普通野生稻线粒体蛋白质编码基因密码子使用偏好性的分析

以普通野生稻(Oryza rufipogon Griff.)线粒体基因组为对象,分析其蛋白质编码基因的密码子使用特征及与亚洲栽培稻(O. sativa L.)的差异,探讨其密码子偏性形成的影响因素和进化过程。结果显示:普通野生稻线粒体基因组编码序列第1、第2和第3位碱基的GC含量依次为49.18%、42.67%和40.86%;有效密码子数(Nc)分布于45.32～61.00之间,其密码子偏性较弱; Nc值仅与GC_3呈显著相关,密码子第3位的碱基组成对密码子偏性影响较大;第1向量轴上显示9.91%的差异,其与GC_3s、Nc、密码子偏好指数(CBI)和最优密码子使用频率(Fop)的相关性均达到显著水平;而GC_3和GC₁₂的相关性未达到显著水平。因此,普通野生稻线粒体基因组密码子的使用偏性主要受自然选择压力影响而形成。本研究确定了21个普通野生稻线粒体基因组的最优密码子,大多以A或T结尾,与叶绿体密码子具有趋同进化,但是与核基因组具有不同的偏好性。同义密码子相对使用度(RSCU)、PR2偏倚分析和中性绘图分析显示,普通野生稻线粒体基因功能和其密码子使用密切相关,且线粒体密码子使用在普通野生稻、粳稻(O. sativa L. subsp. japonica Kato)和籼稻(O. sativa L. subsp.indica Kato)内具有同质性。     

紫花苜蓿叶绿体基因组密码子偏好性分析

为分析紫花苜蓿叶绿体基因组密码子偏好性的使用模式,该文以紫花苜蓿叶绿体基因组中筛选到的49条蛋白质编码序列为研究对象,利用CodonW、CUSP、CHIPS、SPSS等软件对其密码子的使用模式和偏好性进行研究。结果表明:(1)紫花苜蓿叶绿体基因的第3位密码子的平均GC含量为26.44%,有效密码子数(ENC)在40.6～51.41之间,多数密码子的偏好性较弱。(2)相对同义密码子使用度(RSCU)分析发现,RSCU>1 的密码子数目有30个,以A、U结尾的有29个,说明了紫花苜蓿叶绿体基因组A或U出现的频率较高。(3)中性分析发现,GC3与 GC12的相关性不显著,表明密码子偏性主要受自然选择的影响; ENC-plot 分析发现一部分基因落在曲线的下方及周围,表明突变也影响了部分密码子偏性的形成。此外,有17个密码子被鉴定为紫花苜蓿叶绿体基因组的最优密码子。紫花苜蓿叶绿体基因组的密码子偏好性可能受自然选择和突变的共同作用。该研究将为紫花苜蓿叶绿体基因工程的开展和目标性状的遗传改良奠定基础。     

滇楸叶绿体基因组密码子偏好性分析

为分析滇楸(Catalpa fargesii)叶绿体基因组密码子的使用模式,本研究以滇楸叶绿体基因组密码子为研究对象,筛选出了38条蛋白编码序列,并利用CodonW和CUSP在线软件对其进行了中性绘图分析、ENC-plot和PR2-plot分析。结果表明：滇楸叶绿体基因组密码子平均GC含量为39.03%,不同位置上的GC含量依次是GC₁(47.51%)>GC₂ (40.80%)>GC₃(28.78%),说明叶绿体基因组密码子末位碱基偏好以A和U结尾;其有效密码子数(effective number of codons, ENC)的范围为34.93～55.78,平均值为46.61,有25个ENC值大于45,表明其密码子的偏好性较弱;同义密码子相对使用度(relative synonymous codon usage, RSCU)分析表明,RSCU>1的密码子中有30个以A或U作为结尾,说明其密码子偏好以A和U结尾;中性绘图分析显示,GC₁₂和GC₃的相关性不显著...     

思茅松叶绿体基因组密码子偏好性分析

密码子偏好性(codon usage bias)是指同义密码子的使用频率不同的现象,该现象广泛存在于植物中.本研究利用Codon W 1.4.2和CUSP软件分析思茅松(Pinus kesiya var.langbianensis)叶绿体基因组的45条CDS,结果显示思茅松叶绿体基因组密码子第三位碱基的GC含量为29.63％,偏好以AT碱基结尾;ENC值在37.66～60.30之间,且ENC值＞45的CDS有37个,占总参试基因的82.22％;GC1、GC2、GC3与GCall均为极显著相关,GC3与ENC呈显著相关.中性绘图分析显示GC12和GC3的相关系数为-0.1114,回归系数为-0.1111;ENC-plot软件分析显示大部分基因与标准曲线的距离较远;PR2-plot软件分析显示思茅松叶绿体基因组在密码子的碱基使用频率方面,T＞A,G＞C.这些说明思茅松叶绿体基因密码子偏好性的主要影响因素为选择,突变的作用较小.本研究为思茅松种源选择、系统发育等研究提供科学依据.     

栽培大豆和野生大豆线粒体基因组密码子使用偏性的比较分析

为分析栽培大豆和野生大豆线粒体基因组的密码子使用特征差异,该文以其线粒体基因组编码序列为研究对象,比较其密码子偏性形成的影响因素和演化过程。结果表明:(1)栽培大豆和野生大豆线粒体基因组编码区的GC含量分别为44.56%和44.58%,说明栽培大豆和野生大豆线粒体编码基因均富含A/T碱基。(2)栽培大豆和野生大豆线粒体基因组密码子第1位、第2位GC含量平均值与第3位GC含量的相关性均呈极显著水平,说明突变在其密码子偏性形成中的作用不可忽略; PR2-plot分析显示,在同义密码子第3位碱基的使用频率上,嘌呤低于嘧啶; Nc-plot分析中Nc比值位于-0.1～0.2区间的基因数占总基因数的95%以上;突变和选择等多重因素共同作用影响了大豆线粒体基因组编码序列密码子使用偏性的形成。(3)有20、21个密码子分别被确定为栽培大豆和野生大豆线粒体基因组编码序列的最优密码子,其中除丝氨酸TCC密码子外均以A或T结尾。综上结果认为,栽培大豆线粒体密码子偏性的形成受选择的影响要高于野生大豆,这可能是栽培大豆由野生大豆经长期人工栽培驯化的结果。     

糜子叶绿体基因组密码子使用偏性的分析

密码子使用偏性（CUB）是生物体重要的进化特征,对研究物种进化、基因功能以及外源基因表达等具有重要科学意义。本研究利用糜子（Panicum miliaceum L.）叶绿体基因组中筛选出的53条蛋白编码序列,对其密码子使用模式及偏性进行了分析。结果表明,糜子叶绿体基因的有效密码子数（ENC）在37.14~61之间,多数密码子的偏性较弱。相对同义密码子使用度（RSCU）分析发现,RSCU > 1的密码子有32个,其中28个以A、U结尾,表明第3位密码子偏好使用A和U碱基。中性分析发现,GC₃与GC₁₂的相关性不显著,回归曲线斜率为0.2129,表明密码子偏性主要受到自然选择的影响;而ENC-plot分析发现大部分基因落在曲线的上方及周围,表明突变也影响了密码子偏性的形成。进一步的对应性分析发现,第1轴为主要影响因素,解释了17.92%的差异,其与ENC、GC_3S值的相关性均达到显著水平,但与CBI、GC_all不相关。最后,9个密码子被鉴定为糜子叶绿体基因组的最优密码子,糜子叶绿体基因组的密码子使用偏性可能受选择和突变共同作用。     

流感病毒基因的密码子偏好性及聚类分析

流行性感冒病毒是一种造成人类及动物患流行性感冒的RNA病毒,它造成急性上呼吸道感染,并由空气迅速传播,在世界各地常有周期性的大流行。根据该病毒的基因组CDS序列,探讨了基因组序列密码子的使用模式和特性,并进行了病毒间的聚类分析。结果表明:流感病毒的G+C含量均低于A+U含量,偏向使用以A、U结尾的密码子的程度比使用以G、C结尾的较高,CUG、UCA、AGU、AGC、AGA、AGG、GUG、CCA、ACA、GGA、GCA、AUU、UGA、CAU、CAA、AAU、AAA、GAA等18个密码子为流感病毒共有的偏好性密码子,且以A结尾的居多,尤其偏爱AGA、GGA。聚类结果表明首先亚洲流感病毒H2N2和香港流感病毒H2N2聚为一类,亚洲流感病毒H1N1和俄罗斯流感病毒H1N1聚为一类,1997年和2003年~2004年发生的人禽流感聚为一类,说明它们的密码子使用的偏好性相似;而2009年爆发的甲型H1N1流感和任何一个流感的距离都比较远,说明甲型H1N1流感病毒是一种新型的病毒,不同于以往任何一种流感病毒。     

降香黄檀叶绿体基因组密码子偏好性分析

为了解降香黄檀叶绿体基因组密码子使用模式,该文利用Codon W 1.4.2和在线软件CUSP对降香黄檀叶绿体基因组中的52条基因编码序列密码子进行中性绘图、ENC-plot和PR2-plot分析.结果表明:降香黄檀叶绿体基因组密码子的3个位置上GC含量依次为GC1(46.01％)>GC2(38.98％)>GC3(27...     

甘蔗属种及其近缘属种蔗茅的全基因组密码子偏好性分析

【目的】为解析甘蔗基因组的密码子使用特征,提高异源基因在甘蔗中的表达效率。【方法】以已发布的甘蔗属种（热带种LA-purple、割手密NP-X和AP85-441）及其近缘属种蔗茅（Yunnan2009-3）基因组为数据,利用Python、CodonW1.4.2进行密码子偏好性分析,同时通过中性绘图、ENC-plot、PR2-plot等分析探讨密码子偏好性形成的影响因素,并结合转录组测序数据分析密码子偏好性参数与基因表达水平的相关性。最后,基于RSCU均值与7个主要模式生物种（玉米、高粱、水稻、拟南芥、烟草、大肠杆菌、酿酒酵母）的密码子使用模式进行比较分析。【结果】显示热带种、割手密和蔗茅的基因组都富含GC,平均GC含量为56.3%,且GC3>GC1>GC2,倾向于使用以G/C结尾的密码子,平均ENC值为48.45,偏好性较低。中性绘图、ENC-plot和PR2-plot分析表明它们的密码子偏好性受到自然选择、突变压力等多种因素的共同影响,其中自然选择占主导作用。相关性分析表明密码子偏好性参数与基因实际的转录表达水平存在显著相关性,但相关性不强。根据RSCU和?RSCU值,确...     

草菇密码子偏好性分析

以草菇全基因组编码序列为研究对象,利用软件CodonW1.4.2分析草菇基因组密码子使用模式,确定了草菇的24个最优密码子。利用Create a condon usage table(CUSP)程序分析计算草菇密码子使用频率,并将它与人、酵母、拟南芥、小鼠、斑马鱼、果蝇6个代表性物种及灰盖鬼伞、双孢蘑菇、香菇、平菇4个食用菌进行比较。结果显示草菇密码子偏好性与人、酵母、拟南芥、小鼠、斑马鱼、果蝇和平菇都有较大的差异,与灰盖鬼伞、双孢蘑菇、香菇的密码子偏好性差异较小。利用软件SPSS16.0聚类分析表明密码子偏好性差异大小在一定程度上反映物种间的进化关系,可作为研究物种进化关系的参考。首次以食用菌全基因组为分析对象,解析草菇的密码子偏好性,并将其与其他生物进行比较,这些将为不同来源的外源基因在草菇中的异源表达提供重要参考。     

Trends in the codon usage patterns of Chromohalobacter salexigens genes

Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes are separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. Both NC plot and correspondence analysis on Relative Synonymous Codon Usage (RSCU) indicates that the variation in codon usage among the genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. Gene length and the hydrophobicity of the encoded protein also influence the codon usage variation of genes to some extent. A comparison of the relative synonymous codon usage between 10% each of highly and lowly expressed genes determines 23 optimal codons, which are statistically over represented in the former group of genes and may provide useful information for salt-stressed gene prediction and gene-transformation. Furthermore, genes for regulatory functions; mobile and extrachromosomal element functions; and cell envelope are observed to be highly expressed. The study could provide insight into the gene expression response of halophilic bacteria and facilitate establishment of effective strategies to develop salt-tolerant crops of agronomic value.     

A cross talk between codon usage bias in human oncogenes

Background: Oncogenes are the genes that have the potential to induce cancer. The extent and origin of codon usage bias is an important indicator of the forces shaping genome evolution in living organisms. Results: We observed moderate correlations between gene expression as measured by CAI and GC content at any codon site. The findings of our results showed that there is a significant positive correlation (Spearman''s r= 0.45, P<0.01) between GC content at first and second codon position with that of third codon position. Further, striking negative correlation (r = -0.771, P < 0.01) between ENC with the GC3s values of each gene and positive correlation (r=0.644, P<0.01) in between CAI and ENC was also observed. Conclusions: The mutation pressure is the major determining factor in shaping the codon usage pattern of oncogenes rather than natural selection since its effects are present at all codon positions. The results revealed that codon usage bias determines the level of oncogene expression in human. Highly expressed oncogenes had rich GC contents with high degree of codon usage bias.     

Analysis of synonymous codon usage bias in Chlamydia

Chlamydiae are obligate intracellular bacterial pathogens that cause ocular and sexuallytransmitted diseases,and are associated with cardiovascular diseases.The analysis of codon usage mayimprove our understanding of the evolution and pathogenesis of Chlamydia and allow reengineering of targetgenes to improve their expression for gene therapy.Here,we analyzed the codon usage of C.muridarum,C.trachomatis(here indicating biovar trachoma and LGV),C.pneumoniae,and C.psittaci using the codonusage database and the CUSP(Create a codon usage table)program of EMBOSS(The European MolecularBiology Open Software Suite).The results show that the four genomes have similar codon usage patterns,with a strong bias towards the codons with A and T at the third codon position.Compared with Homosapiens,the four chlamydial species show discordant seven or eight preferred codons.The ENC(effectivenumber of codons used in a gene)-plot reveals that the genetic heterogeneity in Chlamydia is constrained bythe G+C content,while translational selection and gene length exert relatively weaker influences.Moreover,mutational pressure appears to be the major determinant of the codon usage variation among the chlamydialgenes.In addition,we compared the codon preferences of C.trachomatis with those of E.coli,yeast,adenovirus and Homo sapiens.There are 23 codons showing distinct usage differences between C.trachomatisand E.coli,24 between C.trachomatis and adenovirus,21 between C.trachomatis and Homo sapiens,butonly six codons between C.trachomatis and yeast.Therefore,the yeast system may be more suitable for theexpression of chlamydial genes.Finally,we compared the codon preferences of C.trachomatis with those ofsix eukaryotes,eight prokaryotes and 23 viruses.There is a strong positive correlation between the differ-ences in coding GC content and the variations in codon bias(r=0.905,P<0,001).We conclude that thevariation of codon bias between C.trachomatis and other organisms is much less influenced by phylogeneticlineage and primarily determined by the extent of disparities in GC content.     

Comparative genome analysis of six malarial parasites using codon usage bias based tools

Codon usage bias (CUB) is an omnipresent phenomenon, which occurs in nearly all organisms. Previous studies of codon bias in Plasmodium species were based on a limited dataset. This study uses whole genome datasets for comparative genome analysis of six Plasmodium species using CUB and other related methods for the first time. Codon usage bias, compositional variation in translated amino acid frequency, effective number of codons and optimal codons are analyzed for P.falciparum, P.vivax, P.knowlesi, P.berghei, P.chabaudii and P.yoelli. A plot of effective number of codons versus GC3 shows their differential codon usage pattern arises due to a combination of mutational and translational selection pressure. The increased relative usage of adenine and thymine ending optimal codons in highly expressed genes of P.falciparum is the result of higher composition biased pressure, and usage of guanine and cytosine bases at third codon position can be explained by translational selection pressure acting on them. While higher usage of adenine and thymine bases at third codon position in optimal codons of P.vivax highlights the role of translational selection pressure apart from composition biased mutation pressure in shaping their codon usage pattern. The frequency of those amino acids that are encoded by AT ending codons are significantly high in P.falciparum due to action of high composition biased mutational pressure compared with other Plasmodium species. The CUB variation in the three rodent parasites, P.berghei, P.chabaudii and P.yoelli is strikingly similar to that of P.falciparum. The simian and human malarial parasite, P.knowlesi shows a variation in codon usage bias similar to P.vivax but on closer study there are differences confirmed by the method of Principal Component Analysis (PCA).

Abbreviations

CDS - Coding sequences, GC1 - GC composition at first site of codon, GC2 - GC composition at second site of codon, GC3 - GC composition at third site of codon, Ala - Alanine, Arg - Arginine, Asn - Asparagine, Asp - Aspartic acid, Cys - Cysteine, Gln - Glutamine Glu - Glutamic acid Gly - Glycine His - Histidine Ile - Isoleucine Leu - Leucine Lys - Lysine Met - Methionine Phe - Phenylalanine Pro - Proline Ser - Serine Thr - Threonine Trp - Tryptophan Tyr - Tyrosine Val - Valine.     

圆红冬孢酵母的密码子用法分析

运用CodonW等软件,分析了圆红冬孢酵母Rhodosporidium toruloides基因组中191个蛋白质编码基因的密码子使用模式,包括密码子3个位置上的GC含量、有效密码子数和密码子使用频率。圆红冬孢酵母有效密码子数ENc值为38.9,密码子GC含量为63%,密码子第三位GC含量为78.3%,且偏好使用G或C结尾的密码子,确定了圆红冬孢酵母R. toruloides的21个高表达优越密码子。研究发现,圆红冬孢酵母与毕赤酵母、酿酒酵母、大肠杆菌和拟南芥在密码子使用频率上有较大差异,而与解脂耶氏酵母和果蝇差异相对较小。研究结果对提高外源基因在圆红冬孢酵母中表达效率及相关代谢工程和合成生物学研究有一定意义。     

云南及周边普通野生稻遗传多样性及其分布特征研究

利用27对SSR标记对云南普通野生稻的2个自然群体进行遗传多样性和起源进化分析,结果发现我国其他省份的材料与东南亚材料的遗传多样性较高,云南元江材料的遗传多样性最低。亲缘关系分析结果表明,云南元江材料与我国其他省份的普通野生稻之间关系较近,云南景洪普通野生稻与缅甸的普通野生稻关系最近,且云南元江和景洪的普通野生稻的遗传结构之间存在明显差异,说明云南普通野生稻属于中国与东南亚普通野生稻的过渡类型,为水稻起源地的"印度阿萨姆——中国云南"学说提供了科学依据。     

Analysis of synonymous codon usage bias in 09H1N1

A novel subtype of influenza A virus 09H1N1 has rapidly spread across the world. Evolutionary analyses of this virus have revealed that 09H1N1 is a triple reassortant of segments from swine, avian and human influenza viruses. In this study, we investigated factors shaping the codon usage bias of 09H1N1 and carried out cluster analysis of 60 strains of influenza A virus from different subtypes based on their codon usage bias. We discovered that more preferentially used codons of 09H1N1 are A-ended or U-ended, and the intra-genomic codon usage bias of 09H1N1 is quite low. Base composition constraint, dinucleotide biases and translational selection are the main factors influencing the codon usage bias of 09H1N1. At the genome level, we find that the codon usage bias of 09H1N1 is similar to H1N1 (A/swine/Kansas/77778/2007H1N1), H9N2 from Asia, H1N2 from Asia and North America and H3N2 from North America. Our results provide insight for understanding the processes governing evolution, regulation of gene expression, and revealing the evolution of 09H1N1.