Department of Animal Science, University of Minnesota, College of Food, Agricultural and Natural Resource Sciences, 1334 Eckles Ave, 350 ABLMS, St. Paul, MN 55108, USA.
Nucleic Acids Res. 2023 Jan 11;51(1):17-28. doi: 10.1093/nar/gkac510.
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.
黑木工蚁（Camponotus pennsylvanicus）是一种广泛分布于北美的有害物种。我从单个个体中使用长读长纳米孔测序技术组装了一个相位二倍体基因组，大小为 306Mb，覆盖率为 60X，质量评估为 97.0%的 BUSCO 分数，优于其他蚂蚁组装。线粒体基因组显示出与其他蚂蚁的微小重排。这些读取还允许组装寄生虫和共生体基因组。我包括一个完整的沃尔巴克氏体细菌组装，大小为 1.2Mb，以及共生体 Blochmannia pennsylvanicus，大小为 791kb。从相同的读取中以碱基对分辨率测量了 DNA 甲基化和羟甲基化，并证实了在 Formicidae 家族中观察到的极低水平。存在中度杂合性，0.16%的碱基来自亲本单倍型。蛋白质预测生成了 14415 个氨基酸序列，具有 95.8%的 BUSCO 分数和 86%与之前已知的蛋白质匹配。所有组装都来自单个 MinION 流动池，产生了 20GB 的序列，成本为 1047 美元，包括耗材试剂。加上设备的固定成本，蚂蚁大小的基因组的总成本不到 5000 美元。所有分析都在一周内在单个台式计算机上进行。
