DFAST and DAGA: web-based integrated genome annotation tools and resources

Abstract

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.

Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov.

“…of low quality reads using FASTQ/A Trimmer in FASTX-toolkit (http://hannonlab.cshl.edu/fastx toolkit/), assembled by SPADES version 3.13.0 [29] and annotated through DFAST program [26].…”

“…In order to reconfirm the above phylogenetic analysis, we also constructed the phylogenetic tree based on the core genome of Bifidobacterium spp. Total 76 type strains of Bifidobacterium were annotated with the DFAST program [26], and 355 orthologous genes were identified as the core retained in all genomes. The amino acid sequences of core genes from each genome were concatenated and aligned using the MAFFT program (version 7.313) [9].…”

Potential Application of Bacteriophages in Enrichment Culture for Improved PrenatalStreptococcus agalactiaeScreening

“…The genome sequences were analyzed by using BLASTn at the National Center for Biotechnology Information (NCBI; https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome; last accessed: 5 May, 2018). The genomes were annotated using a prokaryotic genome annotation pipeline, DFAST (https://dfast.nig.ac.jp/) (19, 20).…”

High-Quality Draft Genome Sequence of Burkholderia contaminans CH-1, a Gram-Negative Bacterium That Metabolizes 2-Azahypoxanthine, a Plant Growth-Regulating Compound

“…The high-quality draft genome of B. contaminans CH-1 contained three circular chromosomes, in which only five gaps remained, as well as a putative linear plasmid (designated pBC453), totaling 8,901,643 bp with a G+C content of 66.0%. The CH-1 genome was annotated using the DFAST-core stand-alone program version 0.9.4 (11) and manually curated. The CH-1 genome contains 8,065 protein-coding sequences, including 85 possible pseudogenes (1.05%), 18 rRNAs (6 clusters of 5S, 16S, and 23S rRNAs), and 82 tRNAs.…”