A critical comparison of technologies for a plant genome sequencing project

Abstract

BackgroundA high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow and expensive, whereas faster, cheaper short-read–only assemblies can be incomplete and highly fragmented, which minimizes their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e.g., human) genomes. However, plant genomes can be much more repetitive and larger than the human genome, and plant biochemistry often makes obtaining high-quality DNA that is free from contaminants difficult. Reflecting their challenging nature, we observe that plant genome assembly statistics are typically poorer than for vertebrates.ResultsHere, we compare Illumina short read, Pacific Biosciences long read, 10x Genomics linked reads, Dovetail Hi-C, and BioNano Genomics optical maps, singly and combined, in producing high-quality long-range genome assemblies of the potato species Solanum verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA compute requirements and sequencing costs.ConclusionsThe field of genome sequencing and assembly is reaching maturity, and the differences we observe between assemblies are surprisingly small. We expect that our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.

High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

“…The weak hint for tetraploidy might be due to a whole genome duplication event early in the diversification of the genus. The N50 of 3.2 Mbp is in the expected range for a long read assembly of a highly heterozygous plant species which contains quite some repetitive sequences as others reported similar values before [49]. Due to regions of merged haplophases the total assembly size of 485 Mbp is smaller than expected for a fully phase separated “diploid” genome sequence based on the haploid genome size estimation of 322 Mbp.…”

“…A higher ploidy would result in more distinct coverage peaks as observed for a genome with up to pentaploid parts [29]. The N50 of 3.2 Mbp is in the expected range for a long read assembly of a highly heterozygous species as others reported similar values before [36]. Due to regions of merged haplophases the total assembly size of 485 Mbp is smaller than expected for a fully phase separated “diploid” genome sequence based on the haploid genome size estimation of 322 Mbp.…”

A guide to sequence your favorite plant genomes

“…Paajanen et al. () recently applied almost all of the methods mentioned above (with the exception of Nanopore) to assemble the Solanum verrucosum Schltdl. genome, and this could be used as a good benchmark reference.…”

High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

“…We demonstrate a high level of completeness of the assembly and identify a number of candidate genes for future analyses on evolutionary adaptations in cetaceans. Scaffolding with Chicago Library method (i.e., in vitro proximity ligation) has previously produced high‐quality genomes in plants (Moll et al., ; Paajanen et al., ), insects (Nosil et al., ; Wachi, Matsubayashi, & Maeto, ) and birds (Holt et al., ). We have applied this method to a sample from a deceased by‐caught cetacean specimen, demonstrating that this approach can be successfully used for nonmodel mammal species and samples of lower quality.…”