A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding

Abstract

SUMMARY The assembly and scaffolding of plant crop genomes facilitate the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato (Solanum lycopersicum) has been improved through the introgression of genetic material from related wild species, including resistance to pandemic strains of tobacco mosaic virus (TMV) from Solanum peruvianum. Here we applied PacBio HiFi and ONT Nanopore sequencing to develop independent, highly contiguous and complementary assemblies of an inbred TMV‐resistant tomato variety. We show specific examples of how HiFi and ONT datasets can complement one another to improve assembly contiguity. We merged the HiFi and ONT assemblies to generate a long‐read‐only assembly where all 12 chromosomes were represented as 12 contiguous sequences (N50 = 68.5 Mbp). This chromosome scale assembly did not require scaffolding using an orthogonal data type. The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato genome assemblies that made use of genetic maps and Hi‐C for scaffolding. Our long‐read‐only assembly reveals that a complex series of structural variants linked to the TMV resistance gene likely contributed to linkage drag of a 64.1‐Mbp region of the S. peruvianum genome during tomato breeding. Through marker studies and ONT‐based comprehensive haplotyping we show that this minimal introgression region is present in six cultivated tomato hybrid varieties developed in three commercial breeding programs. Our results suggest that complementary long read technologies can facilitate the rapid generation of near‐complete genome sequences.

plotsr: visualizing structural similarities and rearrangements between multiple genomes

“…plotsr generates publication-quality visualizations that have already been used by several research groups ( Li et al , 2021 ; van Rengs et al , 2022 ; Zamyatin et al , 2021 ; Zhang et al , 2021 ). We believe that plotsr visualizations will help in getting a better understanding of the genome divergence of a species.…”

Genomic, transcriptomic, and metabolomic analysis of Traditional Chinese Medicine plantOldenlandia corymbosareveals the biosynthesis and mode of action of anti-cancer metabolites

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Towards smart and sustainable development of modern berry cultivars in Europe

“…Recent improvements have made it possible to obtain a phased genome of tetraploid blueberry (Colle et al., 2019). By contrast, improvements in long‐read sequencing technology (Dumschott et al., 2020; van Rengs et al., 2022) coupled with open‐source technologies (Chen et al., 2021; Cheng et al., 2021; Schrinner et al., 2020) have unraveled the black raspberry (VanBuren et al., 2018) and octoploid strawberry (Edger et al., 2019) genomes, and pangenomic analysis has shed light on the evolutionary history of strawberry (Feng et al., 2021; Hardigan et al., 2021; Liston et al., 2020; Qiao et al., 2021). For practical breeding purposes, high‐quality genome resources should reflect the allelic diversity of cultivated strawberry, which was found to be generally high in cosmopolitan collections (Hardigan et al., 2021), but lower in a subset from California (Hardigan et al., 2018).…”