Genome Assembly, Haplotyping And Analysis Of A Heterozygous Diploid Potato

Potato is the most important tuber crop in the world.The wild potato germplasm resources are primarily diploids and tetraploids that are widely used in the breeding systems.The reference genome of potato has been released using a double-haploid plant line DM,which has been boosting the function genomics research.However,the genetic heterozygosity of diploid potatoes is high and the haplotype differences are great(>1%),therefore,the double haploid reference genome provides limited information for diploid potato research,which is insufficient to the need for diploid potato breeding and functional researches.Assembly of diploid potato genome is rather difficult due to the highly heterozygosity.The Potato Genome Sequencing Consortium's failure to assemble RH genome gives us an ab uno disce omnes view of the degree of difficulty.This study uses a 10 X Genomics(10XG)library and high throughput sequencing method,combining the genome assembly and haplotyping pipeline developed by ourselves,successfully assembled,haplotyped and annotated the genome of diploid potato RH.Furthermore,we constructed the genetic map from scratch using the inbred population and anchored the sequences of the assembly onto the genetic map.In addition,we carried out a comparative analysis between the two haplotypes based on the haplotyped assembly,which provide a primitive resolution of the allelic differentiation of this species.This study is an example for the genomic analysis of highly heterozygous species.The conclusions are as follow:(1)Combining 10 XG library and high throughput sequencing technology,we de novo assembled a heterozygous diploid potato genome RH.The assembly is of 1.7 Gb in total with a scaffold N50 of 308 Kb,which comprises of 93.3% of the whole genome.71561 protein-coding genes are annotated on the assembly.(2)We constructed a genetic map of 24 chromosomes from scratch.Approximately 90% of the scaffolds were clustered into 24 linkage groups,which refers to 12 pairs of RH chromosomes.(3)A total of 844 collinear regions are found by analyzing the collinearity between the haplotypes.These areas cover 55.5% of genomic regions,including 36,297 genes,representing a 50.67% of the annotated genes.By analyzing the linear regions of the two haplotypes and their polymorphism,we screened out 5.23 M SNPs and 552 K InDels,representing a heterozygosity >1%.(4)We analyzed genomic regions suffering from distorted segregation in combining with the allelic segregation data from RH inbred population.which preliminarily explain the reason of why distorted segregation happens on a region on chromosome 12 in the light of the changes of gene structure and expression.