Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus
Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus
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DOI：
10.1111/1574-6941.12285
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发表时间：
2014-05-01
影响因子：
4.2
通讯作者：
Garczarek, Laurence
中科院分区：
文献类型：
--
作者：
Humily, Florian;Farrant, Gregory K.;Garczarek, Laurence
聚球藻是海洋生态系统中数量最多的蓝藻之一，具有广泛的色素多样性。然而，色素类型的原位分布在很大程度上仍然未知。在这项研究中，我们结合流式细胞术细胞分选，全基因组扩增，和fosmid库的建设，目标是参与捕光复合物（藻胆体）的生物合成和调控的基因组区域。聚球藻群落组成和异养细菌的相对污染进行了评估，在管道的每个步骤，分别使用终端限制性片段长度多态性靶向petB和16S rRNA基因。这种方法使我们能够控制每种方法固有的偏差，并选择可靠的WGA产品从Roscoff（法国）收集的天然样品中构建fosmid文库。对含有靶向区域的25个磷酶进行测序，导致整个或部分藻胆体区域的组装。大多数重叠群被分配到进化枝I和IV，这与这些进化枝在温带沿海沃茨中的已知优势一致。然而，其中一个化石包含的基因与参考基因组中的直系同源物有很远的关系，这表明它属于一个新的系统发育分支。总之，这项研究提供了新的见解聚球藻群落结构和色素类型的多样性在一个有代表性的沿海站的英吉利海峡。
Synechococcus, one of the most abundant cyanobacteria in marine ecosystems, displays a broad pigment diversity. However, the in situ distribution of pigment types remains largely unknown. In this study, we combined flow cytometry cell sorting, whole-genome amplification, and fosmid library construction to target a genomic region involved in light-harvesting complex (phycobilisome) biosynthesis and regulation. Synechococcus community composition and relative contamination by heterotrophic bacteria were assessed at each step of the pipeline using terminal restriction fragment length polymorphism targeting the petB and 16S rRNA genes, respectively. This approach allowed us to control biases inherent to each method and select reliable WGA products to construct a fosmid library from a natural sample collected off Roscoff (France). Sequencing of 25 fosmids containing the targeted region led to the assembly of whole or partial phycobilisome regions. Most contigs were assigned to clades I and IV consistent with the known dominance of these clades in temperate coastal waters. However, one of the fosmids contained genes distantly related to their orthologs in reference genomes, suggesting that it belonged to a novel phylogenetic clade. Altogether, this study provides novel insights into Synechococcus community structure and pigment type diversity at a representative coastal station of the English Channel.