“红阳”猕猴桃全基因组SSR标记与基因密码子偏性分析

Genome-wide Analysis of SSR Markers and Codon Bias of Actinidia chinensis cv.Hongyang

【目的】为"红阳"猕猴桃种质资源鉴定与分子标记进行辅助育种提供理论基础。【方法】基于红阳猕猴桃全基因组数据,对其进行SSR标记分析以及基因密码子偏性分析。通过生物信息学方法,分别以全基因组及碱基数不小于300 bp的蛋白质编码序列为研究对象,利用GMATA、Codon W和SPSS对红阳猕猴桃进行SSR标记与基因密码子使用偏性分析。【结果】扫描红阳猕猴桃全基因组得到的247012个SSR单元中,二核苷酸重复单元最多,占87.7%;长度为10 bp的SSR占比最高,为33.4%。红阳猕猴桃基因的GC平均含量、GC12含量和GC3含量分别为47.10%、47.6%和45.87%;红阳猕猴桃的密码子使用模式与大肠杆菌和酿酒酵母密码子使用模式差异较大,与毕赤酵母较接近;中性作图表明,GC3s与GC12无明显相关性;ENC作图表明,大部分基因位于曲线周围;红阳猕猴桃28个最优密码子中,除CGA以A结尾外,其他密码子均以C或G结尾,说明红阳猕猴桃最优密码子偏好使用以C/G结尾的密码子。【结论】红阳猕猴桃全基因组具有丰富的SSR位点,可用于高效、快速地进行SSR引物的开发。红阳猕猴桃基因密码子使用模式受压力突变和自然选择等多重因素的影响;选取毕赤酵母作为红阳猕猴桃基因的异源表达宿主较合适。

【Objective】The objective of the paper was to provide the theoretical basis for germplasm identification and marker-assisted selection of the Actinidia chinensis cultivar Hongyang.【Method】SSR markers and codon bias analysis were performed based on the genomic data of Hongyang.The whole genomic sequence and coding sequences larger than 300 bp were analyzed using GMATA,Codon W and SPSS.【Result】Totally 247,012 SSR loci were detected in the Hongyang genome.87.7%of the loci were dinucleotide repeat units,and SSR length of 10 bp had the highest proportion(33.4%).The average content of GC,GC12 and GC3 were 47.10%,47.6%and 45.87%,respectively.The codon usage pattern of Hongyang kiwifruit was quite different from those of Escherichia coli and Saccharomyces cerevisiae,whereas it was similar to that of Pichia pastoris.Besides,the neutrality plot result showed that there was no obvious correlation between GC12 and GC3s,and most genes were located around the curve in the ENC diagram.In addition,among the 28 optimal codons,all of which were ended with C or G excepted that of CGA,suggesting that the Hongyang optimal codons prefer reel to use C or G as the condon end.【Conclusion】The Hongyang genome contained abundant SSR loci,which was beneficial for rapid and efficient development of SSR primers.Otherwise,many factors could influence the usage pattern of codon,like stress mutation and natural selection.In addition,the codon usage pattern of Hongyang kiwi was influenced by multiple factors such as stress mutation and natural selection.Therefore,it was more suitable to select Pichia pastoris as the heterologous expression host for Hongyang kiwifruit genes.