BACKGROUND New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. RESULTS We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. CONCLUSIONS Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

中文翻译：

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进化超级支架和染色体锚定以改善按蚊基因组组装。

背景技术新的测序技术已经降低了全基因组测序的财务障碍，但由此产生的组装通常是碎片化的并且远未“完成”。将多支架草稿更新到染色体水平状态可以通过实验作图或重新测序工作来实现。避免与此类方法相关的成本，基因顺序保守（同线性）的比较基因组分析以预测支架邻居（邻接）为改进草案装配提供了一种潜在有用的补充方法。结果 我们评估并采用了 3 种基于基因同线性的方法，应用于 21 个按蚊组装，以产生一致的支架邻接集。对于程序集的子集，我们将它们与其他支持数据集成以确认和补充基于 synteny 的邻接关系：6 个具有将支架锚定到染色体位置的物理映射数据，13 个具有配对末端 RNA 测序 (RNAseq) 数据，3 个具有基于重新支架或长读数据的新组件。我们的综合分析产生了 20 个具有改进邻接性的新超级支架组件：其中 7 个将非锚定支架分配到染色体臂跨越超过 75% 的组件，另外 7 个具有染色体锚定，包括 88% 的锚定阿拉伯按蚊组件和，分别有 73% 和 84% 的锚定组件具有全面更新的按蚊和斯蒂芬按蚊的细胞遗传学照片。结论 来自探针映射、RNAseq 或长读长技术的实验数据（如果可用）都有助于成功升级草案装配。我们的评估表明，基于基因同线性的计算方法代表了一种有价值的替代或补充方法。我们改进的按蚊参考组件突出了应用比较基因组学方法来改善社区基因组资源的效用。