plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.
Motivation Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth’s virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies. Results We describe a MetaviralSPAdes tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked MetaviralSPAdes on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines. Availability and implementation MetaviralSPAdes includes ViralAssembly, ViralVerify and ViralComplete modules that are available as standalone packages: https://github.com/ablab/spades/tree/metaviral_publication, https://github.com/ablab/viralVerify/ and https://github.com/ablab/viralComplete/. Supplementary information Supplementary data are available at Bioinformatics online.
Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.
Motivation: Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell's chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects. Results: We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes. Availability and implementation: PLASMIDSPADES is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/
To study the relatives of two grasses carrying an unusual 2-chromosome genome, Zingeria biebersteiniana and Colpodium versicolor, we have studied the phylogeny relationships of Colpodium sensu lato species and some other grasses by analysis of ITS1 and ITS2 of nuclear rDNA. Z. biebersteiniana (2n = 4, x = 2), Z. trichopoda (2n = 8, x = 2), and C. versicolor (2n = 4, x = 2) form a well supported clade with a single species of Colpodium s. l. complex,Catabrosella araratica (2n = 42, x = 7). All other Colpodium s.l. complex species form another well supported group [{Catabrosella variegata (2n = 10, x = 5), C. subornata (2 n= ?)} Hyalopoa pontica (2n = 28, x = 7), Paracolpodium altaicum (2n = 42, x = 7){Hyalopoa lanatiflora (2n = 28, x = 7), Catabrosa capusii (2n = 20, x = 5), C. aquatica (2n = 20, x = 5)}]. This clade is sister to group [{Puccinelia distans (2n = 42, x = 7), Sclerochloa dura (2n = 14,x = 7)}, Phippsia concinna (2n = 28, x = 7)].
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