鹿科动物基因组学研究进展

doi:10.16288/j.yczz.20-362

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

鹿科动物基因组学研究进展

巴恒星^1,²(), 胡鹏飞^1,², 李春义^1,²()

^1. 长春科技学院,鹿茸科学与产品技术研究所,长春 130112
^2. 吉林省鹿茸生物学重点实验室,长春 130112

收稿日期:2020-10-28 修回日期:2020-12-29 出版日期:2021-04-20 发布日期:2021-04-20
通讯作者: 巴恒星,李春义 E-mail:bahengxing@caas.cn;lichunyi1959@163.com
作者简介:巴恒星,博士,研究员,研究方向：特种动物基因组学。E-mail: bahengxing@caas.cn
基金资助:
国家自然科学基金项目编号(31402035);国家自然科学基金项目编号(U20A20403);吉林省科技发展计划项目资助编号(20200602013ZP)

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)

摘要/Abstract

摘要：

鹿科动物是世界上最丰富的大型哺乳动物之一,在极北地区、热带地区和高海拔地区都有分布。中国占世界鹿科动物40%以上,是鹿科动物进化的主战场。鹿科动物除了具有反刍动物常见的独特表型特征外,更是进化出周期性再生新器官——鹿茸角。鹿科动物是研究生态学、行为学和进化生物学非常有价值的动物模型,特别是在研究哺乳动物器官再生方面具有重要科学价值。鹿基因组是系统阐述鹿的进化和演变,解析鹿科动物独特生物学性状的依据,对遗传资源保护和利用具有重要意义。目前,随着鹿科动物参考基因组的不断完善,在鹿基础科学研究上取得了诸多重要成果。本文详细综述了鹿科动物基因组学研究进展,主要包括鹿遗传变异数据、适应性进化分子基础、独特性状鹿茸角的起源进化关键基因和功能基因组学,以期为鹿科动物的深入研究奠定理论基础。

关键词: 鹿科动物, 参考基因组, 遗传变异, 适应性进化, 鹿茸角, 功能基因组学

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

巴恒星, 胡鹏飞, 李春义. 鹿科动物基因组学研究进展[J]. 遗传, 2021, 43(4): 308-322.

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

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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

鹿科动物基因组学研究进展

Progress on deer genome research

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