期刊
G3-GENES GENOMES GENETICS
卷 13, 期 4, 页码 -出版社
OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkad030
关键词
ectoparasite; Sturnus vulgaris; PacBio; TELL-Seq; historical effective population size; mitogenome; endosymbiont
Sequencing HMW DNA has greatly improved complete genome sequences for nonmodel organisms. In this study, we used PacBio long reads and TELL-Seq linked reads to assemble and annotate the genome of a single feather louse from a European Starling. We obtained a high-quality genome and annotated numerous genes similar to the human louse genome. This study demonstrates the potential to obtain high-quality genomes from individual small organisms, contributing to our understanding of individual genomic diversity and evolution.
Sequencing high molecular weight (HMW) DNA with long-read and linked-read technologies has promoted a major increase in more complete genome sequences for nonmodel organisms. Sequencing approaches that rely on HMW DNA have been limited to larger organisms or pools of multiple individuals, but recent advances have allowed for sequencing from individuals of small-bodied organisms. Here, we use HMW DNA sequencing with PacBio long reads and TELL-Seq linked reads to assemble and annotate the genome from a single individual feather louse (Brueelia nebulosa) from a European Starling (Sturnus vulgaris). We assembled a genome with a relatively high scaffold N50 (637 kb) and with BUSCO scores (96.1%) comparable to louse genomes assembled from pooled individuals. We annotated a number of genes (10,938) similar to the human louse (Pediculus humanus) genome. Additionally, calling phased variants revealed that the Brueelia genome is more heterozygous (similar to 1%) then expected for a highly obligate and dispersal-limited parasite. We also assembled and annotated the mitochondrial genome and primary endosymbiont (Sodalis) genome from the individual louse, which showed evidence for heteroplasmy in the mitogenome and a reduced genome size in the endosymbiont compared to its free-living relative. Our study is a valuable demonstration of the capability to obtain high-quality genomes from individual small, nonmodel organisms. Applying this approach to other organisms could greatly increase our understanding of the diversity and evolution of individual genomes.
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