ArticleNucleic acids research2023
De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
- Epigenotoxicity: Decoding the epigenetic imprints of genotoxic agents and their implications for regulatory genetic toxicology.Environmental and molecular mutagenesis · 2025Review
- A trove of antiviral TRIM family E3 ligases in reptiles.bioRxiv : the preprint server for biology · 2025Article
- Characterisation and phylogenetic analysis of the complete mitochondrial genome of two endemic lampreys from Greece (Caspiomyzon hellenicus and Caspiomyzon graecus) using Long-Read technology.Molecular biology reports · 2025Article
- Sequencing and assembling the genome of Przewalski's horse in the classroom.Journal of equine veterinary science · 2025Review
- Genome assembly of the temporary socially parasitic spiny ant Polyrhachis lamellidens and its host Camponotus japonicus.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Reference genome of the bicolored carpenter ant, Camponotus vicinus.The Journal of heredity · 2024Article
- Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms.Scientific data · 2023Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.FEMS microbiology reviews · 2023Review
- Single-worm long-read sequencing reveals genome diversity in free-living nematodes.Nucleic acids research · 2023Article
- Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat,NAR genomics and bioinformatics · 2023Article
- Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates.Genome research · 2023Article
- The genome of the soybean gall midge (Resseliella maxima).G3 (Bethesda, Md.) · 2023Article
- The Genome of the Soybean Gall Midge (bioRxiv : the preprint server for biology · 2023Article
- Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates.bioRxiv : the preprint server for biology · 2023Article
- Application of next-generation sequencing to identify different pathogens.Frontiers in microbiology · 2023Review
- Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes.Genome biology and evolution · 2022Article
- Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genusEcology and evolution · 2022Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The black carpenter ant (Camponotus pennsylvanicus) is a pest species found widely throughout North America. From a single individual I used long-read nanopore sequencing to assemble a phased diploid genome of 306 Mb and 60X coverage, with quality assessed by a 97.0% BUSCO score, improving upon other ant assemblies. The mitochondrial genome reveals minor rearrangements from other ants. The reads also allowed assembly of parasitic and symbiont genomes. I include a complete Wolbachia bacterial assembly with a size of 1.2 Mb, as well as a commensal symbiont Blochmannia pennsylvanicus, at 791 kb. DNA methylation and hydroxymethylation were measured at base-pair resolution level from the same reads and confirmed extremely low levels seen in the Formicidae family. There was moderate heterozygosity, with 0.16% of bases being biallelic from the parental haplotypes. Protein prediction yielded 14 415 amino acid sequences with 95.8% BUSCO score and 86% matching to previously known proteins. All assemblies were derived from a single MinION flow cell generating 20 Gb of sequence for a cost of $1047 including consumable reagents. Adding fixed costs for equipment brings the total for an ant-sized genome to less than $5000. All analyses were performed in 1 week on a single desktop computer.
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