004) A 1463 gene cattle–human comparative map with anchor points defined by human genome sequence coordinates. Genome Res 14(7):1424–1437. https://doi.org/10.1101/gr.2554404 CrossRefPubMedPubMedCentralGoogle Scholar
- Everts-van der Wind A, Larkin DM, Green CA, Elliott JS, Olmstead CA, Chiu R, Schein JE, Marra MA, Womack JE, Lewin HA (2005) A high-resolution whole-genome cattle–human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci USA 102(51):18526–18531. https://doi.org/10.1073/pnas.0509285102 CrossRefPubMedGoogle Scholar
- Fisher PJ, Brauning R, McCulloch AF, Smithies RJ, Ward JF, Bixley MJ, Lawley CT, Everett-Hincks JM, McEwan JC (2015) Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk. bioRxiv. https://doi.org/10.1101/027318 Google Scholar
- Frank K, Barta E, Bana N, Nagy J, Horn P, Orosz L, Stéger V (2016) Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae. Acta Biol Hung 67:133–147. https://doi.org/10.1556/018.67.2016.2.2 CrossRefPubMedGoogle Scholar
- Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108(4):1513–1518. https://doi.org/10.1073/pnas.1017351108 CrossRefPubMedGoogle Scholar
- Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883 CrossRefPubMedPubMedCentralGoogle Scholar
- Gustavsson I, Sundt CO (1968) Karyotypes in five species of deer (Alces alces L., Capreolus capreolus L., Cervus elaphus L., Cervus nippon nippon Temm. and Dama dama L.). Hereditas 60:233–248. https://doi.org/10.1111/j.1601-5223.1968.tb02204.x CrossRefPubMedGoogle Scholar
- Gyurján I, Molnár A, Borsy A, Stéger V, Hackler L, Zomborszky Z, Papp P, Duda E, Deák F, Lakatos P, Puskás LG, Orosz L (2007) Gene expression dynamics in deer antler: mesenchymal differentiation toward chondrogenesis. Mol Genet Genom 277:221–235. https://doi.org/10.1007/s00438-006-0190-0 CrossRefGoogle Scholar
- Harris RS (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State UniversityGoogle Scholar
- Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30(9):1236–1240. https://doi.org/10.1093/bioinformatics/btu031 CrossRefPubMedPubMedCentralGoogle Scholar
- Korf I, Yandell M, Bedell J (2003) An essential guide to the basic local alignment search tool: BLAST. O’Reilly & Associates, Inc., SebastopolGoogle Scholar
- Kosambi DD (1943) The estimation of map distance from recombination values. Ann Eugen 12:172–175. https://doi.org/10.1111/j.1469-1809.1943.tb02321.x CrossRefGoogle Scholar
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352 CrossRefPubMedPubMedCentralGoogle Scholar
- Ma RZ, Beever JE, Da Y, Green CA, Russ I, Park C, Heyen DW, Everts RE, Fisher SR, Overton KM, Teale AJ, Kemp SJ, Hines HC, Guérin G, Lewin HA (1996) A male linkage map of the cattle (Bos taurus) genome. J Hered 4:261–271. https://doi.org/10.1093/oxfordjournals.jhered.a022999 CrossRefGoogle Scholar
- Molnár A, Gyurján I Jr, Korpos E, Borsy A, Stéger V, Buzás Z, Kiss I, Zomborszky Z, Papp P, Deák F, Orosz L (2007) Identification of differentially expressed genes in the developing antler of red deer Cervus elaphus. Mol Genet Genom 277:237–248. https://doi.org/10.1007/s00438-006-0193-x CrossRefGoogle Scholar
- Smit AFA, Hubley R, Green P (2013–2015) RepeatMasker Open-4.0. http://www.repeatmasker.org/. Accessed Jan 2016
- Stéger V, Molnár A, Borsy A, Gyurján I, Szabolcsi Z, Dancs G, Molnár J, Papp P, Nagy J, Puskás L, Barta E, Zomborszky Z, Horn P, Podani J, Semsey S, Lakatos P, Orosz L (2010) Antler development and coupled osteoporosis in the skeleton of red deer Cervus elaphus: expression dynamics for regulatory and effector genes. Mol Genet Genom 284:273–287. https://doi.org/10.1007/s00438-010-0565-0 CrossRefGoogle Scholar
- Yao B, Zhao Y, Zhang H, Zhang M, Liu M, Liu H, Li J (2012) Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology. Biotechnol Lett 34:813–822. https://doi.org/10.1007/s10529-011-0841-z CrossRefPubMedGoogle Scholar