Haplotype-resolved Assembly And Analyses Of Heterozygous Potato Genome

Potato(Solanum tuberosum L.)is the most important tuber crop in the world.Tetrasomic inheritance and clonal propagation by tubers are two structural obstacles in cultivated potato breeding.A trend in potato breeding is to transform the crop from a clonal propagated tetraploid into a seed-propagated,inbred line-based diploid.However,this strategy is impeded by self-incompatibility or inbreeding depression of diploid potato.Here we assemble the genomes of diploid potato and autotetraploid potato to explore the features of heterozygous potatoes and facilitate those breeding projects.Although genome assembly is getting routine,construction of a haplotype-resolved genome sequence for the heterozygous species is still challenging.In this study,we combine the 10X Genomics linked reads,the Nanopore long reads and the Hi-C sequencing to hierarchically assemble the two haplotypes of the RH genome.The assembly contains 1.7 Gb sequences and 98%of them are phased and anchored on 12 pairs of chromosomes.To provide a comprehensive vision of heterozygosity between two haplotypes,～20 Mb SNP/InDel and～34,000 structural variants are identified by aligning the syntenic blocks in pairwise,indicationg the～3%intra-genome diversity.In the coding level,0.79 M variants of them may cause the amino acid alteration.Among 22,401 allelic gene pairs,23.6%of them show differential expression and 17.8%of them located in differentially methylated regions.The deleterious mutations were reported to be accumulated in vegetatively propagated species and were assumed as the reason for inbreeding depression.In RH genome,5,428 genes are predicted to harbour deleterious substitutions on only one allele and 2,077 genes harbour deleterious substitutions on both alleles.The difference on the sequence and their function indicates the complementation of the two haplotypes,which might be the genetic basis of agricultural traits of elite heterozygous potatoes.Based on the assembled RH genome,we fine map the plant architecture controlling gene PA1 to a 134 kb region and identify one gene coding EIN3 protein as the reliable candidate.There are expression difference and coding difference between two alleles of the candidate gene.This mapping displays the utilization potential of RH genome on potato breeding.To overcome the obstacles of genome assembly in autotetraploid genome project,we generate and sequence 400 BACpools.By merging the assembly in BAC pools and linking the draft using PacBio long reads,we obtain 2.89 Gb sequences with a scaffold N50 of 386 kb.Through genetic mapping,1.43 Gb sequences are phased into two or four haplotypes.In this thesis,we report the haplotype-resolved genomes of diploid potato and autotetraploid potato and uncover the divergence between haplotypes on sequence and expression level.Our work offers a full picture of the genetic composition of the highly heterozygous potato and facilitates the construction of potato inbred lines.Moreover,the assembly and phasing pipeline developed here provides a practical and innovative solution for research on the complex genome.