A chromosome-level genome assembly of the parasitoid waspPteromalus puparum
A chromosome-level genome assembly of the parasitoid waspPteromalus puparum
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寄生蜂 Pteromalus puparum 的染色体水平基因组组装
DOI：
10.1111/1755-0998.13206
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发表时间：
2020-09-01
影响因子：
7.7
通讯作者：
Ye, Gongyin
中科院分区：
文献类型：
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作者：
Ye, Xinhai;Yan, Zhichao;Ye, Gongyin
寄生蜂在蜂目昆虫中占有很大比例。它们具有复杂的进化历史，是重要的生防因子。为推进寄生蜂研究，采用Illumina短读、PacBio长读和Hi-C支架技术，构建了蛹金小蜂染色体水平的高质量基因组拼接。染色体水平的组装有助于毒液和解毒基因的研究。组装的基因组大小为338 Mb，重叠群N50为38.7 kb，支架N50为1.16 Mb。Hi-C分析将支架组装到五条染色体上，并将支架N50提高到65.8 Mb，其中超过96%的组装碱基位于染色体上。通过RNA测序辅助两种性别和四个不同生命阶段的基因注释。分析检测到98%的BUSCO（基准通用单拷贝直系同源物）基因集，支持高质量的组装和注释。总的来说，40.1%（135.6 Mb）的装配由重复序列组成，并确定了14，946个蛋白质编码基因。虽然毒液基因在寄生蜂生物学中起着重要作用，但其在染色体上的空间分布却知之甚少。定位揭示了丝氨酸蛋白酶、胰腺脂肪酶相关蛋白和犬尿氨酸-酮戊二酸转氨酶的毒液基因串联阵列，这些基因在P.蛹系是从其共同祖先丽翅夜蛾（Nasonia vitripennis）分化而来的。此外，P450基因在家蚕中也有大量扩增。蛹这些例子说明了染色体水平的基因组组装可以为寄生蜂的分子，进化和生物防治研究提供有价值的资源。
Parasitoid wasps represent a large proportion of hymenopteran species. They have complex evolutionary histories and are important biocontrol agents. To advance parasitoid research, a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies was used to develop a high-quality chromosome-level genome assembly forPteromalus puparum, which is an important pupal endoparasitoid of caterpillar pests. The chromosome-level assembly has aided in studies of venom and detoxification genes. The assembled genome size is 338 Mb with a contig N50 of 38.7 kb and a scaffold N50 of 1.16 Mb. Hi-C analysis assembled scaffolds onto five chromosomes and raised the scaffold N50 to 65.8 Mb, with more than 96% of assembled bases located on chromosomes. Gene annotation was assisted by RNA sequencing for the two sexes and four different life stages. Analysis detected 98% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set, supporting a high-quality assembly and annotation. In total, 40.1% (135.6 Mb) of the assembly is composed of repetitive sequences, and 14,946 protein-coding genes were identified. Although venom genes play important roles in parasitoid biology, their spatial distribution on chromosomes was poorly understood. Mapping has revealed venom gene tandem arrays for serine proteases, pancreatic lipase-related proteins and kynurenine-oxoglutarate transaminases, which have amplified in theP. puparumlineage after divergence from its common ancestor withNasonia vitripennis. In addition, there is a large expansion of P450 genes inP. puparum. These examples illustrate how chromosome-level genome assembly can provide a valuable resource for molecular, evolutionary and biocontrol studies of parasitoid wasps.