Genome Sequence of the Banana Aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and Its Symbionts.
Genome Sequence of the Banana Aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and Its Symbionts.
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DOI：
10.1534/g3.120.401358
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发表时间：
2020-12-03
期刊：
影响因子：
--
通讯作者：
Tripathi L
中科院分区：
文献类型：
--
作者：
Mathers TC;Mugford ST;Hogenhout SA;Tripathi L
香蕉蚜虫Pentalonia nigronervosa Coquerel（半翅目：蚜虫科）是栽培香蕉（香蕉属，香蕉束顶病毒（Banana bunchy top virus，BBTV）是世界上最严重的香蕉病毒性疾病。在这里，我们使用单个无PCR的Illumina测序文库产生了黑脉的高度完整的基因组组装。使用相同的序列数据，我们还生成了黑脉黑脉疫霉共生细菌Buchnera aphidicola和Wolbachia的完整基因组组装体。为了改进我们对黑脉黑脉原杆菌的初始组装，我们开发了基于k聚体的去重复流水线以去除源自单倍体组装的基因组支架（组装为单独支架的等位基因变体）。为了证明该管道的有用性，我们将其应用于最近生成的蚜虫Myzus cerasi的组装，将保守的BUSCO基因的重复减少了25%。系统基因组分析表明，黑脉cerasi组装，和七个先前发表的蚜虫基因组，跨越三个蚜虫部落和两个亚科，揭示了黑脉蚜福尔斯落在部落Macrosiphini，但是一个外群到目前为止测序的其他Macrosiphini。因此，这里报道的基因组资源将有助于理解Macrosphini的进化和P. nigronervosa的研究。此外，我们的方法使用低成本，高质量，Illumina短读段来生成未充分研究的蚜虫物种的完整基因组组装，将有助于填补不同蚜虫生命树中的基因组黑点。
The banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae), is a major pest of cultivated bananas (Musa spp., order Zingiberales), primarily due to its role as a vector of Banana bunchy top virus (BBTV), the most severe viral disease of banana worldwide. Here, we generated a highly complete genome assembly of P. nigronervosa using a single PCR-free Illumina sequencing library. Using the same sequence data, we also generated complete genome assemblies of the P. nigronervosa symbiotic bacteria Buchnera aphidicola and Wolbachia. To improve our initial assembly of P. nigronervosa we developed a k-mer based deduplication pipeline to remove genomic scaffolds derived from the assembly of haplotigs (allelic variants assembled as separate scaffolds). To demonstrate the usefulness of this pipeline, we applied it to the recently generated assembly of the aphid Myzus cerasi, reducing the duplication of conserved BUSCO genes by 25%. Phylogenomic analysis of P. nigronervosa, our improved M. cerasi assembly, and seven previously published aphid genomes, spanning three aphid tribes and two subfamilies, reveals that P. nigronervosa falls within the tribe Macrosiphini, but is an outgroup to other Macrosiphini sequenced so far. As such, the genomic resources reported here will be useful for understanding both the evolution of Macrosphini and for the study of P. nigronervosa. Furthermore, our approach using low cost, high-quality, Illumina short-reads to generate complete genome assemblies of understudied aphid species will help to fill in genomic black spots in the diverse aphid tree of life.
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