鹿科动物基因组学研究进展

doi:10.16288/j.yczz.20-362

[an error occurred while processing this directive]

Hereditas(Beijing) ›› 2021, Vol. 43 ›› Issue (4): 308-322.doi: 10.16288/j.yczz.20-362

• Review • Previous Articles Next Articles

Progress on deer genome research

Hengxing Ba^1,²(), Pengfei Hu^1,², Chunyi Li^1,²()

^1. Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130112, China
^2. Jilin Provincial Key laboratory of Deer Antler Biology, Changchun 130112, China

Received:2020-10-28 Revised:2020-12-29 Online:2021-04-20 Published:2021-04-20
Contact: Ba Hengxing,Li Chunyi E-mail:bahengxing@caas.cn;lichunyi1959@163.com
Supported by:
Supported by the National Natural Science Foundation of China Nos(31402035);Supported by the National Natural Science Foundation of China Nos(U20A20403);the Science and Technology Development Project of Jilin Province No(20200602013ZP)

Abstract

Abstract:

Deer family is one of the most abundant mammalian families in the world. Deer species are distributed in wide geographic ranges including the North Pole, tropical regions and high-altitude mountains. Of these deer species, China accounts for more than 40% of them and is the main site for deer evolution. Besides the common phenotypical attributes for ruminants, deer family is evolved to possess the unique head gears with periodic regeneration, i.e. antlers. It is currently well accepted that deer is a very valuable model for the studies of ecology, behavior, evolution and biology, especially for the study of mammalian organ regeneration. Reference deer genome is the basis for systematically illustrating deer evolution, deciphering unique biological attributes of deer species, and is significant in protection and utilization of deer genetic resources. In this review, we summarize the recent progress in the field of deer genome research, including data of deer genetic variation, molecular basis of adaptive evolution, and key genes and functional genomics involved in deer antler origin and evolution. The overall aim of the paper is to provide the reference neccessary for in depth investigation of deer species.

Key words: cervids, deer genome, genetic variation, adaptive evolution, velvet antler, functional genomic

Hengxing Ba, Pengfei Hu, Chunyi Li. Progress on deer genome research[J]. Hereditas(Beijing), 2021, 43(4): 308-322.

Figures/Tables 4

Table 1

Fig. 1

Fig. 2

Table 2

References 107

[1]	盛和林 . 中国鹿科动物. 生物学通报, 1992, ( 05):4-7.
[2]	Li CY, Yang FH, Sheppard A. Adult stem cells and mammalian epimorphic regeneration-insights from studying annual renewal of deer antlers. Curr Stem Cell Res Ther, 2009,4(3):237-251. doi: 10.2174/157488809789057446 pmid: 19492976
[3]	Li ZP, Lin ZS, Ba HX, Chen L, Yang YF, Wang K, Qiu Q, Wang W, Li GY. Draft genome of the reindeer ( Rangifer tarandus). GigaScience, 2017,6(12):1-5.
[4]	Ba HX, Cai ZX, Gao HY, Qin T, Liu WY, Xie LW, Zhang YL, Jing BY, Wang DT, Li CY. Chromosome- level genome assembly of tarim red deer, Cervus elaphus yarkandensis. Sci Data, 2020,7(1):187.
[5]	Johnston SE, Huisman J, Ellis PA, Pemberton JM. A high-density linkage map reveals sexual dimorphism in recombination landscapes in red deer ( Cervus elaphus). G3 (Bethesda), 2017,7(8):2859-2870.
[6]	Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS. Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution. Commun Biol, 2020,3(1):480.
[7]	Ludt CJ, Schroeder W, Rottmann O, Kuehn R. Mitochondrial DNA phylogeography of red deer ( Cervus elaphus). Mol Phylogenet Evol, 2004,31(3):1064-1083.
[8]	Bana NÁ, Nyiri A, Nagy J, Frank K, Nagy T, Stéger V, Schiller M, Lakatos P, Sugár L, Horn P, Barta E, Orosz L. The red deer Cervus elaphus genome cerela1.0: Sequencing, annotating, genes, and chromosomes. Mol Genet Genomics, 2018,293(3):665-684.
[9]	Zhang CZ, Chen L, Zhou Y, Wang K, Chemnick LG, Ryder OA, Wang W, Zhang GJ, Qiu Q. Draft genome of the milu ( Elaphurus davidianus). GigaScience, 2018,7(2).
[10]	Wang W, Yan HJ, Chen SY, Li ZZ, Yi J, Niu LL, Deng JP, Chen WG, Pu Y, Jia XB, Qu Y, Chen A, Zhong Y, Yu XM, Pang S, Huang WL, Han Y, Liu GJ, Yu JQ. The sequence and de novo assembly of hog deer genome. Sci Data, 2019,6:180305. pmid: 30620341
[11]	Russell T, Cullingham C, Kommadath A, Stothard P, Herbst A, Coltman D. Development of a novel mule deer genomic assembly and species-diagnostic snp panel for assessing introgression in mule deer, white-tailed deer, and their interspecific hybrids. G3 (Bethesda), 2019,9(3):911-919.
[12]	Chen L, Qiu Q, Jiang Y, Wang K, Lin ZS, Li ZP, Bibi F, Yang YZ, Wang JH, Nie WH, Su WT, Liu GC, Li QY, Fu WW, Pan XY, Liu C, Yang J, Zhang CZ, Yin Y, Wang Y, Zhao Y, Zhang C, Wang ZK, Qin YL, Liu W, Wang B, Ren YD, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan WT, Zhao RP, Zhu WB, Wang YT, Duan SC, Gao Y, Zhang YE, Chen CY, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang GJ, Heller R, Wang W. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science , 2019, 364(6446): eaav6202.
[13]	de Jong MJ, Li ZP, Qin YL, Quéméré E, Baker K, Wang W, Hoelzel AR. Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the pleistocene. Mol Ecol, 2020,29(15):2777-2792. doi: 10.1111/mec.15450 pmid: 32306438
[14]	Wang Y, Zhang CZ, Wang NN, Li ZP, Heller R, Liu R, Zhao Y, Han JG, Pan XY, Zheng ZQ, Dai XQ, Chen C, Dou M, Peng SJ, Chen XQ, Liu J, Li M, Wang K, Liu C, Lin ZS, Chen L, Hao F, Zhu WB, Song CC, Zhao C, Zheng CL, Wang JM, Hu WS, Li CY, Yang H, Jiang L, Li GY, Liu MJ, Sonstegard TS, Zhang GJ, Jiang Y, Wang W, Qiu Q. Genetic basis of ruminant headgear and rapid antler regeneration. Science , 2019, 364(6446): eaav6335.
[15]	Hassanin A, Delsuc F, Ropiquet A, Hammer C , Jansen van Vuuren B, Matthee C, Ruiz-Garcia M, Catzeflis F, Areskoug V, Nguyen TT, Couloux A. Pattern and timing of diversification of cetartiodactyla( mammalia, laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C R Biol, 2012,335(1):32-50.
[16]	Pitra C, Fickel J, Meijaard E, Groves PC. Evolution and phylogeny of old world deer. Mol Phylogenet Evol, 2004,33(3):880-895. pmid: 15522810
[17]	Leberg P, Smith MH, Brisbin IL. The biology of deer. Springer New York, 1992.
[18]	王宗仁, 杜若甫 . 鹿科动物的染色体组型及其进化. 动物学报, 1983, ( 03):214-222.
[19]	Ba HX, Jia BY, Wang GW, Yang YF, Kedem G, Li CY. Genome-wide snp discovery and analysis of genetic diversity in farmed sika deer ( Cervus nippon) in northeast china using double-digest restriction site-associated DNA sequencing. G3 (Bethesda), 2017,7(9):3169-3176.
[20]	Ba HX, Li ZP, Yang YF, Li CY. Development of diagnostic snp markers to monitor hybridization between sika deer ( Cervus nippon) and wapiti( Cervus elaphus). G3 (Bethesda), 2018,8(7):2173-2179.
[21]	Blåhed IM, Königsson H, Ericsson G, Spong G. Discovery of snps for individual identification by reduced representation sequencing of moose ( Alces alces). PLoS One, 2018,13(5):e0197364.
[22]	Seabury CM, Bhattarai EK, Taylor JF, Viswanathan GG, Cooper SM, Davis DS, Dowd SE, Lockwood ML, Seabury PM. Genome-wide polymorphism and comparative analyses in the white-tailed deer ( Odocoileus virginianus): A model for conservation genomics. PLoS One, 2011,6(1):e15811.
[23]	Wang W, Yan HJ, Yu JQ, Yi J, Qu Y, Fu MZ, Chen A, Tang H, Niu LL. Discovery of genome-widesnps by rad-seqand the genetic diversity of captive hog deer ( Axis porcinus). PLoS One, 2017,12(3):e0174299.
[24]	Haynes GD, Latch EK. Identification of novel single nucleotide polymorphisms (snps) in deer ( Odocoileus spp.) using the bovinesnp50 beadchip. PLoS One, 2012,7(5):e36536.
[25]	Kharzinova VR, Sermyagin AA, Gladyr EA, Okhlopkov IM, Brem G, Zinovieva NA. A study of applicability of snp chips developed for bovine and ovine species to whole-genome analysis of reindeer rangifer tarandus. J Hered, 2015,106(6):758-761. doi: 10.1093/jhered/esv081 pmid: 26447215
[26]	Powell JH, Amish SJ, Haynes GD, Luikart G, Latch EK. Candidate adaptive genes associated with lineage divergence: Identifying snps via next-generation targeted resequencing in mule deer ( Odocoileus hemionus). Mol Ecol Resour, 2016,16(5):1165-1172.
[27]	Hu PF, Xu JP, Ai C, Shao XJ, Wang HL, Dong YM, Cui XZ, Yang FH, Xing XM . Screening weight related genes of velvet antlers by whole genome re-sequencing. Hereditas(Beijing), 2017,39(11):1090-1101.
	胡鹏飞, 徐佳萍, 艾成, 邵秀娟, 王洪亮, 董依萌, 崔学哲, 杨福合, 邢秀梅 . 利用全基因组重测序分析鹿茸重量相关基因. 遗传, 2017,39(11):1090-1101.
[28]	Brauning R, Fisher PJ , McCulloch AF, Smithies RJ, Ward JF, Bixley MJ, Lawley CT, Rowe SJ, McEwan JC. Utilization of high throughput genome sequencing technology for large scale single nucleotide polymerphism discovery in red deer and canadian elk. Biorxiv, 2015: 027318.
[29]	Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML. Special features of rad sequencing data: Implications for genotyping. Mol Ecol, 2013,22(11):3151-3164. pmid: 23110438
[30]	Shafer ABA, Miller JM, Kardos M. Cross-species application of snp chips is not suitable for identifying runs of homozygosity. J Hered, 2016,107(2):193-195. doi: 10.1093/jhered/esv137 pmid: 26774056
[31]	Rowe SJ , Clarke SM, van Stijn TC, Hyndaman DL, ward JF, Km M, Dodds KG, Mcewan JC, Newman S-AN, GW A. Brief communication: Developing genomic tools in the new zealand deer industry.Proceedings of the New Zealand Society of Animal Production, 2015(75):91-93.
[32]	Slate J, Van Stijn TC, Anderson RM , McEwan KM, Maqbool NJ, Mathias HC, Bixley MJ, Stevens DR, Molenaar AJ, Beever JE, Galloway SM, Tate ML. A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes. Genetics, 2002,160(4):1587-1597.
[33]	Hu PF, Shao Y , C Xu JP, Wang TJ, Li YQ, Liu HM, Rong M, Su WL, Chen BX, Cui SH, Cui XZ, Yang FH, Tamate H, Xing XM. Genome-wide study on genetic diversity and phylogeny of five species in the genus cervus. BMC Genomics, 2019,20(1):384. pmid: 31101010
[34]	Zhu LF, Deng C, Zhao X, Ding JJ, Huang HS, Zhu SL, Wang ZW, Qin SS, Ding YH, Lu GQ, Yang ZS. Endangered père david’s deer genome provides insights into population recovering. Evol Appl, 2018,11(10):2040-2053. doi: 10.1111/eva.12705 pmid: 30459847
[35]	Zhao SC, Zheng PP, Dong SS, Zhan XJ, Wu Q, Guo XS, Hu YB, He WM, Zhang SN, Fan W, Zhu LF, Li D, Zhang XM, Chen Q, Zhang HM, Zhang ZH, Jin XL, Zhang J, Yang HM, Wang J, Wang J, Wei FW. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat Genet, 2013,45(1):67-71. pmid: 23242367
[36]	Szyda J, Fraszczak M, Mielczarek M, Giannico R, Minozzi G, Nicolazzi EL, Kamiński S, Wojdak- Maksymiec K. The assessment of inter-individual variation of whole-genome DNA sequence in 32 cows. Mamm Genome, 2015,26(11-12):658-665. doi: 10.1007/s00335-015-9606-7 pmid: 26475143
[37]	Hu PF, Deng YY, Ba HX, Li CY. Association analysis of thirty-one single nucleotide polymorphisms with antler weight in sika deer. Anim Genet, 2020, 51(6):990-991.
[38]	Hu PF, Wang TJ, Liu HM, Xu JP, Wang L, Zhao P, Xing XM. Full-length transcriptome and microrna sequencing reveal the specific gene-regulation network of velvet antler in sika deer with extremely different velvet antler weight. Mol Genet Genomics, 2019,294(2):431-443. doi: 10.1007/s00438-018-1520-8 pmid: 30539301
[39]	Xie LW, Deng YY, Shao XQ, Hu PF, Zhao DW, Li CY, Ba HX. Design of a universal primer pair for the identification of deer species. Conserv Genet Resour, 2020,13(1):9-12.
[40]	Jia BY, Wang GW, Zheng JJ, Yang WY, Chang SZ, Zhang JL, Liu Y, Li QN, Ge CX, Chen G, Liu DD, Yang FH. Development of novel est microsatellite markers for genetic diversity analysis and correlation analysis of velvet antler growth characteristics in sika deer. Hereditas, 2020,157(1):24. doi: 10.1186/s41065-020-00137-x pmid: 32591015
[41]	Jia BY, Ba HX, Wang GW, Yang Y, Cui XZ, Peng YH, Zheng JJ, Xing XM, Yang FH. Transcriptome analysis of sika deer in china. Mol Genet Genomics, 2016,291(5):1941-1953. doi: 10.1007/s00438-016-1231-y pmid: 27423230
[42]	Yang WY, Zheng JJ, Jia BY, Wei HJ, Wang GW, Yang FH. Isolation of novel microsatellite markers and their application for genetic diversity and parentage analyses in sika deer. Gene, 2018,643:68-73. pmid: 29223356
[43]	Tanaka K, Hoshi A, Nojima R, Suzuki K, Takiguchi H, Takatsuki S, Takizawa T, Hosoi E, Tamate HB, Hayashida M, Anezaki T, Fukue Y, Minami M. Genetic variation in y-chromosome genes of sika deer ( Cervus nippon) in japan. Zoolog Sci, 2020,37(5):411-416.
[44]	Frank K, Bana NÁ, Bleier N, Sugár L, Nagy J, Wilhelm J, Kálmán Z, Barta E, Orosz L, Horn P, Stéger V. Mining the red deer genome (cerela1.0) to develop x-and y-chromosome-linked str markers. PLoS One, 2020,15(11):e0242506. doi: 10.1371/journal.pone.0242506 pmid: 33226998
[45]	Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li QY, Zhou Y, Xiong YQ, Johnson JL, Perelman PL, Johnson WE, Warren WC, Kukekova AV, Zhang GJ , O'Brien SJ, Ryder OA, Graphodatsky AS, Ma J, Lewin HA, Larkin DM. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Res, 2019,29(4):576-589. doi: 10.1101/gr.239863.118 pmid: 30760546
[46]	Zhou Q, Huang L, Zhang JG, Zhao XY, Zhang QP, Song F, Chi JX, Yang FT, Wang W. Comparative genomic analysis links karyotypic evolution with genomic evolution in the indian muntjac ( Muntiacus muntjak vaginalis). Chromosoma, 2006,115(6):427-436.
[47]	Lee C, Sasi R, Lin CC. Interstitial localization of telomeric DNA sequences in the indian muntjac chromosomes: Further evidence for tandem chromosome fusions in the karyotypic evolution of the asian muntjacs. Cytogenet Cell Genet, 1993,63(3):156-159. doi: 10.1159/000133525 pmid: 8485991
[48]	Yang F, Carter NP, Shi L, Ferguson-Smith MA. A comparative study of karyotypes of muntjacs by chromosome painting. Chromosoma, 1995,103(9):642-652.
[49]	Yang F , O'Brien PC, Wienberg J, Ferguson-Smith MA. Evolution of the black muntjac ( Muntiacus crinifrons) karyotype revealed by comparative chromosome painting. Cytogenet Cell Genet, 1997,76(3-4):159-163.
[50]	Yang F , O'Brien PC, Wienberg J, Neitzel H, Lin CC, Ferguson-Smith MA. Chromosomal evolution of the chinese muntjac ( Muntiacus reevesi). Chromosoma, 1997,106(1):37-43.
[51]	Tsipouri V, Schueler MG, Hu S, Program NCS, Dutra A, Pak E, Riethman H, Green ED. Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the indian muntjac genome. Genome Biol, 2008,9(10):R155. doi: 10.1186/gb-2008-9-10-r155 pmid: 18957082
[52]	Huang L, Chi J, Nie WH, Wang JH, Yang FT. Phylogenomics of several deer species revealed by comparative chromosome painting with chinese muntjac paints. Genetica, 2006,127(1-3):25-33. doi: 10.1007/s10709-005-2449-5 pmid: 16850210
[53]	Huang L, Chi JX, Wang JH, Nie WH, Su W, Yang FT. High-density comparative bac mapping in the black muntjac ( Muntiacus crinifrons): Molecular cytogenetic dissection of the origin of mcr 1p+4 in the x1x2y1y2y3 sex chromosome system. Genomics, 2006,87(5):608-615.
[54]	Zhou Q, Wang J, Huang L, Nie WH, Wang JH, Liu Y, Zhao XY, Yang FT, Wang W. Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes. Genome Biol, 2008,9(6):R98.
[55]	Huang L, Jing MD, Zhou Q, Yang FT, Wang W . Research advances in genome evolution of muntjacs ( Muntiacinae, Cervidae). Sci China Life Sci, 2012,42(2):87-95.
	黄玲, 靖美东, 周琦, 杨凤堂, 王文 . 鹿科麂属动物基因组演化研究进展. 中国科学:生命科学, 2012,42(2):87-95.
[56]	Lin ZS, Chen L, Chen XQ, Zhong YB, Yang Y, Xia WH, Liu C, Zhu WB, Wang H, Yan BY, Yang YF, Liu X, Sternang Kvie K, Røed KH, Wang K, Xiao WH, Wei HJ, Li GY, Heller R, Gilbert MTP, Qiu Q, Wang W, Li ZP. Biological adaptations in the arctic cervid, the reindeer(Rangifer tarandus). Science, 2019, 364(6446): eaav6312.
[57]	Weldenegodguad M, Pokharel K, Ming Y, Honkatukia M, Peippo J, Reilas T, Røed KH, Kantanen J. Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern eurasia. Sci Rep, 2020,10(1):8980. doi: 10.1038/s41598-020-65487-y pmid: 32488117
[58]	Yang SL, Lu XC, Wang YF, Xu LZ, Chen XY, Yang F, Lai R. A paradigm of thermal adaptation in penguins and elephants by tuning cold activation in trpm8. Proc Natl Acad Sci USA, 2020,117(15):8633-8638.
[59]	Ababaikeri B, Abduriyim S, Tohetahong Y, Mamat T, Ahmat A, Halik M. Whole-genome sequencing of tarim red deer (Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment. Front Zool, 2020,17(1):31.
[60]	Ba HX, Qin T, Cai ZX, Liu WY, Li CY. Molecular evidence for adaptive evolution of olfactory-related genes in cervids. Genes Genomics, 2020,42(4):355-360. doi: 10.1007/s13258-019-00911-w pmid: 31902105
[61]	Li CY, Suttie JM. Deer antlerogenic periosteum: A piece of postnatally retained embryonic tissue? Anat Embryol (Berl), 2001,204(5):375-388.
[62]	Kierdorf U, Li CY, Price JS. Improbable appendages: Deer antler renewal as a unique case of mammalian regeneration. Semin Cell Dev Biol, 2009,20(5):535-542. doi: 10.1016/j.semcdb.2008.11.011 pmid: 19084608
[63]	Price JS, Allen S, Faucheux C, Althnaian T, Mount JG. Deer antlers: A zoological curiosity or the key to understanding organ regeneration in mammals? J Anat, 2005,207(5):603-618. doi: 10.1111/j.1469-7580.2005.00478.x pmid: 16313394
[64]	Randi E, Mucci N, Pierpaoli M, Douzery E. New phylogenetic perspectives on the Cervidae (Artiodactyla) are provided by the mitochondrial cytochrome b gene. Proc Biol Sci, 1998,265(1398):793-801. doi: 10.1098/rspb.1998.0362 pmid: 9628037
[65]	Li CY. Deer antler regeneration: A stem cell-based epimorphic process. Birth Defects Res C Embryo Today, 2012,96(1):51-62. pmid: 22457177
[66]	Li CY, Chu WH. The regenerating antler blastema: The derivative of stem cells resident in a pedicle stump. Front Biosci (Landmark Ed), 2016,21:455-467.
[67]	Rolf HJ, Kierdorf U, Kierdorf H, Schulz J, Seymour N, Schliephake H, Napp J, Niebert S, Wölfel H, Wiese KG. Localization and characterization of stro-1 cells in the deer pedicle and regenerating antler. PLoS One, 2008,3(4):e2064. doi: 10.1371/journal.pone.0002064 pmid: 18446198
[68]	Seo MS, Park SB, Choi SW, Kim JJ, Kim HS, Kang KS. Isolation and characterization of antler-derived multipotent stem cells. Cell Transplant, 2014,23(7):831-843. doi: 10.3727/096368912X661391 pmid: 23294672
[69]	Wang DT, Ba HX, Li CG, Zhao QM, Li CY. Proteomic analysis of plasma membrane proteins of antler stem cells using label-free LC-MS/MS. Int J Mol Sci, 2018,19(11):3477.
[70]	Wang DT, Berg DB, Ba HX, Sun HM, Wang Z, Li CY. Deer antler stem cells are a novel type of cells that sustain full regeneration of a mammalian organ-deer antler. Cell Death Dis, 2019,10(6):443. doi: 10.1038/s41419-019-1686-y pmid: 31165741
[71]	Ba HX, Wang DT, Li CY. Microrna profiling of antler stem cells in potentiated and dormant states and their potential roles in antler regeneration. Mol Genet Genomics, 2016,291(2):943-955. doi: 10.1007/s00438-015-1158-8 pmid: 26738876
[72]	Ba HX, Wang DT, Wu WY, Sun HM, Li CY. Single-cell transcriptome provides novel insights into antler stem cells, a cell type capable of mammalian organ regeneration. Funct Integr Genomics, 2019,19(4):555-564. doi: 10.1007/s10142-019-00659-2 pmid: 30673893
[73]	Li CY, Yang FH, Li GY, Gao XH, Xing XM, Wei HJ, Deng XM, Clark DE. Antler regeneration: A dependent process of stem tissue primed via interaction with its enveloping skin. J Exp Zool A Ecol Genet Physiol, 2007,307(2):95-105. pmid: 17177282
[74]	Dong Z, Ba HX, Zhang W, Coates D, Li CY. Itraq-based quantitative proteomic analysis of the potentiated and dormant antler stem cells. Int J Mol Sci, 2016,17(11):1778.
[75]	Dong Z, Coates D, Liu QX, Sun HM, Li CY. Quantitative proteomic analysis of deer antler stem cells as a model of mammalian organ regeneration. J Proteomics, 2019,195:98-113. doi: 10.1016/j.jprot.2019.01.004 pmid: 30641233
[76]	Dong Z, Haines S, Coates D. Proteomic profiling of stem cell tissues during regeneration of deer antler: A model of mammalian organ regeneration. J Proteome Res, 2020,19(4):1760-1775. doi: 10.1021/acs.jproteome.0c00026 pmid: 32155067
[77]	Sun HM, Sui ZG, Wang DT, Ba HX, Zhao HP, Zhang LH, Li CY. Identification of interactive molecules between antler stem cells and dermal papilla cells using an in vitro co-culture system. J Mol Histol, 2020,51(1):15-31. doi: 10.1007/s10735-019-09853-9 pmid: 31858326
[78]	Li CY, Harper A, Puddick J, Wang WY, McMahon C. Proteomes and signalling pathways of antler stem cells. PLoS One, 2012,7(1):e30026. pmid: 22279561
[79]	Liu Z, Zhao HP, Wang D, McMahon C, Li CY. Differential effects of the pi3k/akt pathway on antler stem cells for generation and regeneration of antlers in vitro. Front Biosci (Landmark Ed), 2018,23:1848-1863.
[80]	Dedhar S, Rennie PS, Shago M, Hagesteijn CY, Yang H, Filmus J, Hawley RG, Bruchovsky N, Cheng H, Matusik RJ. Inhibition of nuclear hormone receptor activity by calreticulin. Nature, 1994,367(6462):480-483. doi: 10.1038/367480a0 pmid: 8107809
[81]	Akhtar RW, Liu Z, Wang DT, Ba HX, Shah SAH, Li CY. Identification of proteins that mediate the role of androgens in antler regeneration using label free proteomics in sika deer (Cervus nippon). Gen Comp Endocrinol, 2019,283:113235. doi: 10.1016/j.ygcen.2019.113235 pmid: 31369730
[82]	Park HJ, Lee DH, Park SG, Lee SC, Cho S, Kim HK, Kim JJ, Bae H, Park BC. Proteome analysis of red deer antlers. Proteomics, 2004,4(11):3642-3653. doi: 10.1002/pmic.200401027 pmid: 15529405
[83]	Yao BJ, Zhao Y, Wang Q, Zhang M, Liu MC, Liu HL, Li J. De novo characterization of the antler tip of chinese sika deer transcriptome and analysis of gene expression related to rapid growth. Mol Cell Biochem, 2012,364(1-2):93-100. doi: 10.1007/s11010-011-1209-3 pmid: 22198337
[84]	Yao BJ, Zhao Y, Zhang HS, Zhang M, Liu MC, Liu HL, Li J. Sequencing and de novo analysis of the chinese sika deer antler-tip transcriptome during the ossification stage using illumina rna-seq technology. Biotechnol Lett, 2012,34(5):813-822.
[85]	Zhao Y, Yao BJ, Zhang M, Wang SM, Zhang H, Xiao W. Comparative analysis of differentially expressed genes in sika deer antler at different stages. Mol Biol Rep, 2013,40(2):1665-1676. doi: 10.1007/s11033-012-2216-5 pmid: 23073784
[86]	Han RB, Han L, Wang SN, Li HP. Whole transcriptome analysis of mesenchyme tissue in sika deer antler revealed the cernas regulatory network associated with antler development. Front Genet, 2019,10:1403. pmid: 32133026
[87]	Zhang YY, Liu HM, Shao YC, Zhou PY, Su Y, Wang L, Xing XM . Comparative proteomic analysis in different growth stages of sika deer velvet antler, Acta Veterinaria et Zootechnica Sinica, 2016,47(3):493-501.
	张然然, 刘华淼, 邵元臣, 周盼伊, 苏莹, 王磊, 邢秀梅 . 不同生长时期梅花鹿鹿茸差异蛋白质组学分析. 畜牧兽医学报, 2016,47(3):493-501.
[88]	Li CY, Clark DE, Lord EA, Stanton JA, Suttie JM. Sampling technique to discriminate the different tissue layers of growing antler tips for gene discovery. Anat Rec, 2002,268(2):125-130. doi: 10.1002/ar.10120 pmid: 12221718
[89]	Ba HX, Wang DT, Yau TO, Shang YD, Li CY. Transcriptomic analysis of different tissue layers in antler growth center in sika deer ( Cervus nippon). BMC Genomics, 2019,20(1):173. doi: 10.1186/s12864-019-5560-1 pmid: 30836939
[90]	Ker DFE, Wang D, Sharma R, Zhang B, Passarelli B, Neff N, Li CY, Maloney W, Quake S, Yang YP. Identifying deer antler uhrf1 proliferation and s100a10 mineralization genes using comparative rna-seq. Stem Cell Res Ther, 2018,9(1):292. doi: 10.1186/s13287-018-1027-6 pmid: 30376879
[91]	Chen DY, Jiang RF, Li YJ, Liu MX, Wu L, Hu W. Screening and functional identification of lncrnas in antler mesenchymal and cartilage tissues using high- throughput sequencing. Sci Rep, 2020,10(1):9492. doi: 10.1038/s41598-020-66383-1 pmid: 32528134
[92]	Yao BJ, Wang CN, Zhou ZW, Zhang M, Zhao DQ, Bai XY, Leng XY. Comparative transcriptome analysis of the main beam and brow tine of sika deer antler provides insights into the molecular control of rapid antler growth. Cell Mol Biol Lett, 2020,25:42. doi: 10.1186/s11658-020-00234-9 pmid: 32944020
[93]	Li CY, Zhao HP, Liu Z, McMahon C. Deer antler--a novel model for studying organ regeneration in mammals. Int J Biochem Cell Biol 2014,56:111-122. pmid: 25046387
[94]	Landete-Castillejos T, Kierdorf H, Gomez S, Luna S, García AJ, Cappelli J, Pérez-Serrano M, Pérez-Barbería J, Gallego L, Kierdorf U. Antlers-evolution, development, structure, composition, and biomechanics of an outstanding type of bone. Bone, 2019,128:115046. doi: 10.1016/j.bone.2019.115046 pmid: 31446115
[95]	Fennessy PF. Deer antlers: Regeneration, function and evolution. J R Soc N Z, 1984,14(3):290-291. doi: 10.1080/03036758.1984.10426948
[96]	Lombard LS, Witte EJ. Frequency and types of tumors in mammals and birds of the philadelphia zoological garden. Cancer Res, 1959,19(2):127-141. pmid: 13629476
[97]	Griner LA. A review of necropsies conducted over a fourteen-year period at the san diego zoo and san diego wild animal park. In: Pathology of Zoo Animals. 1983.
[98]	Rong XL, Chu WH, Zhang HY, Wang YS, Qi XY, Zhang GK, Wang YM, Li CY. Antler stem cell- conditioned medium stimulates regenerative wound healing in rats. Stem Cell Res Ther 2019,10(1):326. doi: 10.1186/s13287-019-1457-9 pmid: 31744537
[99]	Willyard C. Unlocking the secrets of scar-free skin healing. Nature, 2018,563(7732):S86-S88. doi: 10.1038/d41586-018-07430-w pmid: 30464288
[100]	Banks WJ, Epling GP, Kainer RA, Davis RW. Antler growth and osteoporosis. I. Morphological and morphometric changes in the costal compacta during the antler growth cycle. Anat Rec, 1968,162(4):387-397. doi: 10.1002/ar.1091620401 pmid: 5701619
[101]	Jr WJB, Epling GP, Kainer RA, Davis RW. Antler growth and osteoporosis. II. Gravimetric and chemical changes in the costal compacta during the antler growth cycle. Anat Rec, 1968,162(4):399-405. doi: 10.1002/ar.1091620402 pmid: 5701620
[102]	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. Antler development and coupled osteoporosis in the skeleton of red deer cervus elaphus: Expression dynamics for regulatory and effector genes. Mol Genet Genomics, 2010,284(4):273-287. doi: 10.1007/s00438-010-0565-0 pmid: 20697743
[103]	van der Weijden VA, Ulbrich SE. Embryonic diapause in roe deer: A model to unravel embryo-maternal communication during pre-implantation development in wildlife and livestock species. Theriogenology, 2020,158:105-111. doi: 10.1016/j.theriogenology.2020.06.042 pmid: 32947063
[104]	Beyes M, Nause N, Bleyer M, Kaup FJ, Neumann S. Description of post-implantation embryonic stages in european roe deer (capreolus capreolus) after embryonic diapause. Anat Histol Embryol, 2017,46(6):582-591. doi: 10.1111/ahe.12315 pmid: 28960412
[105]	Drews B, Rudolf Vegas A, van der Weijden VA, Milojevic V, Hankele AK, Schuler G, Ulbrich SE. Do ovarian steroid hormones control the resumption of embryonic growth following the period of diapause in roe deer (Capreolus capreolus)? Reprod Biol, 2019,19(2):149-157. doi: 10.1016/j.repbio.2019.04.003 pmid: 31147267
[106]	Korzekwa AJ, Kotlarczyk AM, Zadroga A. Profiles of maternal origin factors during transition from embryonic diapause to implantation in roe deer. Anim Sci J, 2019,90(11):1444-1452. doi: 10.1111/asj.13289 pmid: 31486226
[107]	van der Weijden VA, Puntar B, Rudolf Vegas A, Milojevic V, Schanzenbach CI, Kowalewski MP, Drews B, Ulbrich SE. Endometrial luminal epithelial cells sense embryo elongation in the roe deer independent of interferon-tau†. Biol Reprod, 2019,101(5):882-892. doi: 10.1093/biolre/ioz129 pmid: 31317179

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

物种	发表时间 (年)	测序/组装技术	基因组大小 (去除Gap后) (Gb)	测序深度(×)	Contig/ Scaffold N50 (kb/Mb)	Scaffolds 数量
白尾鹿 (Odocoileus virginianus)^a	2011	Illumina HiSeq/Allpath-lg	2.38 (2.36)	150	122.0/0.9	17,025
西方狍 (Capreolus capreolus)^b	2014	Illumina HiSeq/SOAPdenovo	2.78 (2.74)	24	4.1/0.01	3,088,511
驯鹿 (Rangifer tarandus)^[3]	2017	Illumina HiSeq/SOAPdenovo	2.64 (2.54)	220	89.7/0.94	58,765
赤鹿 (Cervus elaphus)^[8]	2017	Illumina HiSeq/AllPaths	3.40 (1.95)	74	7.9/0.27	34,724
麋鹿 (Elaphurus davidianus)^[9]	2017	Illumina HiSeq/SOAPdenovo	2.52 (2.46)	82	32.7/3.0	46,381
豚鹿 (Axis porcinus)^[10]	2018	Illumina HiSeq/SOAPdenovo	2.68 (2.64)	197	172.8/20.6	136,093
黑尾鹿 (Odocoileus hemionus)^[11]	2018	Illumina HiSeq/BWA; SAMtools	2.34 (2.34)	25	113.3/0.8	838,758
小麂 (Muntiacus reevesi)^[6]	2019	Illumina HiSeq/Supernova; Hi-C	2.58 (2.51)	34	225.1/9.4	29,705
赤麂 (Muntiacus muntjak)^[6]	2019	Illumina HiSeq/SOAPdenovo	2.57 (2.52)	68	215.5/-	25,651
白唇鹿 (Przewalskium albirostris)^[12]	2019	Illumina HiSeq/Platanus	2.69 (2.64)	214	39.6/3.8	171,874
獐 (Hydropotes inermis)^[12]	2019	Illumina HiSeq/Supernova	2.53 (2.48)	76	131.4/13.8	22,246
黑麂 (Muntiacus crinifrons)^[12]	2019	PacBio/FALCON	2.68 (2.67)	116	8.2/1.3	21,052
驼鹿 (Alces alces)^c	2019	Illumina HiSeq/Supernova	2,74 (2,54)	35	131,8/4.1	48,219
东方狍 (Capreolus pygargu)^[13]	2020	Illumina HiSeq/Supernova	2.61 (2,55)	100	-/6.6	92,100
塔里木马鹿 (Cervus elaphus yarkandensis)^[4]	2020	Illumina NextSeq/Supernova; Genetic maps	2.60 (2.56)	63	275.5/31.7	19,010
梅花鹿 (Cervus nippon)^d	2020	PacBio/wtdbg2; Hi-C; Optical maps	2.50 (2.50)	58	23,600/78.8	588

物种	发表时间 (年)	测序平台/方法	个体数量	标记类型	标记数量
白尾鹿 (Odocoileus virginianus)^[22]	2011	Roche 454/简化基因组	16	SNP	13,734^c
白尾鹿 (Odocoileus virginianus)^[24]	2012	Illumina BovineSNP50	10	SNP	469^a
骡鹿 (Odocoileus hemionus)^[24]	2012	Illumina BovineSNP50	4	SNP	429^a
黑尾鹿 (Odocoileus hemionus)^[24]	2012	Illumina BovineSNP50	14	SNP	434^a
驯鹿 (Rangifer tarandus)^[25]	2015	Illumina BovineSNP50+OvineSNP50	4	SNP	4572+1471^a
赤鹿/马鹿 (Cervus elaphus)^[28]	2015	Illumina GAII-X/重测序	7	SNP	1.8×10^5c
骡鹿 (Odocoileus hemionus)^[26]	2016	Illumina HiSeq2000/外显子捕获	7	SNP	23,204^c
梅花鹿 (Cervus nippon)^[19]	2017	Illumina HiSeq2500/双酶切简化基因组	42	SNP	96,188^c
梅花鹿 (Cervus nippon)^[27]	2017	Illumina Hiseq Xten/重测序	100	SNP	38,319,467^c
豚鹿 (Axis porcinus)^[23]	2017	Illumina HiSeq2500/酶切简化基因组	11	SNP	11,155^c
梅花鹿(Cervus nippon)/ 马鹿(Cervus elaphus)/F1^[20]	2018	Illumina HiSeq2500/双酶切简化基因组	30	SNP	2015^b
驼鹿 (Alces alces)^[21]	2018	Illumina HiSeq2500/酶切简化基因组	34	SNP	336^c
梅花鹿 (Cervus nippon)^[42]	2018	Applied Biosystems 3730/基因组	96	SSR	29^a
骡鹿(Odocoileus hemionus)/ 白尾鹿(Odocoileus virginianus)/F₁/F₂^[11]	2019	Illumina CervusSNP50	30	SNP	40^b
狍 (Capreolous capreolus)^[13]	2019	Illumina HiSeq2500/酶切简化基因组	250	SNP	83,893^c
梅花鹿 (Cervus nippon)^[43]	2020	PCR扩增	478	Y-SNP	9^c
梅花鹿 (Cervus nippon)^[40]	2020	Applied Biosystems 3730/转录组	140	SSR	29^a
赤鹿 (Cervus nippon)^[44]	2020	PCR扩增	123	X-/Y-SSR	10/5^a

Progress on deer genome research

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 4

References 107

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Liang Jin, Yujie Chen, Yongjun Chen. Advances in genetic etiology, diagnosis and treatment of developmental and epileptic encephalopathy [J]. Hereditas(Beijing), 2023, 45(7): 553-567.
[2]	Ke Mao, Ziqiu Meng, Yongbiao Zhang. Progress on the regulation of neural crest and the genetics in craniofacial development [J]. Hereditas(Beijing), 2022, 44(12): 1089-1102.
[3]	Shanshan Gao, Jinliang Li, Jiani Yang, Tong Zhou, Rui Liu, Xiaoping Wang, Li Yu. Progresses on adaptive evolution of gliding and flying ability in mammals [J]. Hereditas(Beijing), 2022, 44(1): 46-58.
[4]	Yuxing Zhang, Hong Wu, Li Yu. Progress on coat color regulation mechanism and its association with the adaptive evolution in mammals [J]. Hereditas(Beijing), 2021, 43(2): 118-133.
[5]	Zhichao Mei, Zhujun Wei, Jiahui Yu, Fengdan Ji, Linan Xie. Multi-omics association analysis revealed the role and mechanism of epialleles in environmental adaptive evolution of Arabidopsis thaliana [J]. Hereditas(Beijing), 2020, 42(3): 321-331.
[6]	Yu Meng,Ruolin Yang. Comparative analysis of gene family size provides insight into the adaptive evolution of vertebrates [J]. Hereditas(Beijing), 2019, 41(2): 158-174.
[7]	Pengfei Hu, Jiaping Xu, Cheng Ai, Xiujuan Shao, Hongliang Wang, Yimeng Dong, Xuezhe Cui, Fuhe Yang, Xiumei Xing. Screening weight related genes of velvet antlers by whole genome re-sequencing [J]. Hereditas(Beijing), 2017, 39(11): 1090-1101.
[8]	Fei Chang, Wenchao Zou, Fangluan Gao, Jianguo Shen, Jiasui Zhan. Comparative analysis of population genetic structure of Potato virus Y from different hosts [J]. HEREDITAS(Beijing), 2015, 37(3): 292-301.
[9]	Jing Jiang, Qian Qian, Bojun Ma, Zhenyu Gao. Epigenetic variation and its application in crop improvement [J]. HEREDITAS(Beijing), 2014, 36(5): 469-475.
[10]	Linjiang Zhu, Qi Li. Stress-induced cellular adaptive mutagenesis [J]. HEREDITAS, 2014, 36(4): 327-335.
[11]	. Molecular evolution of the sulphite efflux gene SSU1 in Saccharomy-ces cerevisiae [J]. HEREDITAS, 2013, 35(11): 1317-1326.
[12]	WU Zhi-Jun, JIN Wei, ZHANG Feng-Ru, LIU Yan. Recent advances in natriuretic peptide family genes and cardiovas-cular diseases [J]. HEREDITAS, 2012, 34(2): 127-133.
[13]	Chengcai Chu. The Cover story description [J]. HEREDITAS, 2012, 34(11): 1389-1389.
[14]	OU Shu-Jun, WANG Hong-Ru, CHU Cheng-Cai. Major domestication traits in Asian rice [J]. HEREDITAS, 2012, 34(11): 1379-1389.
[15]	WANG Yan, XIE Hui, CHEN Li-Ping. Progress in research on plant graft-induced genetic variation [J]. HEREDITAS, 2011, 33(6): 585-590.