Dramatic improvement in genome assembly achieved using doubled-haploid genomes

Abstract

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

“…Following hybrid assembly of PacBio and Illumina reads, Li and colleagues 33 reported a N50 of 112 kb, whereas we obtained a N50 of 620 kb at that same step. These results highlight the power of haploids or doubled haploids in genome sequencing projects 48 , particularly in those for apple, which is not only highly heterozygous but has also undergone a recent whole-genome duplication (ref. 6 and this study).…”

“…This affected all types of TEs, suggesting that the precursor of the modern apple underwent environmental changes with resulting stresses that led to the activation of these TEs 50 . The observed TE burst corresponds to the Miocene epoch (23 Mya to 5 Mya) and may coincide with two events: the divergence between pear and apple 48 and an uplift event occurring at the Tian Shan mountains 51 , which cover the region where the ancestor of the apple originates from 52 . We hypothesize that these TE bursts, which presumably must have been very different in the predecessor of pear and apple, have contributed to the diversification, and possibly even speciation, of these plants.…”

Doubled Haploid ‘CUDH2107’ as a Reference for Bulb Onion (Allium cepa L.) Research: Development of a Transcriptome Catalogue and Identification of Transcripts Associated with Male Fertility

“…RNA-seq is a particularly attractive approach in non-model crops that have large genomes, where genomic sequencing is complex and expensive. To aid downstream analysis and avoid detection of false SNPs, a good quality transcriptome assembly is essential [3, 5, 6]. However in species that are highly heterozygous, such as bulb onion, the development of a high quality reference transcriptome is challenging, as it is hard to distinguish the transcripts belonging to different members of a gene family from allelic variants of a particular gene [2, 3, 5].…”

“…However in species that are highly heterozygous, such as bulb onion, the development of a high quality reference transcriptome is challenging, as it is hard to distinguish the transcripts belonging to different members of a gene family from allelic variants of a particular gene [2, 3, 5]. In out-crossing crop plants, such as bulb onion, the complications of heterozygosity can be overcome by using homozygous double haploids [1, 6]. Double haploid (DH) lines have been developed in bulb onion and have proved useful for various genetic and genomic studies [7–10].…”

A novel approach for the assembly of complex genomic DNA cloned into bacterial artificial chromosome vectors: assembly and analysis of Triticum aestivum chromosome arm 7DS

“…This greatly complicates the assembly process (Kajitani et al, 2014). For sequencing and assembly, doubled haploids offer reduced heterozygosity, which has been shown to improve genome assembly (Hong Zhang et al, 2014). …”