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SageHLS联合ONT超长读长测序技术对拟南芥进行高质量的基因组组装和测序



       拟南芥作为模式植物,在植物研究领域具有重要的地位。对拟南芥进行遗传分析、基因克隆和功能基因组等研究,可为粮食增产、农作物抗逆、植物保护等提供新的思路。在遗传研究中,基因的分析往往依赖于参考基因组。理论上,参考基因组应该是一个物种的全基因序列,但实际上,只有极少数动植物有100%的参考基因组。目前,拟南芥参考基因组还存在大量的缺失序列,尤其是在细胞分裂过程中起到重要作用的着丝粒序列和与衰老相关的端粒序列。这些序列存在大量高度重复的片段,给基因组组装带来了巨大困难,阻碍了科学家对该区域序列及其功能的研究。
 
        2021年9月份发表在国际生物信息学著名学术期刊Genomics, Proteomics & Bioinformatics上的一篇文献中,西安交通大学信息与生物医学交叉团队以人工智能算法开发、生物医学大数据挖掘为手段,设计了综合利用Nanopore超长读长测序技术和Pacbio HiFi(高准确率)测序技术相结合的混合测序策略,实现了仅剩两个缺口的高质量拟南芥基因组Col-XJTU。通过该测序方案组装得到的Col-XJTU基因组完成了拟南芥5条染色体中3号、4号及5号染色体着丝粒的无缺口组装,并完成了1号和2号染色体大部分着丝粒的组装。数据显示,Col-XJTU基因组的碱基准确性和结构准确性均高于目前国际通用的、由美国实现的拟南芥参考基因组TAIR10.1。(基因组的碱基准确性和结构准确性是评估参考基因组质量的指标)
 
       值得注意的是,该团队所采用的ONT超长读长测序方案中,SageScience公司的超长DNA片段回收系统SageHLS被用来回收>50kb的基因组片段,然后使用ONT建库试剂盒进行文库构建和下游的测序组装。经过SageHLS自动化片段筛选,可以将<50kb的DNA自动过滤掉,保留符合要求的超长DNA片段(>50kb),最大程度地发挥长读长测序的优势,极大地提高了长读长测序效率。结果表明:经过SageHLS的片段选择和ONT测序后,其N50值可达46,452 bp,最大读长可达495,032 bp,测序覆盖度~388×。
 

SageHLS是目前市面上唯一一款支持客户制备百kb级以上长度文库的设备
 
       此外,SageScience公司的另外一款全长型DNA片段回收系统BluePippin用于PacBio HiFi测序文库构建过程中15kb以上SMRTbell文库的回收。SageHLS与BluePippin两款DNA片段回收系统强强联合,共同助力ONT超长读长测序和Pacbio HiFi测序技术对拟南芥基因组的高质量组装。
 
       原文链接:https://doi.org/10.1016/j.gpb.2021.08.003
 
       SageScience是全球领先的研发和制造Pippin系列全自动核酸电泳片段回收仪的生产厂家,拥有美国技术专利,其生产的Sage系列产品可以高效完成不同长度范围的DNA片段的精准回收,广泛用于二代测序、三代测序以及多个分子生物学相关领域。
 
       环亚生物科技有限公司作为美国SageScience公司在中国区的独家代理商,自2011年以来将SageScience的产品线引入国内,一直为国内用户提供专业的全自动核酸片段回收系统的安装测试、应用培训,技术支持与售后维护工作,赢得客户的一致好评与信任。环亚生物科技有限公司将一如既往地支持越来越多的SageScience用户。


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