Large structural variations in the haplotype-resolved African cassava genome

Abstract

Cassava (Manihot esculenta Crantz, 2n=36) is a global food security crop. Cassava has a highly heterozygous genome, high genetic load, and genotype-dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi-C to resolve each haplotype of the genome of a farmer-preferred cassava line, TME7 (Oko-iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON-Phase and Hi-C read data. The ultra-long-range information from Hi-C sequencing was also used for scaffolding. Comparison of the two phases revealed more than 5,000 large haplotype-specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele specific expression was further explored. RNA-seq data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy-to-use web-based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype-specific structural variation, gene hemizygosity, and allele specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava.

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage

“…In general, the syntenic blocks detected between Amborella and other species were very small (just containing the sMYB– PRR or PIF3– PHYA linkages), suggesting that there is selective pressure to retain these genes in syntenic blocks even as surrounding genes are fractionated. For the CCA1LHY– PRR5/9 and RVE4/8– PRR3/7 linkages there are eight different combinations possible ( Supplemental Figure S7 ), all of which were detected across an array of evolutionarily distinct monocots and eudicots: Cinnamomum camphora (Ranunculales), Aquilegia coerulea (Magnoliids), Manihot esculenta (Malpighiales), Cuscuta australis (Convolvulaceae), Chenopodium quinoa (Caryophyllales), Vaccinium macrocarpon (Asterid), Apostasia shenzhenica (Asparagales), Ananas comosus (Poales), Cocos nucifera (Arecales), Elaeis guineensis (Arecales), and Spirodela polyrhiza (Araceae; Figure 4 ; Supplemental Figures S6 and S7 ; Zhang et al, 2017 ; Sun et al, 2018a ; Ong et al, 2020 ; Kawash et al, 2021 ; Mansfeld et al, 2021 ; Yang et al, 2021b ). In Kalanchoe fedtschenkoi (Saxifragales), a CAM photosynthesis plant that partitions carbon capture by TOD, the LHY– PRR5 linkage has completely converged so the two genes are next to one another (no genes in between; Yang et al, 2017 ).…”

Identifying New Resistance to Cassava Mosaic Disease and Validating Markers for the CMD2 Locus

“…The misallocation of the markers might result from the low quality of genome assembly in certain regions, the complexity of the CMD2 locus [21], or the mismatch during SNP calling. The new haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava varieties facilitate further investigation to figure this out [21,37].…”

Haplotype resolved DNA methylome of African cassava genome

“…Since the cassava genome is highly heterozygous, DNA methylome analysis of the haplotype-collapsed genome misses many features of the methylome. With the development of long read sequencing and chromosomal conformation capture techniques, haplotype resolved genomes are available for highly heterozygous genomes (Mansfeld et al ., 2021; Qi et al ., 2022; Zhou et al ., 2020), which provides high-quality reference genomes facilitating studies of haplotype resolved DNA methylomes.…”

“…To dissect the haplotype resolved DNA methylome of cassava, we conducted whole genome methylome studies in two haplotype genome resolved accessions of cassava (TME7 and TME204) using whole-genome bisulfite sequencing (WGBS) and enzymatic methyl-seq (EM-seq), respectively (Feng et al ., 2020; Mansfeld et al ., 2021; Qi et al ., 2022). Sequencing reads were mapped to different haplotypes individually allowing zero mismatches and one best hit, which allowed the separation of reads belonging to different haplotypes.…”

“…Previous studies have revealed large numbers of haplotype-specific structural variants (SVs) in cassava (Mansfeld et al ., 2021; Qi et al ., 2022). To understand how DNA methylation is associated with these SVs, we analyzed methylation levels of these SVs.…”