Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Udall, Joshua A.; Dawe, R. Kelly

doi:10.1105/tpc.17.00514

Cited by 40 publications

(40 citation statements)

References 47 publications

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“…With additional short-read sequencing data we were able to correct errors in the draft genome assembly, resulting in a basmati genome that was highly complete and accurate. Although the assembly is fragmented into multiple contigs, plant genomes still require additional technologies such as optical mapping or Hi-C sequencing for improving the contiguity of the assembly (Goodwin et al, 2016;Howe and Wood, 2015;Sedlazeck, Lee, et al, 2018;Udall and Dawe, 2018). Regardless, with this genome assembly we were able to make unique inferences on the origin and evolution of the basmati rice group.…”

Section: Discussionmentioning

confidence: 97%

Nanopore-based genome assembly and the evolutionary genomics of basmati rice

Choi

Lye

Groen

et al. 2018

Preprint

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BACKGROUNDThe circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group’s evolutionary history is not fully resolved. To address these gaps, we used long-read nanopore sequencing and assembled the genomes of two circum-basmati rice varieties, Basmati 334 and Dom Sufid.RESULTSWe generated two high-quality, chromosome-level reference genomes that represented the 12 chromosomes of Oryza. The assemblies showed a contig N50 of 6.32Mb and 10.53Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies we characterized structural variations segregating across circum-basmati genomes. We discovered repeat expansions not observed in japonica—the rice group most closely related to circum- basmati—as well as presence/absence variants of over 20Mb, one of which was a circum- basmati-specific deletion of a gene regulating awn length. We further detected strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow had its greatest effect on chromosome 10, causing both structural variation and single nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties showed three major geographically structured genetic groups: (1) Bhutan/Nepal group, (2) India/Bangladesh/Myanmar group, and (3) Iran/Pakistan group.CONCLUSIONAvailability of high-quality reference genomes from nanopore sequencing allowed functional and evolutionary genomic analyses, providing genome-wide evidence for gene flow between circum-aus and circum-basmati, the nature of circum-basmati structural variation, and the presence/absence of genes in this important and iconic rice variety group.

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Section: Discussionmentioning

confidence: 97%

Nanopore-based genome assembly and the evolutionary genomics of basmati rice

Choi

Lye

Groen

et al. 2018

Preprint

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“…To confirm our interpretation of the rice λ-4 event, we analyzed the original T0 plant by Bionano optical mapping, where long DNA molecules were fluorescently labeled at the restriction sites BspQI, imaged, and assembled into megabase-scale restriction map contigs 34 .…”

Section: Creation Of Long Arraysmentioning

confidence: 99%

Genome-scale sequence disruption following biolistic transformation in rice and maize

Liu¹,

Nannas

Fu³

et al. 2018

Preprint

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We biolistically transformed linear 48 kb phage lambda and two different circular plasmids into rice and maize and analyzed the results by whole genome sequencing and optical mapping.While some transgenic events showed simple insertions, others showed extreme genome damage in the form of chromosome truncations, large deletions, partial trisomy, and evidence of chromothripsis and breakage-fusion bridge cycling. Several transgenic events contained megabase-scale arrays of introduced DNA mixed with genomic fragments assembled by non-homologous or microhomology-mediated joining. Damaged regions of the genome, assayed by the presence of small fragments displaced elsewhere, were often repaired without a trace, presumably by homology-dependent repair (HDR). The results suggest a model whereby successful biolistic transformation relies on a combination of end joining to insert foreign DNA and HDR to repair collateral damage caused by the microprojectiles. The differing levels of genome damage observed among transgenic events may reflect the stage of the cell cycle and the availability of templates for HDR.

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“…3 and S4, the chromosomes and/or chromosome arms of all 12 de novo assemblies were highly supported by these ultra-long optical maps. Although www.nature.com/scientificdata www.nature.com/scientificdata/ rare, a few discrepancies between the optical maps and genome assemblies could be found and are likely due to small errors and chimeras that were produced through both the optical map and sequence assembly pipelines 15 .…”

Section: Background and Summarymentioning

confidence: 99%

A platinum standard pan-genome resource that represents the population structure of Asian rice

et al. 2020

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the 3,000 accessions can be subdivided into nine subpopulations, where most accessions from close subgroups could be associated to geographic origin 12. One critical piece of information missing from these analyses is the fact that single nucleotide polymorphisms (SNPs) and structural variations (SVs) present in subpopulation specific genomic regions have yet to be detected because the 3K-RG data set was only aligned to a single reference genome. Therefore, the next logical step, to capture and understand genetic variation pan-subpopulation-wide is to map the 3K-RG dataset to high-quality reference genomes that represent each of the subpopulations of cultivated Asian rice. At present, only a handful high-quality rice genomes for cultivated rice are publicly available 5,6,13,14 , thus, there is an immediate need for such a comprehensive resource to be created, which is the subject of this Data Descriptor. Here we present a reanalysis of the population structure analysis discussed above 12 and show that the 3K-RG dataset can be further subdivided into a total of 15 subpopulations. We then present the generation of 12 new and near-gap-free high-quality PacBio long-read reference genomes from representative accessions of the 12 subpopulations of cultivated Asian rice for which no high-quality reference genomes exist. All 12 genomes were assembled with more than 100x genome coverage PacBio long-read sequence data and then validated with Bionano optical maps 15. The number of contigs covering each of the twelve assemblies, excluding unplaced contigs, ranged from 15 (GOBOL SAIL (BALAM)::IRGC 26624-2) to 104 (IR 64). The contig N50 value for the 12-genome dataset ranged from 7.35 Mb to 31.91 Mb. When combined with 4 previously published genomes (i.e. Minghui 63 (MH 63), Zhenshan 97 (ZS 97) 13,14 , N 22 5 and the IRGSP RefSeq. 6), this 16-genome dataset can be used to represent the K = 15 population/admixture structure of cultivated Asian rice. Methods ethics statement. This work was approved by the University of Arizona (UA),

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Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Cited by 40 publications

References 47 publications

Nanopore-based genome assembly and the evolutionary genomics of basmati rice

Nanopore-based genome assembly and the evolutionary genomics of basmati rice

Genome-scale sequence disruption following biolistic transformation in rice and maize

A platinum standard pan-genome resource that represents the population structure of Asian rice

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