Sensitive protein alignments at tree-of-life scale using DIAMOND

Buchfink, Benjamin; Reuter, Klaus; Drost, Hajk-Georg

doi:10.1038/s41592-021-01101-x

Cited by 1,487 publications

(1,234 citation statements)

References 30 publications

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“…Taxonomic binners group sequences into bins labelled with a taxonomic identifier. For taxonomic binning, we evaluated 547 results for nine methods and versions: LSHVec v.cami2 49 , PhyloPythiaS+ v.1.4 54 , Kraken v.2.0.8-beta 55 and v.0.10.5-beta (cami1), DIAMOND v.0.9.28 56 , MEGAN v.6.15.2 57 , Ganon v.0.1.4 and v.0.3.1 58 , and NBC++ 59 . Of these, 75 were for the marine, 405 for strain madness, and 67 for plant-associated data, on either reads or gold standard assemblies (Supplementary Tables 2).…”

Section: Taxonomic Binning Challengementioning

confidence: 99%

Critical Assessment of Metagenome Interpretation - the second round of challenges

Meyer

Fritz

Deng

et al. 2021

Preprint

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Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from ∼1,700 novel and known microbial genomes, as well as ∼600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results.Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses.

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Section: Taxonomic Binning Challengementioning

confidence: 99%

Critical Assessment of Metagenome Interpretation - the second round of challenges

Meyer

Fritz

Deng

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…Clean data were assembled using SOAPdenovo2 short sequence assembly software [ 58 , 59 ]. The software Augustus 3.2.1 [ 60 ] was used for gene model prediction, and all gene annotations were completed by the software DIAMOND v2.0.7 [ 61 ] against seven databases (SWISS-PROT [ 62 ], COG [ 63 ], GO [ 64 ], KEGG [ 65 ], PHI [ 66 ], CAZy [ 67 ], and NCBI NR). The genomes of three strains of orchid mycorrhizal fungi— Sebacina vermifera (Accession No.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata

Ren

Zhao

Liu

et al. 2021

IJMS

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Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.

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“…The remaining reads were assembled into contigs by Trinityrnaseq [19]. The contigs longer than 500 bp were filtered and dereplicated (nucleotide identity > 95% and coverage rate > 80%) by CD-HIT [20] and aligned against the nonredundant protein database from NCBI (updated in March 2021) for taxonomic classification using Diamond blastX [21]. The BLASTX result was processed by the LCA algorithm (weighted LCA percent = 75%, e-value = 1 × 10 −5 , min Support = 1) with MEGAN [22].…”

Section: Methodsmentioning

confidence: 99%

Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020

Ren

Wang

Shi

et al. 2021

Preprint

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Mosquitoes are medically important arthropod vectors and harbor a great variety of viruses. The population density, species and virome of mosquitoes varies according to geography and climate. To investigate the dynamic changes in the species composition and diversity of mosquitoes and their viromes in Wuhan, China, a total of 2,345 adult mosquitoes collected from different habitats including an urban residential area, two hospitals, a scenic area, and a pig farm in a rural region from April to October 2020 were subjected to morphological identification, RT-qPCR and metagenomic sequencing. The results indicated that the dominant presence of Culex mosquitoes was observed in both urban regions (90.32%, 1538/1703) and the pig farm (54.98%, 353/642). Viromes of Culex showed dynamic changes during the collection time. Several viruses, such as Culex flavivirus, Alphamesonivirus 1, Hubei mosquito virus 2 and Hubei mosquito virus 4, had seasonal changes and unimodal increases or declines. Other viruses, such as Wuhan mosquito virus 6, Hubei virga-like virus 2 and Zhejiang mosquito virus 3, were stable in all collected Culex and should be potential members of "core viromes". This study improves the understanding of the dynamic composition of mosquitoes and the viromes they carry and provides useful information for informing mosquito control and mosquito-borne disease prevention strategies.

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Sensitive protein alignments at tree-of-life scale using DIAMOND

Cited by 1,487 publications

References 30 publications

Critical Assessment of Metagenome Interpretation - the second round of challenges

Critical Assessment of Metagenome Interpretation - the second round of challenges

Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata

Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020

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