Improved maize reference genome with single-molecule technologies

Abstract

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation 1 . These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions 2 . Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome 3 , our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing 4 . In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

A reference genome of the Chinese hamster based on a hybrid assembly strategy

“…Recent studies have highlighted the improvements of SMRT-only assemblies compared to Illumina-only assemblies [Bickhart et al, 2017], [Gordon et al, 2016], [Jiao et al, 2017], [Zhang et al, 2016], [Shi et al, 2016]. Here we found that both the pooled Illumina assembly (with mixed read length) and the PacBio SMRT-only assembly resulted in substantially improved assembly statistics compared to the two published hamster genome assemblies (Table 1), with an order of magnitude fewer scaffolds and 2–4x larger N50 values.…”

“…The acquisition of such contiguous sequences is possible now with third generation sequencing technologies, such as Single Molecule Real Time (SMRT) sequencing technology [Eid et al, 2009], which provide mean read lengths that are more than an order of magnitude larger than earlier sequencing technologies. The reads can span repetitive elements, resulting in longer contigs and minimal gaps within scaffolds [Bickhart et al, 2017], [Jiao et al, 2017], [Gordon et al, 2016]. This enables the routine assembly of mammalian genomes approaching the current quality of the human genome.…”

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

“…We have aligned Bionano genome assemblies to several sequenced genomes using the runCharacterize method from Bionano (Table 1). For example, aligning optical maps to the genome assemblies from two maize inbreds resulted in a high level of congruence between uniquely mapped Bionano consensus molecules and the assembled sequence (96% and 98% mapping rate of B73 and W22, respectively; Jiao et al, 2017). The very high percentage of alignment between the maize optical and sequence maps can in part be attributed to the high N50 of their respective sequence assemblies.…”

“…Michael et al (2017) describe the assembly of an entire Arabidopsis genome using Oxford Nanopore technology and confirm the assembly with Bionano optical mapping. PacBio frequently has been used to assemble the genomes of model species, and it combines well with optical mapping (Jiao et al, 2017), but sufficient coverage can be cost-limiting for many projects.…”

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

“…Such questions will best be approached through a comparative analysis of maize cell types, developmental states, and genetic variants. With the rapidly growing resources available for other maize lines (Lu et al, 2015;Andorf et al, 2016;Hirsch et al, 2016;Jiao et al, 2017), the ability to integrate the multiple kinds of information represented in replication timing profiles will greatly facilitate comparative analyses of the maize pan-genome.…”