The draft nuclear genome assembly ofEucalyptus pauciflora: new approaches to comparingde novoassemblies
Abstract
Background
Selecting the best genome assembly from a collection of draft assemblies for the same species remains a difficult task. Here, we combine new and existing approaches to help to address this, using the non-model plantEucalyptus pauciflora(snow gum) as a test case.Eucalyptus pauciflorais a long-lived tree with high economic and ecological importance. Currently, little genomic information forEucalyptus pauciflorais available.
Findings
We generated high coverage of long-(Nanopore, 174x) and short-(Illumina, 228x) read data from a singleEucalyptus paucifloraindividual and compared assemblies from four assemblers with a variety of settings: Canu, Flye, Marvel, and MaSuRCA. A key component of our approach is to keep a randomly selected collection of ~10% of both long- and short-reads separate from the assemblies to use as a validation set with which to assess the assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in eight ways: contig N50, BUSCO scores, LAI scores, assembly ploidy, base-level error rate, computing genome assembly likelihoods, structural variation and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ~0.006 errors per base.
Conclusions
We report a draft genome ofEucalyptus pauciflora, which will be a valuable resource for further genomic studies of eucalypts. These approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies for a single species.
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