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Comparative Study
. 2019 Mar 1;8(3):giy163.
doi: 10.1093/gigascience/giy163.

A Critical Comparison of Technologies for a Plant Genome Sequencing Project

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Free PMC article
Comparative Study

A Critical Comparison of Technologies for a Plant Genome Sequencing Project

Pirita Paajanen et al. Gigascience. .
Free PMC article

Abstract

Background: A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow and expensive, whereas faster, cheaper short-read-only assemblies can be incomplete and highly fragmented, which minimizes their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e.g., human) genomes. However, plant genomes can be much more repetitive and larger than the human genome, and plant biochemistry often makes obtaining high-quality DNA that is free from contaminants difficult. Reflecting their challenging nature, we observe that plant genome assembly statistics are typically poorer than for vertebrates.

Results: Here, we compare Illumina short read, Pacific Biosciences long read, 10x Genomics linked reads, Dovetail Hi-C, and BioNano Genomics optical maps, singly and combined, in producing high-quality long-range genome assemblies of the potato species Solanum verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA compute requirements and sequencing costs.

Conclusions: The field of genome sequencing and assembly is reaching maturity, and the differences we observe between assemblies are surprisingly small. We expect that our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.

Keywords: 10x Genomics; PacBio; Pacific Biosciences; assembly; long reads; optical mapping; short reads.

Figures

Figure 1:
Figure 1:
Comparison of contig/scaffold lengths and total assembly sizes of the various S. verrucosum assemblies.
Figure 2:
Figure 2:
k-mer spectra plots from the k-mer Analysis Toolkit comparing three S. verrucosum contig assemblies. The heights of the bars indicate how many k-mers of each multiplicity appear in the raw Discovar reads. The colors indicate how many times those k-mers appear in the respective assemblies with black being zero times and red being one time. A colored bar at zero multiplicity indicates k-mers appearing in the assembly that do not appear in the reads. The Falcon assembly has been polished with the Illumina reads using Pilon to reduce the effect of using a different sequencing platform.
Figure 3:
Figure 3:
Busco analysis of supernova-bn, discovar-mp-dt-bn, and falcon-dt-bn using the plant gene dataset.
Figure 4:
Figure 4:
Box and whisker plot showing completeness of the S. tuberosum transcripts in supernova-bn, discovar-mp-dt-bn, and falcon-dt-bn with various levels of minimum percentage identity.
Figure 5:
Figure 5:
A difficult region of the genome that is contiguously assembled with a PacBio BAC but in none of our whole-genome assemblies. The region was correctly scaffolded by Dovetail. The figure shows various alignments and information with respect to the BAC assembly. The top track shows the contigs that appear in the discovar, falcon, and supernova assemblies. The paired-end track shows read coverage of the Discovar paired-end library. The mate-pair and Dovetail tracks show physical/fragment coverage of the mate-pair and Dovetail libraries, respectively. The bottom track shows GC content of the sequence as well as homopolymers sequences of at least 5  bp where A, C, G, and T are colored red, blue, yellow, and green, respectively.
Figure 6:
Figure 6:
Mummer plots showing alignment to chromosome 11 of the S. tuberosum reference version 4.03. The S. tuberosum reference is shown on the x-axis and assembly scaffolds on the y-axis. Alignments shown are at least 10 kbp long and 90% identical.

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