JRA2 : EXPLORING NEW APPROACHES IN SPECIES IDENTIFICATION. Lactobacillus acidophilus CIRM-BIA 442

The complete genome sequences of several pairs of closely related prokaryotes are now available. Surprisingly, even strains of the same species can differ by as much as 20 % in gene content. Several analyses of very closely related genomes comparisons reported over the last years show that there may be as much to learn about diversity. Extensive genomic comparisons are possible not only between representatives of distant evolutionary phyla, but also between species of the same phylogenetic branch where individual evolutionary events can be more readily identified. They also indicate that sequencing of one representative genome give us nowhere near a complete picture of the genetic repertoire of any species, and that new and comparative methods will be required. Remarkable innovation in sequencing technologies has been achieved making them high-throughput, faster and more cost effective. The sequencing field has experienced a major shift by the introduction of innovation sequencing technologies capable of generating sequence data at a fraction of the cost and much quicker when compared to the Sanger method. Bacteria are characterized by extensive intraspecies variation. There is not only the sequence variation found in all species, but also the presence or absence of whole genes or clusters of genes. We propose to apply the sequencing technology developed by Illumina on several strains of Lactobacillus acidophilus and helveticus to enable a comparative study that will link genotype and phenotype at the genomic level.

目前已有多对亲缘关系密切的原核生物（prokaryotes）的完整基因组序列。令人意外的是，即便同一物种的不同菌株，其基因含量差异也可高达20%。过去数年发表的多项针对高度近缘基因组的比较分析研究表明，关于微生物多样性仍有大量内容有待探索。大规模基因组比较不仅可在进化亲缘关系较远的类群代表之间开展，也可在同一系统发育分支的物种之间进行——此时单个进化事件更易于被识别。这些研究同时表明，仅对单个代表性基因组进行测序，远不足以完整呈现任一物种的全套遗传组成，因此亟需开发新型比较基因组学方法。测序技术已取得显著革新，实现了高通量、高速度与低成本的突破。相较于桑格测序法（Sanger method），新型测序技术的问世推动测序领域发生重大变革：其可仅以原成本的一小部分，且用时大幅缩短的方式生成序列数据。细菌的典型特征之一是种内存在广泛的遗传变异，这种变异不仅包括所有物种共有的序列差异，还涉及完整基因或基因簇的有无变化。本研究拟采用伊卢米纳（Illumina）公司开发的测序技术，对若干株嗜酸乳杆菌（Lactobacillus acidophilus）和瑞士乳杆菌（Lactobacillus helveticus）进行测序，以此开展比较基因组学研究，从而在基因组层面关联基因型与表型。