为了解鸡 MyoG 基因的密码子特性，以便于为 MyoG 基因的表达选择合适的外源表达系统，使用在线工具CUSP和CHIPS以及codonW软件对鸡 MyoG 基因进行分析，并与鸡基因、模式动物基因组和其他动物 MyoG 基因进行比较。结果表明，MyoG 基因偏好于G/C结尾的密码子，CDS序列中，GC含量大于AT含量。 MyoG 基因与鸡其他31个基因密码子偏好性相似，均偏好于G/C结尾的密码子。与其他物种基因组密码子偏好性比较结果显示，密码子偏好性与小鼠差异最小，说明小鼠可以作为 MyoG 基因外源表达的宿主。与其他动物 MyoG 基因密码子偏好性比较显示，MyoG 基因在包括京海黄鸡在内的32个物种中均有较高表达，几乎所有 MyoG 基因编码区对GC有较强的偏好性。基于RSCU值的聚类和基于CDS区系统发育树结果显示，亲缘关系近的物种之间倾向于拥有相似的密码子偏好性。
张涛
,
张跟喜
,
韩昆鹏
,
王金玉
,
樊庆灿
,
李婷婷
,
段炼
,
王永娟
. 京海黄鸡MyoG基因密码子特性分析[J]. 华北农学报, 2014
, 29(4)
: 71
-79
.
DOI: 10.7668/hbnxb.2014.04.012
In order to understand the codon characteristics of MyoG gene in chicken and select the appropriate exogenous expression system,online tools CUSP,CHIPS and codonW software were used to analyze MyoG gene. MyoG gene was compared to other genes of chicken,model animal genomes and MyoG gene of other species.Result showed that MyoG of chicken was bias toward the synonymous codons with G and C at the third codon position.GC content was greater than AT content in CDS region. MyoG gene and other thirty-one genes of chicken shared similar codon bias toward the synonymous codons with G and C at the third codon position.Codon bias comparison to other species showed that differences of codon bias between MyoG gene and Mus musculus was the minimum,indicating that Mus musculus could be used as exogenous gene expression host of MyoG gene.Codon bias comparison to the MyoG gene of other species indicated that MyoG gene expressed high in all the thirty-two species,including Jinghai yellow chicken.Almost all the thirty-two MyoG genes were bias toward to GC.Result of clustering based on RSCU value and phylogenetic tree based on CDS region showed that species with close genetic relationship tend to have similar codon bias.
[1] Urrutia A O,Hurst L D.Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans,but this is not evidence for selection[J].Genetics,2001,159(3):1191-1199.
[2] Sueoka N,Kawanishi Y.DNA G+C content of the third codon position and codon usage biases of human genes[J].Gene,2000,261(1):53-62.
[3] 李平,白云凤,冯瑞云,等.籽粒苋苹果酸酶(NAD-ME)基因密码子偏好性分析[J].应用与环境生物学报,2011,17(1):12-17.
[4] Bulmer M.The selection-mutation-drift theory of synonymous codon usage[J].Genetics,1991,129(3):897-907.
[5] 张乐,金龙国,罗玲,等.大豆基因组和转录组的核基因密码子使用偏好性分析[J].作物学报,2011,37(6):965-974.
[6] 吴正常,王靖,赵乔辉,等.猪脂多糖结合蛋白基因(LBP)的密码子偏好性分析[J].农业生物技术学报,2013,21(10):1135-1144.
[7] Wright W E,Sassoon D A,Lin V K.Myogenin,a factor regulating myogenesis,has a domain homologous to Myo D[J].Cell,1989,56(4):607-617.
[8] Rudnicki M A,Jaenisch R.The Myo D family of transcription factors and skeletal MyoGenesis[J].Bioessays,1995,17(3):203-209.
[9] Edmondson,Olson E.Helix-loop-helix proteins as regulators of muscle-specific transcription[J].J Biol Chem,1993,268(2):755-758.
[10] Olson E N,Klein W H.bHLH factors in muscle development:deadlines and commitments,what to leave in and what to leave out[J].Genet Dev,1994,8.pp:1-8.
[11] 高光宇,王杰,王永,等.成都麻羊 MyoG 基因的克隆与测序分析[J].西南民族大学学报:自然科学版,2009,35(1):84-88.
[12] Hasty P,Bradley A,Morris J H,et al.Muscle deficiency and neonatal death in mice with a targeted mutation in the MyoG enin gene[J].Nature,1993,364:501-506.
[13] 郭秀丽,王玉,杨路成,等.茶树 CBF1 基因密码子使用特性分析[J].遗传,2012,34(12):1614-1623.
[14] 刘庆坡,谭军,薛庆中.籼稻品种 93-11 同义密码子的使用偏性[J].遗传学报,2003,30(4):335-340.
[15] 赵耀,刘汉梅,顾勇,等.玉米 waxy 基因密码子偏好性分析[J].玉米科学,2008,16(2):16-21.
[16] Sharp P M,Li W H.An evolutionary perspective on synonymous codon usage in unicellular organisms[J].Journal of Molecular Evolution,1986,24(12):28-38.
[17] 刘汉梅,赵耀,顾勇,等.几种植物 waxy 基因的密码子用法特性分析[J].核农学报,2010,24(3):476-481.
[18] 马晓霞,冯玉萍,赵永清,等.口蹄疫病毒密码子使用偏性的位点差导[J].华北农学报,2013,28(2):32-37.
[19] 晁岳恩,常阳,王美芽,等.7种作物叶绿体基因的密码子偏好性及聚类分析[J].华北农学报,2012,27(4):60-64.
[20] 杨平.水稻HKT基因家族密码子使用特性分析[J].山西农业科学,2011,39(11):1137-1140,1145.
[21] Christianson M L.Codon usage patterns distort phylogenies from or of DNA sequences[J].American Journal of Botany,2005,92(8):1221-1233.
