DOI: 10.5061/dryad.msbcc2g3j
title: A high-quality genome assembly for Dillenia turbinata (Dilleniales)

description: Objectives: Dillenia turbinata (Dilleniaceae) is a member of the order
 Dilleniales, an enigmatic clade of critical importance for understanding
 the diversification history of flowering plants but for which genome
 sequences are not available. We have produced and annotated a
 chromosome-scale whole genome assembly for D. turbinata through the
 resources of the 10KP (10,000 Plants) Genomes Project. The genome assembly
 and associated data provided here will serve as a useful resource for
 comparative and evolutionary genomics research across the flowering
 plants. Data description: The D. turbinata genome was assembled from
 Oxford Nanopore Technology (ONT) and whole-genome shotgun (WGS) sequences,
 and scaffolded into chromosome-scale pseudomolecules using Hi-C data. The
 genome assembly is 723,739,077 base pairs in length with a BUSCO
 completeness score of 97%.  Twenty-eight scaffolds contain more
 than 99% of the assembly. The repeat-masked genome sequence is annotated
 with 36,967 protein-coding gene models (93% BUSCO completeness) supported
 by transcriptome/protein evidence and/or Pfam domain content. These
 measures indicate high contiguity and completeness for the D. turbinata
 genome.
description: <strong>Genome assembly and
 annotation</strong> Raw nanopore reads in fastq format were
 assembled with Canu v2.2 (Koren et al. 2017) using an estimated genome of
 900Mb to guide coverage parameters during the read correction, trimming,
 and assembly steps of the pipeline. The resulting primary assembly was
 polished with the WGS reads using NextPolish v1.3.1 (Hu et al. 2020), and
 duplicated constructs were removed by Purge Haplotigs (Roach et al. 2018).
 The set of deduplicated contigs was scaffolded on the basis of Hi-C reads
 using the Juicer pipeline (Durand et al. 2016) and 3d-dna tools (Dudchenko
 et al. 2017) with default parameters. Genome annotation was
 performed using the MAKER-P pipeline
 (Campbell et al. 2014) supplied with coding DNA sequences
 (CDS) from a
 Trinity (Grabherr et al. 2011) assembly of
 the
 <em>Dillenia</em> transcriptome reads, proteomes from four publicly available eudicot genomes —<em>Arabidopsis thaliana</em>, <em>Aquilegia coerulea</em>, <em>Nelumbo nucifera</em>, and <em>Vitis vinifera</em>, and a custom repeat library of transposable elements (TEs) produced by RepeatModeler2 (Flynn et al. 2020) for the <em>Dillenia </em>genome. Gene models were predicted from the masked assemblies using the SNAP (Korf 2004) and AUGUSTUS<sup> </sup>(Stanke and Waack 2003) <em>ab initio</em> gene predictors after three rounds of training on interim high-quality (AED &lt;= 0.25; length &gt;= 50 amino acids) and BUSCO gene models, respectively. All evidence-based and <em>ab initio</em> gene predictions that were supported by the presence of functional protein domains were retained in the final genome annotation.
description: The included data files may be opened with MS Word (Detailed
 Methods.docx), MS Ecel (Dillenia.genome.assembly.stats.xlsx), standard
 image viewer software (Dillenia.BUSCO.summaries.png), and standard text
 editor programs (Dillenia.genome.fasta and
 Dillenia.maker.predict.36967.final.gff), .