WebQUAST: online evaluation of genome assemblies

Mikheenko, Alla; Saveliev, Vladislav; Hirsch, Pascal; Gurevich, Alexey

doi:10.1093/nar/gkad406

“…De novo contigs were annotated using RAST-tk v.1.3.0 [12], as implemented in BV-BRC. Lastly, WebQUAST (http://cab.cc.spbu.ru/quast/) [13], an online server for quality assessment and comparison of genome assemblies based on the QUAST tool [14], was used to evaluate our genome assembly and completeness, using C. abortus strain 84/2334 as the reference genome ().…”

Section: Methodsmentioning

confidence: 99%

“…De novo contigs were annotated using RAST-tk v.1.3.0 [ 12 ], as implemented in BV-BRC. Lastly, WebQUAST ( http://cab.cc.spbu.ru/quast/ ) [ 13 ], an online server for quality assessment and comparison of genome assemblies based on the QUAST tool [ 14 ], was used to evaluate our genome assembly and completeness, using C. abortus strain 84/2334 as the reference genome ( Table 1 ). Average nucleotide identity (ANI) was calculated using CJ Bioscience’s online ANI calculator [ 15 ] utilizing the OrthoANIu algorithm with default parameters for comparison of de novo contigs of strains C1, C2 and C3 and selected avian chlamydial genomes (Table S5).…”

Section: Methodsmentioning

confidence: 99%

Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways

Kasimov,

White,

Jelocnik

2023

Microbial Genomics

0

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Chlamydia abortus, an obligate intracellular bacterium, is a major causative agent of reproductive loss in ruminants, with zoonotic potential. Though this pathogen is primarily known to infect livestock, recent studies have detected and isolated genetically distinct avian strains of C. abortus from wild birds globally. Before this study, only five avian C. abortus genomes were publicly available. Therefore, we performed culture-independent probe-based whole-genome sequencing on clinical swabs positive for avian C. abortus obtained from Australian Torresian crows (Corvus orru) in 2019 and 2020. We successfully obtained draft genomes for three avian C. abortus strains (C1, C2 and C3), each comprising draft chromosomes with lengths of 1 115 667, 1 120 231 and 1 082 115 bp, and associated 7 553 bp plasmids, with a genome completeness exceeding 92 %. Molecular characterization revealed that these three strains comprise a novel sequence type (ST333), whilst phylogenetic analyses placed all three strains in a cluster with other avian C. abortus genomes. Interestingly, these three strains share a distant genomic relation (2693 single nucleotide variants) with the reference strain 15-58d/44 (ST152), isolated from a Eurasian magpie (Pica pica) in Poland, highlighting the need for more publicly available genomes. Broad comparative analyses with other avian C. abortus genomes revealed that the three draft genomes contain conserved Chlamydia genomic features, including genes coding for type III secretion system and polymorphic membrane proteins, and potential virulence factors such as the large chlamydial cytotoxin, warranting further studies. This research provides the first avian C. abortus draft genomes from Australian birds, highlighting Torresian crows as novel reservoir hosts for these potential pathogens, and demonstrates a practical methodology for sequencing novel Chlamydia genomes without relying on traditional cell culture.

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