A Hybridde novoAssembly of the Sea Pansy (Renilla muelleri) Genome

Abstract

24Background: Over 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range 25 of environments, from shallow tropical seas to the deep-ocean floor. They are important 26 foundation species that create coral "forests" which provide unique niches and three-dimensional 27 living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves 28 in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially 29 interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and 30 produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although 31 several cnidarian genomes are currently available, the majority are from hexacorals. Here, we 32 present a de novo assembly of the R. muelleri genome, making this the first complete draft 33 genome from an octocoral. 34 Findings: We generated a hybrid de novo assembly using the Maryland Super-Read Celera 35 Assembler v.3.2.6 (MaSuRCA). The final assembly included 4,825 scaffolds and a haploid 36 genome size of 172 Mb. A BUSCO assessment found 88% of metazoan orthologs present in the 37 genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had 38 detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or 39 to the Uniprot database. Although the R. muelleri genome is smaller (172 Mb) than other 40 publicly available, hexacoral genomes (256-448 Mb), the R. muelleri genome is similar to the 41 hexacoral genomes in terms of the number of complete metazoan BUSCOs and predicted gene 42 models. 43 Conclusions: The R. muelleri hybrid genome provides a novel resource for researchers to 44 investigate the evolution of genes and gene families within Octocorallia and more widely across 45 3Anthozoa. It will be a key resource for future comparative genomics with other corals and for 46 understanding the genomic basis of coral diversity. 47 48

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

“…De novo genome assembly of short and long reads was performed with the Maryland Super-Read Celera Assembler pipeline, MaSuRCA (Zimin et al, 2013;. This is one of the most common assemblers for performing short and long reads hybrid genome assemblies of eukaryotes, with consistently good results across studies (Jiang et al, 2019;Tan et al, 2018;Thai et al, 2019). In brief, MaSuRCA typically works as follows: Illumina pairedend short reads are first assembled into non-ambiguous super-reads, which are then mapped to Nanopore reads to further assemble them in long, high-quality pre-mega-reads.…”

Hybrid genome assembly and annotation of Danionella translucida, a transparent fish with the smallest known vertebrate brain

“…Multiple published assembly pipelines utilise a combination of short-and long-read sequencing. Our assembler of choice was MaSuRCA v3.2.6 (13), since it has already been used to generate high-quality assemblies of fish genomes, providing a large continuity boost even with low amount of input Nanopore reads (8,9). Briefly, Illumina paired-end shotgun reads were non-ambiguously extended into the superreads, which were mapped to Nanopore reads for error correction, resulting in megareads.…”

“…Long-read techniques, such as PacBio and Nanopore, can generate reads up to 2 Mb (7), but they are prone to er- rors, including frequent indels, which can lead to artefacts in long-read-only assemblies (6). Combining short-and longread sequencing technologies in hybrid assemblies recently produced high-quality genomes in fish (8,9). Here we report the hybrid Illumina/Nanopore-based assembly of the Danionella translucida genome.…”

HASLR: Fast Hybrid Assembly of Long Reads

“…Although LRs are becoming more widely used for de novo genome assembly, using hybrid approaches (that utilize a complementary SR dataset) is still popular for several reasons: (1) SRs have higher accuracy and can be generated by Illumina sequencers at a high throughput for a lower cost; (2) plenty of SR datasets are already publicly available for many genomes; (3) for some basic tasks such as variant calling (SNV and short indel detection), SRs still provide better resolution owing to their high accuracy, which often motivates researchers to generate SRs even when LRs are in hand; and (4) unlike PacBio assemblies whose accuracy increases with the depth of coverage thanks to their unbiased random error model (Myers, 2014), constructing reference quality genomes solely from ONT reads remains challenging owing to biases in base calling, even with a high coverage Antipov et al, 2015). As a result, hybrid assembly approaches are still useful (Jaworski et al, 2019;Jiang et al, 2019;Kadobianskyi et al, 2019).…”