A high-quality de novo genome assembly from a single parasitoid wasp

Sequencing and assembling a genome with a single individual have several advantages, such as lower heterozygosity and easier sample preparation. However, the amount of genomic DNA of some small sized organisms might not meet the standard DNA input requirement for current sequencing pipelines. Althou...

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Bibliographic Details
Published inbioRxiv
Main Authors Ye, Xinhai, Yang, Yi, Tian, Zhaoyang, Xu, Le, Yu, Kaili, Xiao, Shan, Yin, Chuanlin, Xiong, Shijiao, Fang, Qi, Hu, Chen, Li, Fei, Ye, Gongyin
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 14.07.2020
Subjects
Deoxyribonucleic acid
DNA
DNA sequencing
Genomes
Heterozygosity
Nucleotide sequence
Population genetics
Rare species
Synteny
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Summary:Sequencing and assembling a genome with a single individual have several advantages, such as lower heterozygosity and easier sample preparation. However, the amount of genomic DNA of some small sized organisms might not meet the standard DNA input requirement for current sequencing pipelines. Although few studies sequenced a single small insect with about 100 ng DNA as input, it may still be challenging for many small organisms to obtain such amount of DNA from a single individual. Here, we use 20 ng DNA as input, and present a high-quality genome assembly for a single haploid male parasitoid wasp (Habrobracon hebetor) using Nanopore and Illumina. Because of the low input DNA, a whole genome amplification (WGA) method is used before sequencing. The assembled genome size is 131.6 Mb with a contig N50 of 1.63 Mb. A total of 99% Benchmarking Universal Single-Copy Orthologs are detected, suggesting the high level of completeness of the genome assembly. Genome comparison between H. hebetor and its relative Bracon brevicornis shows a high-level genome synteny, indicating the genome of H. hebetor is highly accurate and contiguous. Our study provides an example for de novo assembling a genome from ultra-low input DNA, and will be used for sequencing projects of small sized species and rare samples, haploid genomics as well as population genetics of small sized species. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2020.07.13.200725