牦牛DRA基因克隆测序及生物信息学分析

doi:10.3969/j.issn.1004-1524.20212021

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (7): 1564-1570.DOI: 10.3969/j.issn.1004-1524.20212021

牦牛DRA基因克隆测序及生物信息学分析

张丽(), 王媛媛, 王瑞, 刘丽霞()

西北民族大学生命科学与工程学院,甘肃兰州 730030

收稿日期:2021-12-14 出版日期:2023-07-25 发布日期:2023-08-17
作者简介:张丽(1980—),女,宁夏石嘴山人,博士,副教授,主要从事现代生物技术与动物遗传育种研究。E-mail:280082343@xbmu.edu.cn
通讯作者: *刘丽霞,E-mail:skllx@xbmu.edu.cn
基金资助:
西北民族大学中央高校基本科研业务费资金资助项目(31920200074);西北民族大学中央高校基本科研业务费资金资助项目(31920210061);西北民族大学研究生科研创新项目(Yxm2021074)

Cloning sequencing and bioinformatics analysis of DRA gene of yak

ZHANG Li(), WANG Yuanyuan, WANG Rui, LIU Lixia()

College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China

Received:2021-12-14 Online:2023-07-25 Published:2023-08-17
Contact: LIU Lixia

摘要/Abstract

摘要：

为全面解析牦牛MHCⅡ类基因结构与功能,采用分子克隆测序技术对大通牦牛DRA基因编码区进行等位基因频率估算并进行生物信息学分析。结果显示:大通牦牛DRA基因编码区含有762 bp的开放阅读框,共编码253个氨基酸;共有3个SNPs(g.2376C>T、g.2851C>G、g.3016C>A),其中第2、3外显子分别存在1个C→T的同义突变和C→A的错义突变(L→M),这两个突变均降低了大通牦牛DRA基因mRNA二级结构的稳定性;g.3016C>A突变前后编码蛋白质的分子量、原子总数、脂肪系数、不稳定系数、总平均亲水性方面存在差异;生物信息学的方法分析显示,BoLA-DRA基因是MHC基因家族中高度保守的基因。该研究结果可以为大通牦牛DRA基因结构与功能的研究奠定基础。

关键词: DRA基因, 编码区克隆, 突变位点, 生物信息学

Abstract:

In order to comprehensively analyze the structure and function of yak MHCⅡ gene, molecular cloning and sequencing technology was used to estimate the coding region of DRA gene of Datong yak and conduct bioinformatics analysis. The results showed a DRA gene open reading frame in the coding region containing 762 bp, a total of 253 amino acids encoding; a total of 3 SNPs (g.2376C>T, g.2851C>G, g.3016C>A). In exons 2 and 3, there was one synonymous mutation in C→T and a missense mutation (L→M) in C→A, respectively, both mutations reduced the stability of mRNA secondary structure of DRA gene. There were differences in the molecular mass, total number of atoms, fat coefficient, instability coefficient, and total average hydrophilicity of the protein encoded by the g.3016C>A mutation. Methodological analysis by bioinformatics revealed that the BoLA-DRA gene were highly conserved genes in the MHC gene family. The results laid the foundation for the structure and function of DRA in Datong yak.

Key words: DRA gene, coding region cloning, mutation site, bioinformatics

中图分类号:

S823.85

张丽, 王媛媛, 王瑞, 刘丽霞. 牦牛DRA基因克隆测序及生物信息学分析[J]. 浙江农业学报, 2023, 35(7): 1564-1570.

ZHANG Li, WANG Yuanyuan, WANG Rui, LIU Lixia. Cloning sequencing and bioinformatics analysis of DRA gene of yak[J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1564-1570.

图/表 9

参考文献 18

[1]	O‘BRIEN S J, YUHKI N. Comparative genome organization of the major histocompatibility complex: lessons from the Felidae[J]. Immunological Reviews, 1999, 167(1): 133-144.
[2]	ANDERSSON L, BÖHME J, RASK L, et al. Genomic hybridization of bovine class II major histocompatibility genes: 1. Extensive polymorphism of DQα and DQβ genes[J]. Animal Genetics, 1986, 17(4): 95-112.
[3]	NEPOM G T. The major histocompatibility complex[J]. Clinical Immunotherapeutics, 1994, 2(2): 79-83.
[4]	SENA L, SCHNEIDER M P C, BRENIG B, et al. Polymorphisms in MHC-DRA and -DRB alleles of water buffalo (Bubalus bubalis) reveal different features from cattle DR alleles[J]. Animal Genetics, 2003, 34(1): 1-10.
[5]	张丽, 刘丽霞, 李强子, 等. 天祝白牦牛MSTN基因编码区克隆及生物信息学分析[J]. 浙江农业学报, 2017, 29(4): 618-624.
	ZHANG L, LIU L X, LI Q Z, et al. Cloning and bioinformatics analysis of MSTN gene of Tianzhu white yak[J]. Acta Agriculturae Zhejiangensis, 2017, 29(4): 618-624. (in Chinese with English abstract)
[6]	张丽, 刘丽霞, 戴洪伟, 等. 静宁鸡肌肉生长抑制素基因单核苷酸多态性筛查及生物信息学分析[J]. 浙江大学学报(农业与生命科学版), 2018, 44(5): 629-637.
	ZHANG L, LIU L X, DAI H W, et al. Single nucleotide polymorphism screening and bioinformatics analysis of myostatin gene in Jingning chicken[J]. Journal of Zhejiang University(Agriculture & Life Sciences), 2018, 44(5): 629-637. (in Chinese with English abstract)
[7]	张丽, 农伟伦, 卢建雄, 等. 八眉猪FABPs主要家族基因单核苷酸多态性筛查及生物信息学分析[J]. 浙江大学学报(农业与生命科学版), 2019, 45(1): 109-118.
	ZHANG L, NONG W L, LU J X, et al. Single nucleotide polymorphism screening and bioinformatics analysis of the main family genes of FABPs in Bamei pig[J]. Journal of Zhejiang University(Agriculture & Life Sciences), 2019, 45(1): 109-118. (in Chinese with English abstract)
[8]	BECK T W, MENNINGER J, MURPHY W J, et al. The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region[J]. Immunogenetics, 2005, 56(10): 702-709.
[9]	DUKKIPATI V, BLAIR H T, GARRICK D J, et al. ‘Ovar-Mhc’-Ovine major histocompatibility complex: role in genetic resistance to diseases[J]. New Zealand Veterinary Journal, 2006, 54(4): 153-160.
[10]	SHOOK G E. Genetic improvement of mastitis through selection on somatic cell count[J]. Veterinary Clinics of North America: Food Animal Practice, 1993, 9(3): 563-577.
[11]	李彥清, 牛晓亮, 胡江, 等. 牦牛和普通牛BoLA-DRA* Exon2-intron2多态性分析[J]. 华北农学报, 2015, 30(4): 72-77.
	LI Y Q, NIU X L, HU J, et al. Polymorphism of BoLA-DRA*Exon2-intron2 in yak and bovine[J]. Acta Agriculturae Boreali-Sinica, 2015, 30(4): 72-77. (in Chinese with English abstract)
[12]	安添午. 甘肃牦牛DRA、TLR1、TLR2和TLR5-9基因分子生物学特性研究[D]. 兰州: 甘肃农业大学, 2011.
	AN T W. Study on molecular biological characteristics of DRA, TLR1, TLR2 and TLR5-9 genes in Gansu yak[D]. Lanzhou: Gansu Agricultural University, 2011. (in Chinese with English abstract)
[13]	付保强, 虎红红, 刘丽霞. 荷斯坦牛BoLA-DRA基因外显子1生物信息学分析[J]. 现代畜牧兽医, 2018(6): 18-21.
	FU B Q, HU H H, LIU L X. Bioinformatics analysis of BoLA-DRA exon1 gene in Holstein cattle[J]. Modern Journal of Animal Husbandry and Veterinary Medicine, 2018(6): 18-21. (in Chinese with English abstract)
[14]	高树新, 许尚忠, 高雪, 等. 两种兼用型牛BoLA-DRA*exon2多态性及其与乳房炎的关联分析[J]. 华北农学报, 2008, 23(1): 211-213.
	GAO S X, XU S Z, GAO X, et al. Analysis of polymorphisms of BoLA-DRA*exon2 and the relationship between the gene and mastitis in two dual-purpose breed cattle[J]. Acta Agriculturae Boreali-Sinica, 2008, 23(1): 211-213. (in Chinese with English abstract)
[15]	蒲兰屏, 席冬梅, 樊月园, 等. 犏牛主要组织相容性复合物DRA基因(MHC-ClassⅡ-DRA)的分子特征分析[J]. 中国畜牧兽医, 2012, 39(9): 12-17.
	PU L P, XI D M, FAN Y Y, et al. Analysis of the molecular characteristics of Chinese yakow major histocompatibility complex DRA gene (MHC-ClassⅡ-DRA)[J]. China Animal Husbandry & Veterinary Medicine, 2012, 39(9): 12-17. (in Chinese with English abstract)
[16]	SWATHI K, PRAKASH M G, SAKARAM D, et al. Molecular characterization of MHC class II DRA cDNA in Deoni cattle[J]. Indian Journal of Animal Research, 2018, DOI:10.18805/ijar.B-3592.
[17]	SAKARAM D, NIRANJAN S K, KUMAR S, et al. cDNA characterization and molecular analysis of buffalo MHC class II gene, DRA(Bubu-DRA)[J]. Journal of Applied Animal Research, 2010, 37(1): 73-76.
[18]	刘丽霞, 张丽, 田晓静, 等. 猪SLA-DRA基因SNP位点筛选及其生物信息学分析[J]. 浙江农业学报, 2017, 29(7): 1077-1085.
	LIU L X, ZHANG L, TIAN X J, et al. SNP screening and bioinformatics analysis of SLA-DRA gene in pigs[J]. Acta Agriculturae Zhejiangensis, 2017, 29(7): 1077-1085. (in Chinese with English abstract)

编辑推荐

Metrics

阅读次数

全文

486

HTML			PDF

最新录用	在线预览	正式出版	最新录用	在线预览	正式出版
0	0	5	0	0	481

来源	本网站	其他网站

次数	309	177
比例	64%	36%

摘要

326

最新录用	在线预览	正式出版

0	0	326

	来源	本网站

	次数	326
	比例	100%

位置 Location	引物序列 Primer sequence(5'→3')	退火温度 Annealing temperature/℃	片段长度 Fragment length/bp
外显子1 Exon1(1~93 bp) 外显子2 Exon2(263~508 bp)	F:CACCAAAGAAGTGGCC R:CCACAGTTCATTTCTCCGAAGC F:CCTGACCCCCTTTCTTGTCT R:AGGAGGACTGGAGCAGAGGT	57.3 58.5	93 246
外显子3 Exon3(938~1 219 bp)	F:GTCAGCCTCGATGGGACGAA R:CTCACCCCAGTGCTTGAGAA	63.0	282
外显子4 Exon4(1 510~1 664 bp)	F:GTGCTAAGCTGCTCCCTA R:TCCTCTGACCACAGCAGACTC	61.2	155

位置 Location	引物序列 Primer sequence(5'→3')	退火温度 Annealing temperature/℃	片段长度 Fragment length/bp
外显子1 Exon1(1~93 bp) 外显子2 Exon2(263~508 bp)	F:CACCAAAGAAGTGGCC R:CCACAGTTCATTTCTCCGAAGC F:CCTGACCCCCTTTCTTGTCT R:AGGAGGACTGGAGCAGAGGT	57.3 58.5	93 246
外显子3 Exon3(938~1 219 bp)	F:GTCAGCCTCGATGGGACGAA R:CTCACCCCAGTGCTTGAGAA	63.0	282
外显子4 Exon4(1 510~1 664 bp)	F:GTGCTAAGCTGCTCCCTA R:TCCTCTGACCACAGCAGACTC	61.2	155

蛋白质理化特性 Physicochemical properties of proteins	突变类型Mutation type
蛋白质理化特性 Physicochemical properties of proteins	突变前Before mutation	突变后After mutation
分子量Molecular weight/u	28 407.01	28 425.04
原子总数Total number of atoms	4 035	4 033
消光系数Extinction coefficients	28 085/27 960	28 085/27 960
等电点Theoretical pI	5.41	5.41
分子式Formula	C₁₃₀₅H₂₀₃₀N₃₃₀O₃₆₁S₉	C₁₃₀₄H₂₀₂₈N₃₃₀O₃₆₁S₁₀
不稳定系数The instability index (Ⅱ)	38.81	39.78
脂肪系数Aliphatic index	100.16	98.62
总平均亲水性Grand average of hydropathicity (GRAVY)	0.056	0.049
半衰期Estimated half-life/h	30	30
正电荷残基数Total number of negatively charged residues (Asp+Glu)	31	31
负电荷残基数Total number of positively charged residues (Arg+Lys)	23	23

蛋白质理化特性 Physicochemical properties of proteins	突变类型Mutation type
蛋白质理化特性 Physicochemical properties of proteins	突变前Before mutation	突变后After mutation
分子量Molecular weight/u	28 407.01	28 425.04
原子总数Total number of atoms	4 035	4 033
消光系数Extinction coefficients	28 085/27 960	28 085/27 960
等电点Theoretical pI	5.41	5.41
分子式Formula	C₁₃₀₅H₂₀₃₀N₃₃₀O₃₆₁S₉	C₁₃₀₄H₂₀₂₈N₃₃₀O₃₆₁S₁₀
不稳定系数The instability index (Ⅱ)	38.81	39.78
脂肪系数Aliphatic index	100.16	98.62
总平均亲水性Grand average of hydropathicity (GRAVY)	0.056	0.049
半衰期Estimated half-life/h	30	30
正电荷残基数Total number of negatively charged residues (Asp+Glu)	31	31
负电荷残基数Total number of positively charged residues (Arg+Lys)	23	23

突变位点 Mutant site	突变位置 Mutant location	突变类型 Mutation type	氨基酸变化 Amino acid variation	等位基因频率Allele frequency
突变位点 Mutant site	突变位置 Mutant location	突变类型 Mutation type	氨基酸变化 Amino acid variation	突变前Before mutation	突变后After mutation
g.2376C>T	Exon2	同义突变	—	0.156 2	0.843 8
		Synonymous mutation
g.2851C>G	Intron2	—	—	0.343 7	0.656 3
g.3016C>A	Exon3	错义突变	L→M	0.333 3	0.666 7
		Missense mutation

牦牛DRA基因克隆测序及生物信息学分析

Cloning sequencing and bioinformatics analysis of DRA gene of yak

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 9

参考文献 18

相关文章 15

编辑推荐

Metrics

本文评价

突变类型 Mutation type	α螺旋 α-Helix	β转角 β-Turn	β折叠 β-Sheet	无规则卷曲 Random coil
突变前Before mutation	18.58(47)	6.72(17)	38.58(49)	44.66(113)
突变后After mutation	18.58(47)	6.72(17)	30.04(76)	47.43(120)

[1]	庞雪晴, 唐诗, 曾红梅, 赵位, 王印, 罗燕, 姚学萍, 任梅渗, 任永军, 杨泽晓. 两株GI.1型和GI.2型兔出血症病毒RdRp基因的克隆与分析[J]. 浙江农业学报, 2023, 35(6): 1286-1296.
[2]	张新业, 李文静, 朱姝, 孙艳香, 王聪艳, 闫训友, 周志国. 三种伞形科蔬菜作物棕榈酰基转移酶基因家族的鉴定与分析[J]. 浙江农业学报, 2023, 35(6): 1315-1327.
[3]	宋雅萍, 雷召雄, 赵毅昂, 姜超, 王兴平, 罗仍卓么, 马云, 魏大为. 牛FoxO1基因CDS区克隆及其在脂肪细胞分化过程中的表达分析[J]. 浙江农业学报, 2023, 35(5): 1016-1027.
[4]	燕存尧, 贾凯, 闫会转, 高杰. 芜菁BrrLOX7基因克隆、表达及生物信息学分析[J]. 浙江农业学报, 2023, 35(4): 831-840.
[5]	韩雪杨, 刘宁, 温鑫, 魏继承, 任如意, 郝爱平. 植物发育相关miR828基因家族靶基因预测及生物信息学分析[J]. 浙江农业学报, 2023, 35(3): 515-522.
[6]	季美君, 曹孜怡, 王翌婷, 陆静茹, 汪保华. 陆地棉NCS1基因家族的全基因组成员鉴定及分析[J]. 浙江农业学报, 2023, 35(2): 249-258.
[7]	梁成刚, 汪燕, 关志秀, 韦春玉, 邓娇, 黄娟, 孟子烨, 石桃雄. 苦荞蔗糖转运体家族FtSUCs的鉴定与生物信息学分析[J]. 浙江农业学报, 2022, 34(8): 1591-1598.
[8]	向淅, 王思悦, 蒲俊宏, 唐雯璐, 陈清. 低温短日照诱导五叶草莓成花诱导的机理研究[J]. 浙江农业学报, 2022, 34(8): 1661-1668.
[9]	楚志刚, 田云芳. 蕙兰一个PEBP家族基因的克隆及生物信息学分析[J]. 浙江农业学报, 2022, 34(8): 1679-1691.
[10]	刘鹏程, 张继, 邱淦远, 龚俞, 李雪松, 李维, 张依裕, 刘若余. 关岭牛TBC1D7基因单核苷酸多态性筛查及生物信息学分析[J]. 浙江农业学报, 2022, 34(7): 1402-1411.
[11]	李文辰, 刘鑫, 齐泽铮, 于璐, 王芳. 灰皮支黑豆GmPUB24基因的生物信息学与胞囊线虫诱导表达分析[J]. 浙江农业学报, 2022, 34(6): 1124-1132.
[12]	刘凯, 谢楠, 郭炜, 马恒甲. 三角鲂MHCⅠα基因全长cDNA克隆与生物信息学分析[J]. 浙江农业学报, 2022, 34(6): 1162-1174.
[13]	夏煜琪, 孙宇, 刘志鑫, 孙瑞青, 杨楠, 蒲金基, 张贺. 杧果转录因子BES1s家族全基因组鉴定及生物信息学分析[J]. 浙江农业学报, 2022, 34(5): 984-994.
[14]	樊有存, 张红岩, 杨旭升, 韩芊, 刘玉皎, 武学霞. 蚕豆耐盐相关基因VfHKT1;1的克隆、生物信息学分析及表达特性[J]. 浙江农业学报, 2022, 34(4): 756-765.
[15]	李小兰, 张瑞, 郝兰兰, 王鸿. 桃NAC家族基因生物信息学分析及其响应低温胁迫的表达特征[J]. 浙江农业学报, 2022, 34(4): 766-780.