Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

Nurk, Sergey; Bankevich, Anton; Antipov, Dmitry; Gurevich, Alexey; Korobeynikov, Anton; Lapidus, Alla; Prjibelski, Andrey D.; Pyshkin, Alex; Sirotkin, Alexander; Sirotkin, Yakov; Stepanauskas, Ramunas; Clingenpeel, Scott; Woyke, Tanja; McLean, Jeffrey S.; Lasken, Roger S.; Tesler, Glenn; Alekseyev, Max A.; Pevzner, Pavel A.

doi:10.1089/cmb.2013.0084

Cited by 1,203 publications

(882 citation statements)

References 34 publications

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“…Therefore, to obtain a high-quality genome sequence, two different methods were used, Illumina MiSeq and PacBio, using DNA from a nonaxenic laboratory culture of Moorea producens PAL. Both the short and long reads were assembled together (described as "hybrid assembly") using standard settings of SPAdes 3.5 (14), and yielded 47 linear contigs larger than 500 bp along with one circular contig of 35.5 kb (a candidate cyanobacterial plasmid). Hybrid assembly has previously been used to improve overall draft genome quality; however, in this case, it was still fragmented because large repeated regions remained unresolved (15).…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea

Leão

Castelão

Korobeynikov

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Cyanobacteria are major sources of oxygen, nitrogen, and carbon in nature. In addition to the importance of their primary metabolism, some cyanobacteria are prolific producers of unique and bioactive secondary metabolites. Chemical investigations of the cyanobacterial genus Moorea have resulted in the isolation of over 190 compounds in the last two decades. However, preliminary genomic analysis has suggested that genome-guided approaches can enable the discovery of novel compounds from even well-studied Moorea strains, highlighting the importance of obtaining complete genomes. We report a complete genome of a filamentous tropical marine cyanobacterium, Moorea producens PAL, which reveals that about one-fifth of its genome is devoted to production of secondary metabolites, an impressive four times the cyanobacterial average. Moreover, possession of the complete PAL genome has allowed improvement to the assembly of three other Moorea draft genomes. Comparative genomics revealed that they are remarkably similar to one another, despite their differences in geography, morphology, and secondary metabolite profiles. Gene cluster networking highlights that this genus is distinctive among cyanobacteria, not only in the number of secondary metabolite pathways but also in the content of many pathways, which are potentially distinct from all other bacterial gene clusters to date. These findings portend that future genome-guided secondary metabolite discovery and isolation efforts should be highly productive.

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Section: Resultsmentioning

confidence: 99%

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea

Leão

Castelão

Korobeynikov

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…The whole set of reads was trimmed using Trimmomatic (21) and then preassembled with Anytag software v2.5 (22) to produce pseudoreads. Spades assembler (23,24) was then used to assemble these reads, and the contigs obtained were combined using SSPACE v2.0 (25) and Opera software v1.4 (26), assisted by GapFiller v1. 10 (27), to reduce the set.…”

Section: Flow Cytometric Analyses (I) Detection Of Amoeba Lysis By Fmentioning

confidence: 99%

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Reteno

Benamar

Khalil

et al. 2015

J Virol

176

233

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Giant viruses are protist-associated viruses belonging to the proposed order Megavirales; almost all have been isolated from Acanthamoeba spp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage from Vermamoeba vermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of Ϸ200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes Ϸ3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy. IMPORTANCEBy using Vermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the family Asfarviridae. Moreover, the faustovirus gene repertoire is Ϸ3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database). G iant viruses were first described in 2003, with the discovery of Acanthamoeba polyphaga mimivirus (1, 2). They are protistassociated viruses that belong to a major monophyletic group of double-stranded DNA (dsDNA) viruses known as nucleocytoplasmic large DNA viruses (NCLDVs), and they have been classified under the proposed order Megavirales (3). Since the first description of Acanthamoeba polyphaga mimivirus, giant viruses have been isolated from other phagocytic protists, primarily Acanthamoeba spp. (4-6). Because these giant viruses are resistant to killing by phagocytic protists, we hypothesized that they may also reproduce in macrophages and might therefore infect humans. This proposition was validated experimentally by the isolation of mimivirus from atypical pneumonia patients and by the detection of marseilleviruses in blood donors and in human lymph nodes (7-9). Moreover, we and others identified sequences associated with giant viruses in metagenomes generated from human tissues, suggesting that giant viruses are a component of the human virome (10). Because the investigation of a virome typically starts with a filtration procedure that eliminates giant viruses (11), we developed a new culture approach that does not prevent the detection of these viruses.In the present study, we de...

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“…Quality trimmed forward and reverse sequences were merged and assembled into contigs using SPAdes 3.7.0 (Nurk et al, 2013) with the "-meta" option. The number of contigs, contig length, GC content, N50, and L50 assembly statistics were calculated with metaQUAST (Mikheenko et al, 2016;Supplementary Table 2).…”

Section: Metagenomic Analysismentioning

confidence: 99%

Metagenomic Binning Recovers a Transcriptionally Active Gammaproteobacterium Linking Methanotrophy to Partial Denitrification in an Anoxic Oxygen Minimum Zone

et al. 2017

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Diverse planktonic microorganisms play a crucial role in mediating methane flux from the ocean to the atmosphere. The distribution and composition of the marine methanotroph community is determined partly by oxygen availability. The low oxygen conditions of oxygen minimum zones (OMZs) may select for methanotrophs that oxidize methane using inorganic nitrogen compounds (e.g., nitrate, nitrite) in place of oxygen. However, environmental evidence for methane-nitrogen linkages in OMZs remains sparse, as does our knowledge of the genomic content and metabolic capacity of organisms catalyzing OMZ methane oxidation. Here, binning of metagenome sequences from a coastal anoxic OMZ recovered the first near complete (95%) draft genome representing the methanotroph clade OPU3. Phylogenetic reconstruction of concatenated single copy marker genes confirmed the OPU3-like bacterium as a divergent member of the type Ia methanotrophs, with an estimated genome size half that of other sequenced taxa in this group. The proportional abundance of this bacterium peaked at 4% of the total microbial community at the top of the anoxic zone in areas of nitrite and nitrate availability but low methane concentrations. Genes mediating dissimilatory nitrate and nitrite reduction were identified in the OPU3 genome, and transcribed in conjunction with key enzymes catalyzing methane oxidation to formaldehyde and the ribulose monophosphate (RuMP) pathway for formaldehyde assimilation, suggesting partial denitrification linked to methane oxidation. Together, these data provide the first field-based evidence for methanotrophic partial denitrification by the OPU3 cluster under anoxic conditions, supporting a role for OMZs as key sites in pelagic methane turnover.

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Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

Cited by 1,203 publications

References 34 publications

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Metagenomic Binning Recovers a Transcriptionally Active Gammaproteobacterium Linking Methanotrophy to Partial Denitrification in an Anoxic Oxygen Minimum Zone

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