A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates.
A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates.
复制标题
抑制消减杂交方法揭示了可能与海洋聚球藻分离株躲避捕食者有关的生态位特异性基因。
DOI：
10.1128/aem.72.4.2730-2737.2006
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发表时间：
2006
影响因子：
4.4
通讯作者：
Jones H
中科院分区：
文献类型：
--
作者：
Jones H
海洋微囊藻是海洋初级生产的重要贡献者，在世界海洋中普遍存在。该属在遗传上是多样化的，至少有10个离散的谱系或支系已被鉴定为系统发育。然而，人们对特定谱系的遗传属性或特定品系独有的遗传属性知之甚少。在这里，我们使用抑制消减杂交(SSH)方法在两个特征良好的实验室菌株-聚球藻中鉴定了菌株和分支特异的基因。菌株WH8103(支系III)和聚球藻。菌株WH7803(分支V)。在被确定为每个菌株潜在独特的基因中，有编码可能涉及特定捕食者避免的蛋白质的基因，包括菌株WH8103的糖基转移酶和WH7803的ABC类型的多糖/多元醇磷酸输出系统的渗透酶成分。在这项工作中，其中一种菌株WH7803的基因组变得可用。这使得能够评估SSH丰富序列中存在的假阳性序列(即，存在于测试者基因组中的序列)的数量。我们发现大约9%的WH8103序列是潜在的假阳性序列，这表明当使用这项技术来评估遗传相似的细菌菌株的基因组差异时应该谨慎使用。
Picocyanobacteria of the genusSynechococcusare important contributors to marine primary production and are ubiquitous in the world's oceans. This genus is genetically diverse, and at least 10 discrete lineages or clades have been identified phylogenetically. However, little if anything is known about the genetic attributes which characterize particular lineages or are unique to specific strains. Here, we used a suppression subtractive hybridization (SSH) approach to identify strain- and clade-specific genes in two well-characterized laboratory strains,Synechococcussp. strain WH8103 (clade III) andSynechococcussp. strain WH7803 (clade V). Among the genes that were identified as potentially unique to each strain were genes encoding proteins that may be involved in specific predator avoidance, including a glycosyltransferase in strain WH8103 and a permease component of an ABC-type polysaccharide/polyol phosphate export system in WH7803. During this work the genome of one of these strains, WH7803, became available. This allowed assessment of the number of false-positive sequences (i.e., sequences present in the tester genome) present among the SSH-enriched sequences. We found that approximately 9% of the WH8103 sequences were potential false-positive sequences, which demonstrated that caution should be used when this technology is used to assess genomic differences in genetically similar bacterial strains.