Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

Gautam, Anupam; Felderhoff, Hendrik; Bağcı, Caner; Huson, Daniel H.

doi:10.1128/msystems.01408-21

Cited by 23 publications

(20 citation statements)

References 46 publications

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“…The persistent genomes of species group A and B comprise 4,129 and 4,014 CDSs respectively or 79.93% and 76.63% of their mean gene number (Supplementary data). The detected coding sequences were further compared to the PlaBA-db and Annotree databases (Gautam et al, 2022;Mendler et al, 2019;Patz et al, 2021Patz et al, , 2024. In both cases, gene function does segregate the different strains into the previously determined species groups, suggesting different metabolic capacities and different ecologies (Figure 1F & 1G).…”

Section: Strains Affiliated To P Polymyxa Segregate Into Distinct Spe...mentioning

confidence: 86%

Genomic diversity inPaenibacillus polymyxa: Unveiling distinct species groups and functional variability

Wallner,

Antonielli,

Mesguida

et al. 2024

Preprint

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Paenibacillus polymyxa is a bacterial species of high interest, as suggested by the increased number of publications on its functions in the past years. Accordingly, the number of described strains and sequenced genomes is also on the rise. While functional diversity was repeatedly suggested for this species, the available genomic data is now sufficient to confidently segregate strains affiliated to P. polymyxa into two major species groups. As these strains exhibit considerable potential in agriculture, medicine, and bioremediation, it is preferable to clarify their taxonomic affiliation to facilitate reliable and durable approval as active ingredients. Strains currently affiliated to P. polymyxa can be separated into two major species groups with differential potential in nitrogen fixation, plant interaction, secondary metabolism, and antimicrobial resistance, as inferred from genomic data.

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Section: Strains Affiliated To P Polymyxa Segregate Into Distinct Spe...mentioning

confidence: 86%

Genomic diversity inPaenibacillus polymyxa: Unveiling distinct species groups and functional variability

Wallner,

Antonielli,

Mesguida

et al. 2024

Preprint

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show abstract

“…In addition, the sequences of proteins such as RdRp (RNA-directed RNA polymerase), Rep (replication-associated protein) and NS1 (non-structural protein) were also downloaded from the RefSeq database to align contigs with sequence length > 1500 bp. The rma2info program built into MEGAN6[ 30 ] was used to perform taxonomic identification. Putative open reading frames (ORFs) were predicted by Geneious Prime with built-in parameters (Minimum size: 100)[ 27 ], and were further checked through comparing to related viruses.…”

Section: Methodsmentioning

confidence: 99%

Characterization of a novel papillomavirus identified from a whale (Delphinapterus leucas) pharyngeal metagenomic library

Zhu

Dai

2023

Virol J

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Here, using viral metagenomic method, a novel whale papillomavirus (temporarily named wPV, GenBank accession number OP856597) was discovered in a whale (Delphinapterus leucas) pharyngeal metagenomic library. The complete genome size of wPV is 7179 bp, with GC content of 54.4% and a nucleotide composition of 23.4% A, 22.3% T, 28.4% G, and 25.9% C. The viral genome has a typical papillomavirus organization pattern, and five ORFs were predicted, including two late genes encoding L1 and L2, and three early genes encoding E1, E2, and E6. Pairwise sequence comparison and phylogenetic analysis based on the L1 gene sequence indicated that wPV may be a novel species within genus Dyodeltapapillomavirus. In addition, the E2 region of wPV was predicted to have a potential recombination event. The discovery of this novel papillomavirus increases our understanding of the viral ecology of marine mammals, providing insights into possible future infectious diseases.

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“…As an additional control, the HQ reads were analyzed using the DIAMOND+MEGAN pipeline [ 25 , 26 ]. DIAMOND [ 27 ] blastx mode (–top 10 -f 100 -b24 -c1) was used to align the reads against the NCBI-nr database, and then the daa-meganizer tool (MEGAN Ultimate Edition version 6.22.1; -mdb megan-map-Feb2021-ue.db) [ 28 , 29 ] was used to perform taxonomic binning. Then, the daa2info tool was used to check the alignment (-c2c Taxonomy -u true -n true), establishing that a high percentage of reads were aligned to S. cerevisiae .…”

Section: Methodsmentioning

confidence: 99%

Easy efficient HDR-based targeted knock-in in Saccharomyces cerevisiae genome using CRISPR-Cas9 system

et al. 2022

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During the last two decades, yeast has been used as a biological tool to produce various small molecules, biofuels, etc., using an inexpensive bioprocess. The application of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein (Cas) techniques in yeast genetic and metabolic engineering has made a paradigm shift, particularly with a significant improvement in targeted chromosomal integration using synthetic donor constructs, which was previously a challenge. This study reports the CRISPR-Cas9-based highly efficient strategy for targeted chromosomal integration and in-frame expression of a foreign gene in the genome of Saccharomyces cerevisiae ( S. cerevisiae ) by homology-dependent recombination (HDR); our optimized methods show that CRISPR-Cas9-based chromosomal targeted integration of small constructs at multiple target sites of the yeast genome can be achieved with an efficiency of 74%. Our study also suggests that 15 bp microhomology flanked arms are sufficient for 50% targeted knock-in at minimal knock-in construct concentration. Whole-genome sequencing confirmed that there is no off-target effect. This study provides a comprehensive and streamlined protocol that will support the targeted integration of essential genes into the yeast genome for synthetic biology and other industrial purposes. Highlights • CRISPR-Cas9 based in-frame expression of foreign protein in Saccharomyces cerevisiae using Homology arm without a promoter. • As low as 15 base pairs of microhomology (HDR) are sufficient for targeted integration in Saccharomyces cerevisiae . • The methodology is highly efficient and very specific as no off-targeted effects were shown by the whole-genome sequence.

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

Cited by 23 publications

References 46 publications

Genomic diversity inPaenibacillus polymyxa: Unveiling distinct species groups and functional variability

Genomic diversity inPaenibacillus polymyxa: Unveiling distinct species groups and functional variability

Characterization of a novel papillomavirus identified from a whale (Delphinapterus leucas) pharyngeal metagenomic library

Easy efficient HDR-based targeted knock-in in Saccharomyces cerevisiae genome using CRISPR-Cas9 system

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