A combined de novo assembly approach increases the quality of prokaryotic draft genomes

Çabuk, Uğur; Ünlü, Ercan Selçuk

doi:10.1007/s12223-022-00980-7

Cited by 2 publications

(2 citation statements)

References 30 publications

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“…Additionally, pair-end filtered reads were assembled individually by SPAdes v3.13.0 (-k 21,33,55,77,99,127) 51 . In order to recover additional complete viral genomes from the assembly sequences, genomes were assembled applying the Trusted contigs strategy 52 , available in SPADEs, that used the ΦCrAss001 genome 13 as a reference to provide a guidance during de novo assembly. ORF prediction was carried out using Prodigal 53 .…”

Section: Methodsmentioning

confidence: 99%

Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

et al. 2023

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Crassvirales (crAss-like phages) are an abundant group of human gut-specific bacteriophages discovered in silico. The use of crAss-like phages as human fecal indicators is proposed but the isolation of only seven cultured strains of crAss-like phages to date has greatly hindered their study. Here, we report the isolation and genetic characterization of 25 new crAss-like phages (termed crAssBcn) infecting Bacteroides intestinalis, belonging to the order Crassvirales, genus Kehishuvirus and, based on their genomic variability, classified into six species. CrAssBcn phage genomes are similar to ΦCrAss001 but show genomic and aminoacidic differences when compared to other crAss-like phages of the same family. CrAssBcn phages are detected in fecal metagenomes around the world at a higher frequency than ΦCrAss001. This study increases the known crAss-like phage isolates and their abundance and heterogeneity open the question of what member of the Crassvirales group should be selected as human fecal marker.

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Section: Methodsmentioning

confidence: 99%

Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

et al. 2023

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“…To correct this error in the remaining PB strains, we re-assembled their genomes using the reference-guided method (Cabuk and Unlu, 2022) in Spades v3.10.1 with the parameter of “-- untrusted-contigs” (Bankevich et al, 2012). For each assembled genome, genes were predicted using Prokka v1.12 (Seemann, 2014) and annotated using the Cluster of Orthologous Genes (COG) database (Galperin et al, 2020) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (Kanehisa et al, 2023; Kanehisa et al, 2004) .…”

Section: Supplementary Text: Methodsmentioning

confidence: 99%

Correlating phylogenetic and functional diversity of thenod-free but nodulatingBradyrhizobiumphylogroup

Lü

Camuel

Wang

et al. 2023

Preprint

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Bradyrhizobium is a main rhizobial lineage of which the majority of its members nodulate legume plants using Nod factors (NFs) encoded by the nod genes. However, the photosynthetic phylogroup within Bradyrhizobium (PB) does not contain nod genes but are still capable of establishing a nitrogen-fixing symbiosis with some tropical legumes of the Aeschynomene genus. Furthermore, members of this phylogroup colonize rice roots and promote plant growth. Despite this unique combination of ecological features, genomes of only 13 PB members are sequenced, and almost all are isolated from Aeschynomene spp. nodules. Here, we sequenced 208 new PB members predominantly associated with rice. The extended PB phylogroup comprises three main clades: a basal clade with significant expansion of its diversity, followed by the diversification of a singleton clade from a new clade exclusively represented by our strains. Although the PB strains universally lack the canonical nod genes, all 27 assayed strains representing the broad diversity of these clades induced nodules on Aeschynomene indica. Interestingly, significant differences in the efficiency of symbiosis between the main clades were observed and the singleton clade showed an intermediate symbiotic phenotype aligning well with its intermediate phylogenetic position. Our strain collection expands the phylogenetic and ecological diversity of the nod-free but nodulating Bradyrhizobium and shows that the NF-independent nodulation of Aeschynomene is a common trait of this phylogroup, in contrast to the photosynthetic trait originally thought as its unifying feature.

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A combined de novo assembly approach increases the quality of prokaryotic draft genomes

Cited by 2 publications

References 30 publications

Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

Correlating phylogenetic and functional diversity of thenod-free but nodulatingBradyrhizobiumphylogroup

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