Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]
Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]
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DOI：
10.1534/g3.120.401200
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发表时间：
2020-06
期刊：
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通讯作者：
Xiaozhu Wang;Yogeshwar D. Kelkar;Xiao Xiong;Ellen O. Martinson;Jeremy A. Lynch;Chao Zhang;J. Werren;Xu Wang
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文献类型：
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作者：
Xiaozhu Wang;Yogeshwar D. Kelkar;Xiao Xiong;Ellen O. Martinson;Jeremy A. Lynch;Chao Zhang;J. Werren;Xu Wang
石蜂属宝石蜂是一种单倍体性别决定的寄生蜂，发育迅速，易于实验室培养。它们是昆虫遗传学、基因组学、表观遗传学、发育和进化的优秀模型。vitripennis （Nv）和N. giraulti （Ng）是亲缘关系密切的物种，特别是在去除细胞内细菌沃尔巴克氏体（Wolbachia）后，它们可以相互交叉，这是绘制和定位克隆形态、行为、表达和甲基化表型的有力工具。Nv参考基因组使用Sanger， PacBio和Nanopore方法组装，并使用广泛的RNA-seq数据进行注释。相比之下，Ng基因组只能通过低覆盖率重测序获得。因此，de novo Ng组装迫切需要推进该系统。在这项研究中，我们报告了一个高质量的Ng组装，使用10X Genomics的连锁reads，测序深度为670X。目前在3160个支架中组装的基因组大小为259,040,977 bp， G-C为38.05%，BUSCO完整性评分为98.6%。97%的RNA读数与基因组完全对齐，表明高质量的连续性和完整性。Ng基因组共有14,777个基因被注释，其中72%的注释基因在Nv基因组中有一对一的同源基因。我们报道了500万个Ng-Nv snp，这将为纳索尼亚的定位和种群基因组研究提供便利。此外，通过与Nv基因组和注释的比较，鉴定出42个ng特异性基因。这是这一重要物种在纳索尼亚模式系统中的首次重新组装，提供了一个有用的新基因组工具包。
Jewel wasps in the genus of Nasonia are parasitoids with haplodiploidy sex determination, rapid development and are easy to culture in the laboratory. They are excellent models for insect genetics, genomics, epigenetics, development, and evolution. Nasonia vitripennis (Nv) and N. giraulti (Ng) are closely-related species that can be intercrossed, particularly after removal of the intracellular bacterium Wolbachia, which serve as a powerful tool to map and positionally clone morphological, behavioral, expression and methylation phenotypes. The Nv reference genome was assembled using Sanger, PacBio and Nanopore approaches and annotated with extensive RNA-seq data. In contrast, Ng genome is only available through low coverage resequencing. Therefore, de novo Ng assembly is in urgent need to advance this system. In this study, we report a high-quality Ng assembly using 10X Genomics linked-reads with 670X sequencing depth. The current assembly has a genome size of 259,040,977 bp in 3,160 scaffolds with 38.05% G-C and a 98.6% BUSCO completeness score. 97% of the RNA reads are perfectly aligned to the genome, indicating high quality in contiguity and completeness. A total of 14,777 genes are annotated in the Ng genome, and 72% of the annotated genes have a one-to-one ortholog in the Nv genome. We reported 5 million Ng-Nv SNPs which will facility mapping and population genomic studies in Nasonia. In addition, 42 Ng-specific genes were identified by comparing with Nv genome and annotation. This is the first de novo assembly for this important species in the Nasonia model system, providing a useful new genomic toolkit.