Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Apr 15;20(1):184.
doi: 10.1186/s12859-019-2782-9.

FGMP: assessing fungal genome completeness

Ousmane H Cissé  1   2 , Jason E Stajich  3
Affiliations

FGMP: assessing fungal genome completeness

Ousmane H Cissé et al. BMC Bioinformatics. .

Abstract

Background: Inexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems. However, the quality of the assemblies of sampled genomes can vary greatly which hampers utility for comparisons and meaningful interpretation. The uncertainty of the completeness of a given genome sequence can limit feasibility of asserting patterns of high rates of gene loss reported in many lineages.

Results: We propose a computational framework and sequence resource for assessing completeness of fungal genomes called FGMP (Fungal Genome Mapping Project). Our approach is based on evolutionary conserved sets of proteins and DNA elements and is applicable to various types of genomic data. We present a comparison of FGMP and state-of-the-art methods for genome completeness assessment utilizing 246 genome assemblies of fungi. We discuss genome assembly improvements/degradations in 57 cases where assemblies have been updated, as recorded by NCBI assembly archive.

Conclusion: FGMP is an accurate tool for quantifying level of completion from fungal genomic data. It is particularly useful for non-model organisms without reference genomes and can be used directly on unassembled reads, which can help reducing genome sequencing costs.

Keywords: Assembly; Conserved elements; Gene model.

PubMed Disclaimer

Conflict of interest statement

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
The FGMP workflow. A typical workflow consists of three sequential modules (indicated by the boxes). The first module (FGMP_PROT) automates the use of different programs to evaluate the genome completeness based on pre-defined protein and nucleotide markers. Additional modules evaluate the patterns of conservation fungal multi-copy protein families. FGMP protein and nucleotide datasets are derived from 25 and nine fungal species, respectively (indicated as dotted arrows)
Fig. 2
Fig. 2
Estimation of genome completeness in fungal genomes. A comparison of genome completeness by multiple software tools using initial and latest genome assembly versions of 45 fungi. Genome completeness expressed as a percentage of expected markers (y-axis) is plotted against assembly size in megabases (x-axis). a FGMP completeness estimates based exclusively on protein markers are shown; (b) FGMP estimation based exclusively on highly conserved nucleotide segments; (c, d) BUSCO fungi and CEGMA completeness estimates respectively. In each plot, the dots represent distinct assemblies and color represents their status (red for the initial version and light blue for the latest version), and the diameters are proportional to the N50, a measure of assembly contiguity. Three representative species are highlighted in all panels (ellipses) to show the evolution of genome completeness between assembly versions. e Heat map of FGMP, BUSCO and CEGMA completeness estimates
Fig. 3
Fig. 3
Genomic loss simulations. The genomes of 57 fungal species were randomly truncated to evaluate accuracy of FGMP, BUSCO and CEGMA. The density plots represent the differences (expressed as percentages) between completeness estimates from the full and truncated assemblies
See this image and copyright information in PMC

References

    1. Sohn JI, Nam JW. The present and future of de novo whole-genome assembly. Brief Bioinform. 2018;19:23–40. - PubMed
    1. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499:431–437. doi: 10.1038/nature12352. - DOI - PubMed
    1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449:804–810. doi: 10.1038/nature06244. - DOI - PMC - PubMed
    1. Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, Stuber K, van Themaat EV, Brown JK, Butcher SA, Gurr SJ, Lebrun MH, Ridout CJ, Schulze-Lefert P, Talbot NJ, Ahmadinejad N, Ametz C, Barton GR, Benjdia M, Bidzinski P, Bindschedler LV, Both M, Brewer MT, Cadle-Davidson L, Cadle-Davidson MM, Collemare J, Cramer R, Frenkel O, Godfrey D, Harriman J, Hoede C, King BC, Klages S, Kleemann J, Knoll D, Koti PS, Kreplak J, Lopez-Ruiz FJ, Lu X, Maekawa T, Mahanil S, Micali C, Milgroom MG, Montana G, Noir S, O'Connell RJ, Oberhaensli S, Parlange F, Pedersen C, Quesneville H, Reinhardt R, Rott M, Sacristan S, Schmidt SM, Schon M, Skamnioti P, Sommer H, Stephens A, Takahara H, Thordal-Christensen H, Vigouroux M, Wessling R, Wicker T, Panstruga R. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science. 2010;330:1543–1546. doi: 10.1126/science.1194573. - DOI - PubMed
    1. Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canback B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Dore J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Hogberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Mycorrhizal Genomics Initiative C, Tunlid A, Grigoriev IV, Hibbett DS, Martin F. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet. 2015;47:410–415. doi: 10.1038/ng.3223. - DOI - PubMed