ArticleGigaScience2020
The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 60 citations in OpenAlex.
- Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.Molecular ecology resources · 2025Article
- A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world's tallest trees.BMC genomics · 2024Article
- Plant genome evolution in the genusGenome research · 2024Article
- Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome ofFrontiers in plant science · 2024Article
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- Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms.Scientific data · 2023Article
- A practical assembly guideline for genomes with various levels of heterozygosity.Briefings in bioinformatics · 2023Article
- Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus.G3 (Bethesda, Md.) · 2023Article
- Complete Genome of Rose Myrtle,Plants (Basel, Switzerland) · 2023Article
- A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes.GigaScience · 2022Article
- Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids.GigaScience · 2022Article
- Establishing MinION Sequencing and Genome Assembly Procedures for the Analysis of the Rooibos (Plants (Basel, Switzerland) · 2022Article
- The Australian dingo is an early offshoot of modern breed dogs.Science advances · 2022Article
- Green plant genomes: What we know in an era of rapidly expanding opportunities.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Can Forest Trees Cope with Climate Change?-Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change.International journal of molecular sciences · 2021Review
- LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology.Genome biology · 2021Article
- Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation.Genomics & informatics · 2021Article
- Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom.Scientific reports · 2021Article
- An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome.Molecular ecology resources · 2021Article
- GSER (a Genome Size Estimator using R): a pipeline for quality assessment of sequenced genome libraries through genome size estimation.Interface focus · 2021Article
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Authors and funding
7 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEucalyptus pauciflora (the snow gum) is a long-lived tree with high economic and ecological importance. Currently, little genomic information for E. pauciflora is available. Here, we sequentially assemble the genome of Eucalyptus pauciflora with different methods, and combine multiple existing and novel approaches to help to select the best genome assembly.
findingsWe generated high coverage of long- (Nanopore, 174×) and short- (Illumina, 228×) read data from a single E. pauciflora individual and compared assemblies from 5 assemblers (Canu, SMARTdenovo, Flye, Marvel, and MaSuRCA) with different read lengths (1 and 35 kb minimum read length). A key component of our approach is to keep a randomly selected collection of ∼10% of both long and short reads separated from the assemblies to use as a validation set for assessing assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in 8 ways: contig N50, BUSCO scores, LAI (long terminal repeat assembly index) scores, assembly ploidy, base-level error rate, CGAL (computing genome assembly likelihoods) scores, 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.
conclusionsWe report a draft genome of E. pauciflora, which will be a valuable resource for further genomic studies of eucalypts. The approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies from a single dataset.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.