Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection

Abstract

Background: Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemblies. Nowadays, technologies such as DNA long read sequencing and optical mapping have revolutionized the understanding of SVs in genomes, due to the enhancement of the power of SVs detection. This study aims to investigate performance of two techniques, 1) long-read sequencing obtained with the MinION device (Oxford Nanopore Technologies) and 2) optical mapping obtained with Saphyr device (Bionano Genomics) to detect and characterize SVs in the genomes of the two ecotypes of Arabidopsis thaliana, Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1).

Results: We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 against the public reference genome Col-0 TAIR10.1. After filtering (SV > 1 kb), 1184 and 591 Ler-1 SVs were retained from ONT and Bionano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted.

Conclusions: Structural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference genome, most of the detected SVs discovered by both technologies were found in the same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the latter being more efficient to characterize large SVs. Even if both technologies are complementary approaches, ONT data appears to be more adapted to large scale populations studies, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference.

Keywords: Arabidopsis thaliana; Bionano Genomics optical mapping; High molecular weight DNA; Oxford Nanopore technologies; Structural variations.

Fig. 1

Circos visualization of Evry.Ler-1 SVs landscape. All comparisons were performed against the Col-0 TAIR10.1 reference genome per 100kb bins. From external to internal layer (Circle1 to Circle7): Circle1: Col-0 TAIR10.1 chromosomes (ticks every 100 kb): black and light grey rectangles represent centromeric and NOR regions respectively; Circle2: Average mapping coverage for Evry.Col-0 ONT reads (grey line) and Evry.Ler-1 ONT reads (orange line) with dark orange if coverage > 46X; Circle3: DLE-1 label density as purple line (dark purple if density > 18 label per 100 kb); Circle4: Genes density as green line (dark green if density > 23), NLR Genes [58] indicated as green rectangles; Circle5: TEs density as blue line (dark blue if density > 58); Circle6: ONT SVs occurrences as orange outward bars (dark orange bars represent ONT- specific SVs); Circle7: Bionano SVs occurrences as purple inward bars (dark purple bars represent Bionano-specific SVs)

Fig. 2

Number of Evry.Ler-1 structural variations detected by ONT and Bionano against the Col-0 TAIR10.1 reference genome and overlaps in locations between the two technologies. The bars and circles colored in orange and purple correspond respectively to the ONT and Bionano technologies. A Barplot of SV number for insertions (INS), deletions (DEL), inversions (INV), translocations (TRA) and all SVs (TOTAL) obtained using ONT and Bionano technologies. B Venn diagramm of common and specific locations detected by ONT and Bionano technologies

Fig. 3

Focus of large structural variations (MU) located in complex locations. For each location, optical maps are colored in green for the Col-0 TAIR10.1 reference maps (ChrM for mitochondrial chromosome map) and light blue for Evry.Ler-1 maps. Consistent DLE-1 enzyme label between reference and Evry.Ler-1 maps are represented by dark blue bars with grey links between the genome maps. Inconsistent DLE-1 enzyme label are shown by yellow bars on the two genome maps. The purple bars represent the insertion events on the Evry.Ler-1 maps / read / assembly, and the black, yellow and pink bars correspond to deletions, inversions and translocations respectively. Araport11 annotation of the Col-0 TAIR10.1 reference (Genes and TE) and IGV view of the Evry.Ler-1 trimmed ONT reads and SMARTdenovo contigs minimap alignments are also presented. A Bionano Chr2 Evry.Ler-1 translocations against Col-0 TAIR10.1 reference genome (MU_153). B Bionano Chr4 Evry.Ler-1 extra-range size inversion against Col-0 TAIR10.1 reference genome (MU_097). C Bionano Chr4 Evry.Ler-1 large deletion against Col-0 TAIR10.1 reference genome (MU_102). D Bionano Chr5 Evry.Ler-1 inversion against Col-0 TAIR10.1 reference genome (MU_138)

Fig. 4

Size distribution and median comparison of ONT and Bionano SV. All p-values were obtained with a two-sided oriented Wilcoxon rank-sum test. Hypothesis H0 was “median of ONT SV size is less than Bionano one”. ONT and Bionano boxplots are colored in orange and purple respectively. Medians are represented by red dots. A Boxplot of ONT (n=1184) and Bionano (n=591) SV>1kb. B Boxplot of ONT (n=1169) and Bionano (n=573) 1kb<SV<50kb. C Boxplot of ONT (n=591) and Bionano (n=289) INS>1kb. D Boxplot of ONT (n=588) and Bionano (n=282) 1kb<INS<50kb. E Boxplot of ONT (n=581) and Bionano (n=295) DEL>1kb. F Boxplot of ONT (n=571) and Bionano (n=288) 1kb<DEL<50kb