- 著者
- Yasuhiro TANIZAWA Takatomo FUJISAWA Eli KAMINUMA Yasukazu NAKAMURA Masanori ARITA
- 出版者
- BMFH出版会
- 雑誌
- Bioscience of Microbiota, Food and Health (ISSN:21863342)
- 巻号頁・発行日
- vol.35, no.4, pp.173-184, 2016 (Released:2016-10-28)
- 参考文献数
- 49
- 被引用文献数
- 188
Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus, obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii, whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.
- 著者
- Yasuhiro TANIZAWA Hisami KOBAYASHI Eli KAMINUMA Mitsuo SAKAMOTO Moriya OHKUMA Yasukazu NAKAMURA Masanori ARITA Masanori TOHNO
- 出版者
- BMFH出版会
- 雑誌
- Bioscience of Microbiota, Food and Health (ISSN:21863342)
- 巻号頁・発行日
- vol.36, no.3, pp.129-134, 2017 (Released:2017-07-13)
- 参考文献数
- 28
- 被引用文献数
- 2
Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573T to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L. parakefiri in functional foods such as kefir grains.