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.
Highlights
Advances in genomic approaches addressing questions in ecology and evolution have led to a dramatic increase in the number of de novo whole genome assemblies of non-model organisms[1]
The C. vrolikii genome presented here will serve as a starting point for many future studies on speciation, taxonomy, and the evolution of color and hybridization
In an analogous analysis of 248 core eukaryotic genes (CEGs)[10], we found that 238 were represented (224 complete)
Summary
Advances in genomic approaches addressing questions in ecology and evolution have led to a dramatic increase in the number of de novo whole genome assemblies of non-model organisms[1]. De novo assemblies face many challenges, such as the presence of large genomic portions of repetitive content, including the repetitive structure near centromeres and telomeres, large paralogous gene families, and interspersed nuclear elements such as LINEs and SINEs, which often lead to fragmented assemblies. To overcome these challenges, various long read sequencing platforms have emerged, such as Single Molecule, Real-Time (SMRT) Sequencing (PacBio), nanopore sequencing (Oxford Nanopore and Nabsys), and various methods that take advantage of chromosomal structure and patterns (Illumina TruSeq Synthetic Long Read, BioNano Genomics, Dovetail’s Chicago method, and 10× Genomics). This genome is an important contribution to the list of marine vertebrate genomes, which currently lags far behind the list of terrestrial vertebrate genomes[1]
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