利用连接读取技术对 Nasonia oneida 中的 A 组沃尔巴克氏体进行基因组组装。

Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology.

机构信息

Department of Pathobiology, Auburn University.

Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.

出版信息

Genome Biol Evol. 2019 Oct 1;11(10):3008-3013. doi: 10.1093/gbe/evz223.

DOI:10.1093/gbe/evz223

PMID:31596462

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6821208/

Abstract

Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Genome sequences have been generated from arthropod samples following enrichment for the intracellular bacteria, and genomes have also been assembled from arthropod whole-genome sequencing projects. However, these methods remain challenging for infections that occur at low titers in hosts. Here we report the first Wolbachia genome assembled from host sequences using 10× Genomics linked-reads technology. The high read depth attainable by this method allows for recovery of intracellular bacteria that are at low concentrations. Based on the depth differences (714× for the insect and 59× for the bacterium), we assembled the genome of a Wolbachia in the parasitoid jewel wasp species Nasonia oneida. The final draft assembly consists of 1,293, 06 bp in 47 scaffolds with 1,114 coding genes and 97.01% genome completeness assessed by checkM. Comparisons of the five Multi Locus Sequence Typing genes revealed that the sequenced Wolbachia genome is the A1 strain (henceforth wOneA1) previously reported in N. oneida. Pyrosequencing confirms that the wasp strain lacks A2 and B types previously detected in this insect, which were likely lost during laboratory culturing. Assembling bacterial genomes from host genome projects can provide an effective method for sequencing bacterial genomes, even when the infections occur at low density in sampled tissues.

摘要

沃尔巴克氏体是一种专性细胞内细菌，通常感染各种线虫和节肢动物。已经从经过细胞内细菌富集的节肢动物样本中生成了基因组序列，并且还从节肢动物全基因组测序项目中组装了基因组。然而，对于在宿主中低滴度发生的感染，这些方法仍然具有挑战性。在这里，我们报告了使用 10× Genomics 链接读取技术从宿主序列组装的第一个沃尔巴克氏体基因组。该方法可达到的高读取深度允许回收浓度较低的细胞内细菌。基于深度差异（昆虫为 714×，细菌为 59×），我们组装了寄生性宝石蜂种纳索尼亚·奥内达（Nasonia oneida）中的沃尔巴克氏体基因组。最终的草案组装由 1,293,06 个碱基对组成，包含 47 个支架，其中 1,114 个编码基因，97.01%的基因组完整性通过 checkM 评估。对五个多基因座序列分型基因的比较表明，测序的沃尔巴克氏体基因组是 A1 株（以下简称 wOneA1），以前在 N. oneida 中报道过。焦磷酸测序证实，这种黄蜂株缺乏以前在这种昆虫中检测到的 A2 和 B 型，这可能是在实验室培养过程中丢失的。从宿主基因组项目组装细菌基因组可以为测序细菌基因组提供一种有效方法，即使在采样组织中感染密度较低的情况下也是如此。