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. 2018 Jan 24;8(1):1498.
doi: 10.1038/s41598-018-19430-x.

Whole-genome Assembly of the Coral Reef Pearlscale Pygmy Angelfish (Centropyge Vrolikii)

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Free PMC article

Whole-genome Assembly of the Coral Reef Pearlscale Pygmy Angelfish (Centropyge Vrolikii)

Iria Fernandez-Silva et al. Sci Rep. .
Free PMC article

Abstract

The diversity of DNA sequencing methods and algorithms for genome assemblies presents scientists with a bewildering array of choices. Here, we construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae). The best candidate assembly combined all four data types and had a scaffold N50 127.5 times higher than the candidate assembly obtained from shotgun data only. Our best candidate assembly had a scaffold N50 of 8.97 Mb, contig N50 of 189,827, and 97.4% complete for BUSCO v2 (Actinopterygii set) and 95.6% complete for CEGMA matches. These contiguity and accuracy scores are higher than those of any other fish assembly released to date that did not apply linkage map information, including those based on more expensive long-read sequencing data. Our analysis of how different data types improve assembly quality will help others choose the most appropriate de novo genome sequencing strategy based on resources and target applications. Furthermore, the draft genome of the Pearlscale Pygmy angelfish will play an important role in future studies of coral reef fish evolution, diversity and conservation.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
The Pearlscale Pygmy Angelfish, Centropyge vrolikii.
Figure 2
Figure 2
Flow chart of each of the eight candidate assemblies. Colored ovals represent each of the eight assemblies with color indicating which sources of DNA were used. The bold oval represents our highest scoring and final assembly C_vrolikii_CAS243847_v1.0.
Figure 3
Figure 3
Comparison of four contiguity and accuracy statistics among the eight candidate assemblies described in Fig. 2. Contig N50, scaffold N50, scaffold N90 and the proportion of at least partial (complete and fragmented) genes present in our assembly of a set of 3,023 highly conserved single-copy orthologs (BUSCO score), considering fragments longer than 500 bp.
Figure 4
Figure 4
Comparison of the Pearlscale Pygmy Angelfish assembly with 18 other recently published fish assemblies. Assemblies are ranked by scaffold N50 and color coded by type of data that was utilized to generate the assembly (See also information in Table S3). Only scaffolds 1,000 bp and longer were considered for calculating scaffold N50 and CEGMA scores.
Figure 5
Figure 5
SyMAP synteny analyses between C. vrolikii and O. niloticus. (A) Syntenic mapping of C. vrolikii contigs to the O. niloticus chromosomes (a.k.a. linkage groups). (B) Whole genome dot plot. Dots represent anchors (“sequence matches”) and blue boxes indicate synteny blocks determined by the SyMap synteny-finding algorithm. (C) Circular view of the synteny between C. vrolikii contigs and the O. niloticus chromosomes.

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