Abstract

背景回顾：Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. 

主要发现：Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (P. sitchensis) together with improved and more contiguous genome assemblies for white spruce (P. glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). 

研究结果：The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of nonsynonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. 

研究结论：These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests.

 摘 要 

云杉是广泛分布于北半球北方地区和山地森林的针叶树种，具有巨大的经济价值，并且对于全球碳汇作用巨大。云杉的基因组巨大，重复序列含量较高，从而阻碍了对于其基因组的精确解析。本文中，作者报道并比较了4个不同的北美云杉基因组，其中恩格曼云杉（Picea engelmannii）和西加云杉（P. Sitchensis）的基因组为从头组装，而白云杉（P. Glauca）以及三者的自然种间杂种内陆云杉（P. engelmannii × glauca × sitchensis）基因组则为改良版。作者发现，这四个云杉的基因组结构大体相似，并且大部分的scaffolds都可以挂载到遗传图谱上。内陆云杉的基因组组成表明其三个祖先基因组的贡献不均等。作者通过对核基因和细胞器基因的系统发育分析建立了一个能够反映祖先网状结构的拓扑关系。不同云杉基因组中基因家族的扩张模式存在差异，并且与推定的多样生态适应有关。作者鉴定了快速演化的基因，相比于同义多态位点，这些基因含有更高比例的非同义多态位点，表明其存在正选择效应或搭便车效应。在适应相反生态的物种间，快速演化基因集明显不同，并且作者还鉴定到了趋同的平衡选择信号。对于扩张的基因家族和快速演化基因的功能分析发现，这些基因大多胁迫和刺激响应有关。基因扩张和快速演化在基因组演化过程中是互补的，共同作用于对假定适应环境的趋异演化。本研究报道的改良版云杉基因组有助于加强我们对针叶树基因组结构和演化的理解，这些云杉基因组间的比较为从基因组水平上理解针叶树适应和生态的遗传基础提供了线索。另外，它们还将为更好地监测自然遗传多样性和改善针叶林管理提供了新的工具。