An Improved Method for Large Size DNA Recovery Facilitates Fosmid Library Preparation

doi:10.13560/j.cnki.biotech.bull.1985.2019-0935

Abstract

Abstract: The Fosmid library with inserted DNA of around 40 kb has been widely used in genomics research. However,the traditional method of agarose gel separation and electroelution into dialysis bag has long been used for large DNA fragment isolation,which makes it difficult to obtain sufficient amount of DNA fragments for ligation,thus dramatically reduces the success rate in Fosmid library preparation. In this study,a simple,convenient and efficient method for 40 kb DNA fragments recovery was established exploiting a modified program on SageELF,a fully automated nucleic acid / protein recovery system. The method was used to prepare Fosmid libraries with improved quality successfully. Through Sanger sequencing and restriction fragment analysis of 25 random selected Fosmid clones,we found the size of the inserted DNA was 37.9 ± 5.2 kb. These results showed that,our improved method could recover 40 kb DNA accurately,simply and efficiently;In addition,the inserts of the Fosmid library constructed with the recovered 40 kb DNA were more concentrated,which will facilitate the following genomics analysis.

Key words: fosmid library, large size DNA recovery, dialysis bag

ZHANG Cui-cui, ZHAO Sheng, WANG Yue, ZHANG Peng, CHANG Yu-xiao. An Improved Method for Large Size DNA Recovery Facilitates Fosmid Library Preparation[J]. Biotechnology Bulletin, 2020, 36(7): 220-227.

References

[1] Dai Z, Li T, Li J, et al.High-throughput long paired-end sequencing of a Fosmid library by PacBio[J]. Plant Methods, 2019, 15:142.
[2] 丁小维, 田文婷, 张波, 等. 盐湖微生物Fosmid文库纤维素酶克隆的筛选及产酶研究[J]. 陕西理工学院学报:自然科学版, 2016, 32:59-63.
[3] 董亮, 俞勤丽, 董志扬, 等. 沤麻废水处理池微生物多样性分析及其Fosmid文库酶活初步筛选[J]. 食品工业科技, 2015, 36:167-172.
[4] 窦怀乾, 李仰平, 吕佳, 等. 基于WGP物理作图法的虾夷扇贝Fosmid克隆混池策略及解码率研究[J]. 中国海洋大学学报:自然科学版, 2019, 49:44-51.
[5] 华金玲, 施其成, 郁冯艳, 等. 黄淮白山羊瘤胃微生物Fosmid文库的构建与分析[J]. 东北农业大学学报, 2019, 50:52-58.
[6] 李昂, 吴志明, 周志林, 等. 甘薯近缘种Ipomoea trifida(Kunth)G. Don基因组Fosmid文库构建及PCR筛选体系建立[J]. 华北农学报, 2014, 29:45-50.
[7] 李昂, 张安, 唐君, 等. Fosmid基因组文库构建及应用现状[J]. 江苏农业科学, 2013, 41:28-30.
[8] 李碧凤, 朱雅新, 苟潇, 等. 云南大额牛瘤胃宏基因组Fosmid文库的构建与分析[J]. 中国畜牧兽医, 2013, 40:61-65.
[9] 苏俊, 律娜, 朱宝利, 等. 版纳微型猪近交系清瘦亚系和肥胖亚系猪Fosmid基因组文库的构建[J]. 农业生物技术学报, 2017, 25:2052-2057.
[10] 吴晓军, 徐丽, 王守才, 等. 玉米基因组Fosmid文库构建及类受体激酶基因(Psy1和Psy2)筛选[J]. 农业生物技术学报, 2014, 22:1306-1313.
[11] 薛鹏飞, 柳鹏福, 史吉平, 等. 盐单胞菌Fosmid文库构建及群体感应淬灭酶的筛选[J]. 江苏农业科学, 2016, 44:88-91.
[12] Liu C, Liu X, Lei L, et al.Fosmid library construction and screening for the maize mutant gene Vestigial glume 1[J]. The Crop Journal, 2016, 4:55-60.
[13] Preston CM, Wu KY, Molinski TF, et al.A psychrophilic crenarchaeon inhabits a marine sponge:Cenarchaeum symbiosum gen. nov. , sp. nov[J]. PNAS, 1996, 93:6241-6246.
[14] Fitz-Gibbon S, Choi AJ, Miller JH, et al.A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum[J]. Extremophiles, 1997, 1:36-51.
[15] Deckert G, Warren PV, Gaasterland T, et al.The complete genome of the hyperthermophilic bacterium Aquifex aeolicus[J]. Nature, 1998, 392:353-358.
[16] Cui Y, Brugiere N, Jackman L, et al.Structural and transcriptional comparative analysis of the S locus regions in two self-incompatible Brassica napus lines[J]. Plant Cell, 1999, 11:2217-2231.
[17] Bovee D, Zhou Y, Haugen E, et al.Closing gaps in the human genome with fosmid resources generated from multiple individuals[J]. Nature Genetics, 2008, 40:96-101.
[18] Du H, Yu Y, Ma Y, et al.Sequencing and de novo assembly of a near complete indica rice genome[J]. Nature Communications, 2017, 8:15324.
[19] Zhao Y, Huang J, Wang Z, et al.Allelic diversity in an NLR gene BPH9 enables rice to combat planthopper variation[J]. PNAS, 2016, 113:12850-12855.
[20] Zhang CZ, Huang L, Zhang HF, et al.An ancestral NB-LRR with duplicated 3'UTRs confers stripe rust resistance in wheat and barley[J]. Nature Communication, 2019, 10:4023.
[21] Zimin A, Stevens KA, Crepeau MW, et al.Sequencing and assembly of the 22-gb loblolly pine genome[J]. Genetics, 2014, 196:875-890.
[22] Dohm JC, Minoche AE, Holtgrawe D, et al.The genome of the recently domesticated crop plant sugar beet(Beta vulgaris)[J]. Nature, 2014, 505:546-549.
[23] Suk EK, Schulz S, Mentrup B, et al.A fosmid pool-based next generation sequencing approach to haplotype-resolve whole genomes[M]. New York:Springer New York, 2017.
[24] Zou C, Li L, Miki D, et al.The genome of broomcorn millet[J]. Nature Communications, 2019, 10:436.
[25] Ufarté L, Bozonnet S, Laville E, et al.Functional metagenomics:construction and high-throughput screening of fosmid libraries for discovery of novel carbohydrate-active enzymes[M]. New York:Springer New York, 2016.
[26] Riesenfeld CS, Schloss PD, Handelsman J.Metagenomics:genomic analysis of microbial communities[J]. Annual Review of Genetics, 2004, 38:525-552.
[27] Kim UJ, Shizuya H, de Jong PJ, et al. Stable propagation of cosmid sized human DNA inserts in an F factor based vector[J]. Nucleic Acids Research, 1992, 20:1083-1085.
[28] 萨姆布鲁克, 拉塞尔, 黄培堂, 等. 分子克隆实验指南[M]. 第3版. 北京:科学出版社, 2002.
[29] Heavens D, Accinelli GG, Clavijo B, et al.A method to simultaneously construct up to 12 differently sized Illumina Nextera long mate pair libraries with reduced DNA input, time, and cost[J]. Biotechniques, 2015, 59:42-45.
[30] Williams LJ, Tabbaa DG, Li N, et al.Paired-end sequencing of Fosmid libraries by Illumina[J]. Genome Research, 2012, 22:2241-2249.
[31] Murray MG, Thompson WF.Rapid isolation of high molecular weight plant DNA[J]. Nucleic Acids Research, 1980, 8:4321-4325.