Although massively parallel sequencing approaches have been widely used to study genomic variation, simple alignment of short reads to a reference genome cannot be used to investigate the full range of structural variation and phased diploid architecture, which are important for precision medicine. By contrast, the single-molecule real-time (SMRT) sequencing platform produces long reads that can resolve repetitive structures effectively. We integrated this technology with several other sequencing approaches to construct a high-quality

Five subspecies of Fusobacterium nucleatum have been classified: animalis, nucleatum, polymorphum, vincentii, and fusiforme. F. nucleatum subsp. animalis ChDC F324 (KCOM 1325) was isolated from a human subgingival plaque in the Republic of Korea. Here, we report the draft genome sequence of the strain.

Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated as containing 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence (Wm82.a2.v1) revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel subfamilies, we found that soybean contains four clearly separated subfamilies of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

The genus Peptoniphilus comprises butyrate-producing, nonsaccharolytic species that use peptone and amino acids as major energy sources. The novel Peptoniphilus sp. strain ChDC B134 (=KCOM 1628) was isolated from a human periapical abscess lesion. Here, we report the draft genome sequence of the strain.

Fusobacterium nucleatum is a Gram-negative anaerobe and is one of the causative agents of periodontal diseases, including peri-implantitis. Fusobacterium nucleatum subsp. nucleatum ChDC F316 (KCOM 1322) was isolated from a human peri-implantitis lesion. Here, we report the draft genome sequence of this strain.

Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel groups, we found that soybean contains four clearly separated groups of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

Recently, five strains were isolated from human subgingival plaques and were proposed as a novel subspecies of Fusobacterium nucleatum. Here, we report the draft genome sequences of the strains, except one for which the draft sequence was already introduced.

Fusobacterium nucleatum is a Gram-negative, nonmotile, obligately anaerobic rod bacterium which might play an important role in the initiation and progression of periodontal diseases. F. nucleatum subsp. vincentii ChDC F8 (KCOM 1231) was isolated from a human gingivitis lesion. Here, we report the draft genome sequence of the strain.