The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

Background Cassava ( Manihot esculenta ) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding is limited because cassava has a highly heterozygous, repetitive and difficult to assemble genome. Findings Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present two chromosome scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. Genome comparisons revealed extensive chromosome re-arrangements and abundant intra-genomic and inter-genomic divergent sequences despite high gene synteny, with most large structural variations being LTR-retrotransposon related. Allele-specific expression analysis of different tissues based on the haplotype-resolved transcriptome identified both stable and inconsistent alleles with imbalanced expression patterns, while most alleles expressed coordinately. Among tissue-specific differentially expressed transcripts, coordinately and biasedly regulated transcripts were functionally enriched for different biological processes. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding. Conclusions The haplotype-resolved genome allows the first systematic view of the heterozygous diploid genome organization in cassava. The completely phased and annotated chromosome pairs will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy and continuity. ### Competing Interest Statement The authors have declared no competing interest. * ### List of abbreviations ASE : allele-specific expression BAC : bacterial artificial chromosome BP : biological process CCS : circular consensus sequence CDS : coding sequence CLR : continuous long reads CMD : Cassava Mosaic Diseases DE : differentially expressed/differential expression DET : differentially expressed transcript ENA : European Nucleotide Archive GO : gene ontology HiFi : high-fidelity HMW : high molecular weight Indel : insertion and deletion IPA : improved Phased Assembler MF : molecular function NCBI : National Center for Biotechnology Information numt’s : nuclear mitochondrial pseudogene regions PacBio : Pacific Biosciences PE : paired-end QV : quality value SMRT : Single Molecule Real-Time SNP : single nucleotide polymorphism SV : structural variation TPM : transcript per million UDI : Unique Dual Indices VGP : the Vertebrate Genome Project