Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

Abstract

Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wildtype samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

“…The genomes were assembled using Platanus version 1.21 35 . Our genome-assembly pipeline involved assembling of DNA sequences using different parameters, merging results from different assemblies, removing redundant scaffolds, further scaffolding using transcripts, filling the gaps and correcting the errors ( Supplementary Fig.…”

Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

“…Paired-end and mate pair libraries of 2 kb and 5 kb insert sizes of T. transversa gDNA were sequenced using the Illumina HiSeq 2000 platform. We first trimmed Illumina adapters with Cutadapt 1.4.2 (93), then assembled the paired-end reads into contigs, scaffolded the assembly with the mate pair reads, and closed the gaps using Platanus 1.21 (94). The genomic scaffolds of T. transversa including Hox genes are available in the GenBank database (accession nos.…”

A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly

“…Genomic DNA was extracted from one wild-caught larva of P. xuthus (Tokyo, Japan) and one inbred larva of P. polytes. The draft genomes for P. polytes and P. xuthus were assembled with Illumina reads using Platanus (version 1.2.1) 6 , and validation and annotation of protein-coding genes were performed. Details have been provided in the Supplementary Note.…”

“…1a). During de novo genome assembly using Platanus 6 , we found some long regions with high allelic divergence in P. polytes but not in P. xuthus; these regions were further selected on the basis of having a coverage depth ≤350, which was approximately half of the peak for homozygous loci at 600 (Fig. 2b, bottom).…”