牦牛基因组和转录组研究进展
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摘要
为了解牦牛基因组和转录组研究现状,以"牦牛、基因组、转录组和高通量测序"为关键词,对2012—2018年的研究进展进行文献检索。研究发现:在牦牛基因组研究方面,已有研究对牦牛基因组进行了首次测序和重测序分析,构建了基因组"草图"和变异图谱,比较了家、野牦牛及与其他物种间全基因组水平上的异同,阐释了牦牛高原适应的遗传学机制,探究了牦牛的驯化和群体历史发展动态,初步揭示了牦牛与普通牛种间杂交渐渗状况,并对部分性状(如角、多肋性状)进行了全基因组关联分析和遗传机理揭示;在牦牛转录组研究方面,已有研究对牦牛睾丸、卵巢、心脏等多个组织器官及不同发育阶段的卵母细胞和胚胎细胞进行了转录组分析,发掘出一批潜在的与牦牛经济性状及一些生物学变化相关的差异表达基因。为推动牦牛分子育种进程,应进一步利用高通量测序技术获得牦牛大数据,继续完善牦牛全基因组结构。
To investigate the progress of yak genome and transcriptome,literatures related to yak genome and transcriptome researches over 2012-2018 were summarized in this paper by using "yak,genome,transcriptome and high throughput sequencing" as keywords.The results showed: On the aspect of genome,the genome of yak was sequenced for the first time in 2012 and subsequently re-sequenced.The yak genome "sketch frame" and the corresponding genetic variations profile were constructed.The genome similarities and differences between the domestic yak,wild yak and other species were compared.The genetic mechanism of yak plateau adaptation was explained,and the domestication and demographic history of domestic yak were explored.The adaptation introgression between yak and cattle,and the genetic mechanism of some traits(i.e.horns and multi-ribs traits) in yak also were revealed.The whole genome association analysis in yak was used;On the aspect of yak transcriptome study,the transcriptional analysis of the testis,ovary and heart etc.,as well as the oocyte and embryo cells of the yak were carried out to discover a number of potential differentially expressed genes(DEGs) related to the economic traits and some biological changes.Future work should focus on Big Data obtained by high throughput sequencing technology to assist yak molecular breeding.
To investigate the progress of yak genome and transcriptome,literatures related to yak genome and transcriptome researches over 2012-2018 were summarized in this paper by using "yak,genome,transcriptome and high throughput sequencing" as keywords.The results showed: On the aspect of genome,the genome of yak was sequenced for the first time in 2012 and subsequently re-sequenced.The yak genome "sketch frame" and the corresponding genetic variations profile were constructed.The genome similarities and differences between the domestic yak,wild yak and other species were compared.The genetic mechanism of yak plateau adaptation was explained,and the domestication and demographic history of domestic yak were explored.The adaptation introgression between yak and cattle,and the genetic mechanism of some traits(i.e.horns and multi-ribs traits) in yak also were revealed.The whole genome association analysis in yak was used;On the aspect of yak transcriptome study,the transcriptional analysis of the testis,ovary and heart etc.,as well as the oocyte and embryo cells of the yak were carried out to discover a number of potential differentially expressed genes(DEGs) related to the economic traits and some biological changes.Future work should focus on Big Data obtained by high throughput sequencing technology to assist yak molecular breeding.
引文
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[7] Wang K,Hu Q J,Ma H,Wang L Z,Yang Y Z,Luo W C,Qiu Q.Genome-wide variation within and between wild and domestic yak[J].Molecular Ecology Resources,2014,14(4):794-801
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[12] Xie X,Yang Y,Ren Q,Ding X,Bao P,Yan B,Yan X,Han J,Yan P,Qiu Q.Accumulation of deleterious mutations in the domestic yak genome[J].Animal Genetics,2018,49(5):384-392
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[14] Ma Z J.Genome-wide characterization of perfect microsatellites in yak (Bos grunniens)[J].Genetica,2015,143(4):515-520
[15] Qi W H,Jiang X M,Du L M,Xiao G S,Hu T Z,Yue B S,Quan Q M.Genome-wide survey and analysis of microsatellite sequences in Bovid species[J].PLoS One,2015,10(7):e0133667
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[17] Wu D D,Ding X D,Wang S,Wójcik J M,Zhang Y,Tokarska M,Li Y,Wang M S,Faruque O,Nielsen R,Zhang Q,Zhang Y P.Pervasive introgression facilitated domestication and adaptation in the Bos species complex[J].Nature Ecology & Evolution,2018,2(7):1139-1145
[18] 曾贤彬,柴志欣,王永,马志杰,杨琴,宋乔乔,钟金城.犏牛精子发生阻滞的比较转录组研究[J].中国科学:生命科学,2014,44(6):584-601Zeng X B,Cai Z X,Wang Y,Ma Z J,Yang Q,Song Q Q,Zhong J C.Comparative transcriptome analysis of spermatogenesis arrest in cattle-yak[J].Science China:Life Sciences,2014,44(6):584-601 (in Chinese)
[19] Cai X,Yu S M,Mipam T,Yang F,Zhao W S,Liu W J,Cao S Z,Shen L H,Zhao F F,Sun L,Xu C F,Wu S X.Comparative analysis of testis transcriptomes associated with male infertility in cattle-yak[J].Theriogenology,2017,88:28-42
[20] Xu C F,Wu S X,Zhao W S,Mipam T,Liu J B,Liu W J,Yi C P,Shah M A,Yu S M,Cai X.Differentially expressed microRNAs between cattle-yak and yak testis[J].Scientific Reports,2018,8:592
[21] Wang H,Zhong J C,Chai Z X,Zhu J,Xin J W.Comparative expression profile of microRNAs and piRNAs in three ruminant species testes using next-generation sequencing[J].Reproduction in Domestic Animals,2018,53(4):963-970
[22] 兰道亮,熊显荣,位艳丽,徐通,钟金城,字向东,王永,李键.基于RNA-Seq高通量测序技术的牦牛卵巢转录组研究:进一步完善牦牛基因结构及挖掘与繁殖相关新基因[J].中国科学:生命科学,2014,44(3):307-317Lan D L,Xiong X R,Wei Y L,Xu T,Zhong J C,Zi X D,Wang Y,Li J.RNA-Seq analysis of yak ovary:Improving yak gene structure information and mining reproduction-related genes[J].Science China:Life Sciences,2014,44(3):307-317 (in Chinese)
[23] 兰道亮,熊显荣,柴志欣,艾鷖,黄偲,李键.牦牛发情期卵巢比较转录组学研究[J].畜牧兽医学报,2016,47(9):1830-1839Lan D L,Xiong X R,Chai Z X,Ai Y,Huang C,Li J.Comparative transcriptome analysis between yak and cattle estrus ovary[J].Chinese Journal of Animal and Veterinary Sciences,2016,47(9):1830-1839 (in Chinese)
[24] 杨琦玥,陈通,兰道亮,熊显荣,候定超,李键.牦牛肺转录组图谱绘制及特有正选择遗传进化基因探究[J].畜牧兽医学报,2017,48(7):1202-1211Yang Q Y,Chen T,Lan D L,Xiong X R,Hou D C,Li J.Mapping of transcriptome and identification of positively selected genes in lung in yak[J].Chinese Journal of Animal and Veterinary Sciences,2017,48(7):1202-1211 (in Chinese)
[25] Lan D L,Xiong X R,Ji W H,Li J,Mipam T D,Ai Y,Chai Z X.Transcriptome profile and unique genetic evolution of positively selected genes in yak lungs[J].Genetica,2018,146(2):151-160
[26] Tang Q Z,Gu Y R,Zhou X M,Jin L,Guan J Q,Liu R,Li J,Long K R,Tian S L,Che T D,Hu S L,Liang Y,Yang X M,Tao X,Zhong Z J,Wang G S,Chen X H,Li D Y,Ma J D,Wang X,Mai M M,Jiang A N,Luo X L,Lv X,Gladyshev V N,Li X W,Li M Z.Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives[J].GigaScience,2017,6(12):1-9
[27] 刘祥军.镉胁迫下牦牛肝脏组织转录组学及蛋白组学研究[D].西宁:青海大学,2017Liu X J.Study on transcriptome and proteomics of yak liver under cadmium stress[D].Xining:Qinghai University,2017 (in Chinese)
[28] Fan J F,Luo Y Z,Yu S J,Cui Y,Xu G Q,Wang L B,Pan Y Y,He H H.Transcriptional profiling of two different physiological states of the yak mammary gland using RNA sequencing[J].PLoS One,2018,13(7):e0201628 (in Chinese)
[29] 兰道亮,熊显荣,林宝山,陈亚冰,胡敏,苏小珊,李键.基于微量RNA高通量测序技术的牦牛MⅡ期卵母细胞转录组研究[J].畜牧兽医学报,2014,45(5):722-732Lan D L,Xiong X R,Lin B S,Chen Y B,Hu M,Su X S,Li J.Transcriptome analysis of yak metaphase Ⅱ(MⅡ) oocytes by a micro-transcriptome sequencing method[J].Chinese Journal of Animal and Veterinary Sciences,2014,45(5):722-732 (in Chinese)
[30] 字向东,罗斌,夏威,郑玉才,熊显荣,李键,钟金城,朱江江,张正帆.基于RNA-Seq技术的牦牛体外受精胚胎发育转录组分析[J].中国农业科学,2018,51(8):1577-1589Zi X D,Luo B,Xia W,Zheng Y C,Xiong X R,Li J,Zhong J C,Zhu J J,Zhang Z F.Transcriptomicanalysis of IVF embryonic development in the yak (Bos grunniens) via RNA-Seq[J].Scientia Agricultura Sinica,2018,51(8):1577-1589 (in Chinese)
[31] Zi X D,Liu S,Xia W,Xiong X R,Luo B.Transcriptional profiles of crossbred embryos derived from yak oocytes in vitro fertilized with cattle sperm[J].Scientific Reports,2018,8(1):11571
[32] 蒲思颖,郑杰,杨远潇,王琴,杨绕芬,字向东.牦牛新鲜囊胚与玻璃化冻融囊胚转录组的比较分析[J].畜牧兽医学报,2018,49 (4):709-717Pu S Y,Zheng J,Yang Y X,Wang Q,Yang R F,Zi X D.Comparative transcriptome analysis between fresh and vitrified-thawed blastocysts of the yak (Bos grunniens)[J].Acta Veterinaria et Zootechnica Sinica,2018,49 (4):709-717 (in Chinese)
[33] E.科佩莱恩,J.图梅拉,P.萨默沃著.陈建国,张海谋译.RNA-seq 数据分析实用方法[M].北京:科学出版社.2018CopellineE,Tumela J,Summero P,Chen J G,Zhang H M.RNA-seq Practical Method of Data Analysis[M].Beijing:Science Press.2018 (in Chinese)
[2] 马志杰,钟金城,韩建林,徐惊涛,刘仲娜,白文林.牦牛分子遗传多样性研究进展[J].遗传,2013,35(2):151-160Ma Z J,Zhong J C,Han J L,Xu J T,Liu Z N,Bai W L.Research progress on molecular genetic diversity of the yak (Bos grunniens)[J].Hereditas,2013,35(2):151-160 (in Chinese)
[3] 马志杰.牦牛线粒体基因组研究进展[J].中国农业大学学报,2014,19(3):154-161Ma Z J.Research progress of the yak (Bos grunniens) mitochondrial genome[J].Journal of China Agricultural University,2014,19(3):154-161 (in Chinese)
[4] 马志杰.牦牛Y染色体分子遗传学研究进展[J].中国农业大学学报,2016,21(2):93-99Ma Z J.Research progress on molecular genetics of the yak Y chromosome[J].Journal of China Agricultural University,2016,21(2):93-99 (in Chinese)
[5] Qiu Q,Zhang G J,Ma T,Qian W B,Wang J Y,Ye Z Q,Cao C C,Hu Q J,Kim J,Larkin D M,Auvil L,Capitanu B,Ma J,Lewin H A,Qian X J,Lang Y S,Zhou R,Wang L Z,Wang K,Xia J Q,Liao S G,Pan S K,Lu X,Hou H L,Wang Y,Zang X T,Yin Y,Ma H,Zhang J,Wang Z F,Zhang Y M,Zhang D W,Yonezawa T,Hasegawa M,Zhong Y,Liu W B,Zhang Y,Huang Z Y,Zhang S X,Long R J,Yang H M,Wang J,Lenstra J A,Cooper D N,Wu Y,Wang J,Shi P,Wang J,Liu J Q.The yak genome and adaptation to life at high altitude[J].Nature Genetics,2012,44(8):946-949
[6] Qiu Q,Wang L Z,Wang K,Yang Y Z,Ma T,Wang Z F,Zhang X,Ni Z Q,Hou F J,Long R J,Abbott R,Lenstra J,Liu J Q.Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions[J].Nature Communications,2015,6:10283
[7] Wang K,Hu Q J,Ma H,Wang L Z,Yang Y Z,Luo W C,Qiu Q.Genome-wide variation within and between wild and domestic yak[J].Molecular Ecology Resources,2014,14(4):794-801
[8] Zhang X,Wang K,Wang L Z,Yang Y Z,Ni Z Q,Xie X Y,Shao X M,Han J,Wan D S,Qiu Q.Genome-wide patterns of copy number variation in the Chinese yak genome[J].BMC Genomics,2016,17:379
[9] Medugorac I,Graf A,Grohs C,Rothammer S,Zagdsuren Y,Gladyr E,Zinovieva N,Barbieri J,Seichter D,Russ I,Eggen A,Hellenthal G,Brem G,Blum H,Krebs S,Capitan A.Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks[J].Nature Genetics,2017,49(3):470-475
[10] Liang C N,Wang L Z,Wu X Y,Wang K,Ding X Z,Wang M C,Chu M,Xie X Y,Qiu Q,Yan P.Genome-wide association study identifies loci for the polled phenotype in yak[J].PLoS One,2016,11(7):e0158642
[11] Lan D L,Xiong X R,Mipam T D,Fu C X,Li Q,Ai Y,Hou D C,Chai Z X,Zhong J C,Li J.Genetic diversity,molecular phylogeny and selection evidence of Jinchuan yak revealed by whole-genome resequencing[J].G3-Genes/Genomes/Genetics,2018,8(3):945-952
[12] Xie X,Yang Y,Ren Q,Ding X,Bao P,Yan B,Yan X,Han J,Yan P,Qiu Q.Accumulation of deleterious mutations in the domestic yak genome[J].Animal Genetics,2018,49(5):384-392
[13] 宋乔乔.牦牛和普通牛基因组的密码子使用分析[D].成都:西南民族大学.2015Song Q Q.Analysis of the use of codons in yak and cattle genomes[D].Chengdu:Southwest University for Nationalities.2015 (in Chinese)
[14] Ma Z J.Genome-wide characterization of perfect microsatellites in yak (Bos grunniens)[J].Genetica,2015,143(4):515-520
[15] Qi W H,Jiang X M,Du L M,Xiao G S,Hu T Z,Yue B S,Quan Q M.Genome-wide survey and analysis of microsatellite sequences in Bovid species[J].PLoS One,2015,10(7):e0133667
[16] 赵芳芳.牦牛基因组微卫星挖掘与筛选验证[D].绵阳:西南科技大学.2015Zhao F F.Microsatellite mining and screening verification of yak genome[D].Mianyang:Southwest University of Science and Technology.2015 (in Chinese)
[17] Wu D D,Ding X D,Wang S,Wójcik J M,Zhang Y,Tokarska M,Li Y,Wang M S,Faruque O,Nielsen R,Zhang Q,Zhang Y P.Pervasive introgression facilitated domestication and adaptation in the Bos species complex[J].Nature Ecology & Evolution,2018,2(7):1139-1145
[18] 曾贤彬,柴志欣,王永,马志杰,杨琴,宋乔乔,钟金城.犏牛精子发生阻滞的比较转录组研究[J].中国科学:生命科学,2014,44(6):584-601Zeng X B,Cai Z X,Wang Y,Ma Z J,Yang Q,Song Q Q,Zhong J C.Comparative transcriptome analysis of spermatogenesis arrest in cattle-yak[J].Science China:Life Sciences,2014,44(6):584-601 (in Chinese)
[19] Cai X,Yu S M,Mipam T,Yang F,Zhao W S,Liu W J,Cao S Z,Shen L H,Zhao F F,Sun L,Xu C F,Wu S X.Comparative analysis of testis transcriptomes associated with male infertility in cattle-yak[J].Theriogenology,2017,88:28-42
[20] Xu C F,Wu S X,Zhao W S,Mipam T,Liu J B,Liu W J,Yi C P,Shah M A,Yu S M,Cai X.Differentially expressed microRNAs between cattle-yak and yak testis[J].Scientific Reports,2018,8:592
[21] Wang H,Zhong J C,Chai Z X,Zhu J,Xin J W.Comparative expression profile of microRNAs and piRNAs in three ruminant species testes using next-generation sequencing[J].Reproduction in Domestic Animals,2018,53(4):963-970
[22] 兰道亮,熊显荣,位艳丽,徐通,钟金城,字向东,王永,李键.基于RNA-Seq高通量测序技术的牦牛卵巢转录组研究:进一步完善牦牛基因结构及挖掘与繁殖相关新基因[J].中国科学:生命科学,2014,44(3):307-317Lan D L,Xiong X R,Wei Y L,Xu T,Zhong J C,Zi X D,Wang Y,Li J.RNA-Seq analysis of yak ovary:Improving yak gene structure information and mining reproduction-related genes[J].Science China:Life Sciences,2014,44(3):307-317 (in Chinese)
[23] 兰道亮,熊显荣,柴志欣,艾鷖,黄偲,李键.牦牛发情期卵巢比较转录组学研究[J].畜牧兽医学报,2016,47(9):1830-1839Lan D L,Xiong X R,Chai Z X,Ai Y,Huang C,Li J.Comparative transcriptome analysis between yak and cattle estrus ovary[J].Chinese Journal of Animal and Veterinary Sciences,2016,47(9):1830-1839 (in Chinese)
[24] 杨琦玥,陈通,兰道亮,熊显荣,候定超,李键.牦牛肺转录组图谱绘制及特有正选择遗传进化基因探究[J].畜牧兽医学报,2017,48(7):1202-1211Yang Q Y,Chen T,Lan D L,Xiong X R,Hou D C,Li J.Mapping of transcriptome and identification of positively selected genes in lung in yak[J].Chinese Journal of Animal and Veterinary Sciences,2017,48(7):1202-1211 (in Chinese)
[25] Lan D L,Xiong X R,Ji W H,Li J,Mipam T D,Ai Y,Chai Z X.Transcriptome profile and unique genetic evolution of positively selected genes in yak lungs[J].Genetica,2018,146(2):151-160
[26] Tang Q Z,Gu Y R,Zhou X M,Jin L,Guan J Q,Liu R,Li J,Long K R,Tian S L,Che T D,Hu S L,Liang Y,Yang X M,Tao X,Zhong Z J,Wang G S,Chen X H,Li D Y,Ma J D,Wang X,Mai M M,Jiang A N,Luo X L,Lv X,Gladyshev V N,Li X W,Li M Z.Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives[J].GigaScience,2017,6(12):1-9
[27] 刘祥军.镉胁迫下牦牛肝脏组织转录组学及蛋白组学研究[D].西宁:青海大学,2017Liu X J.Study on transcriptome and proteomics of yak liver under cadmium stress[D].Xining:Qinghai University,2017 (in Chinese)
[28] Fan J F,Luo Y Z,Yu S J,Cui Y,Xu G Q,Wang L B,Pan Y Y,He H H.Transcriptional profiling of two different physiological states of the yak mammary gland using RNA sequencing[J].PLoS One,2018,13(7):e0201628 (in Chinese)
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