基于NCBI核酸数据库资源的产黄青霉微卫星序列的筛选

Screening of Microsatellite DNA in Penicillium chrysogenum based on NCBI Nucleic Acid Database Resources

利用生物信息学方法在产黄青霉基因组中筛选微卫星序列,并对其基因组中微卫星数量和丰度进行了研究.利用SSRHunter1.3软件在长度为30 090 464 bp的产黄青霉基因组中共找到163个微卫星序列.其中以两碱基重复类型数目最多,为133个,占重复序列总数目的 81.60%;其次是三碱基重复为29个,占17.79%;最后是四碱基1个,占0.61%.在两碱基重复序列中,AT(44.79%)重复类别最多,其次是AG(23.92%).在三碱基重复序列中,共发现9种重复类别,其中以AAG和ACT重复类型最多,为6个(3.68%),其次是ACC(2.45%),最少的是AGC(0.61%).四碱基重复中,只有1种重复类别,为ATGT(0.61%).同时选取二碱基的重复次数在7以上和三碱基的重复次数在6以上的微卫星序列,利用Primer Premier 5.0软件设计了引物,共得到30对引物.本研究不仅为后续产黄青霉微卫星标记的筛选奠定了基础,也丰富了其基因组学资源,对产黄青霉的种群遗传结构分析、分子标记选育和遗传多样性有重要意义.

Microsatellite sequences in Penicillium ehrysogenum are screened using SSRHunterl. 3 software. One hundred and sixty-three mierosatellites are found in the 30 090 464 bp genome sequence. The numbers and abun- dance of the microsatellites are investigated using bioinformatic method. Among the 163 microsatellites in P. ehry- sogenurn, there are 133 two-base repeats, 29 three-base repeats and one four-base repeats, accounting for 81.60% , 17.79% and 0.61% of the total microsatellites, respectively. Most of the two-base repeat sequences are AT repeats, followed by AG repeats, representing 44.79% and 23.92% of the total two-base repeats, respective- ly. We find nine classes of the three-base repeat sequences, AAG and ACT are the most frequent ones, followed by the ACC and AGC, accounting for 3.68% , 2.45% and 0.61% of the total microsatellites, respectively. Only one four-base repeat sequence, ATGT, is found, which accounts for 0.61% of the total mierosatellites. Meanwhile, thirty PCR primer pairs for two-base repeats occurred over seven times and three-base repeats occurred over six times are designed using Primer Premier 5.0 software. This study provided useful information for microsatellite marker screening, and enriches the genomic database in P. chrysogenum, which is important for genetic structure analysis, molecular marker breeding and genetic diversity analysis.