De Novo Assembly Of Maize Mo17 Genome And Its Comparison With Other Maize Genomes

Maize is one of the most important food crops in the world,as well as vital animal food and industrial raw materials.It is the model organism for plant genetics analysis and also regarded as perfect material in comparative genomics,functional genomics,quantitative genetics and other subjects as its complex genome structure and rich genetic information.Additionally,maize has high levels of heterosis and rich morphological and genetic diversities between different inbred lines.Thus studying this kind of genetic diversity will help us uncover the mechanisms of heterosis and facilitate the gene cloning,genetic breeding and improvement.So in this study,we deep sequenced and assembled the genome of maize inbred line Mol7,and compared with B73 and PH207 genomes to detect the differences between these three inbred lines.The main results are as follows:1.We sequenced and assembled the genome of Mo 17 through a combination of three technologies:PacBio single-molecule real time(SMRT)sequencing,BioNano optical map and Illumina sequencing.The assembled genome size of Mo17 is about 2.18 Gb,and the N50 lengths of contigs and scaffolds are 1.48 Mb and 10.2Mb respectively.Based on the GBS pan-genome genetic map,we anchored 2.104 Gb scaffold sequences onto Mo 17 chromosomes,which occupied 96.5%of the total assembled size.At the same time,evaluation results showed high accuracy of the assembly using the Mo 17 BAC sequences,Mo17 physical map,GBS pan-genome genetic map and BUSCO software.2.1.8 Gb of the Mo17 sequences were annotated as repeats,occupying about 83.83%of the whole assembled sequences.Moreover,the percentages of the repeats in B73 and PH207 were 83.76%and 81%respectively,and also there is no significant difference in each sub-class of them.The insertion time of high-confidence full-length long tenninal repeat(LTR)retrotransposons showed that the expansion of LTR retrotransposons occurred mainly within the past 1 million years in both B73 and Mo 17 genomes,which indicates that transposons of maize have always been in the active state.Then,we annotated 38,620 high-confidence protein coding genes in Mo17 assembled genome by Maker-P pipeline,and 37,830 genes(97.95%)were anchored onto Mo17 chromosomes.3.Comparing B73,Mo17 and PH207 genome sequences,we found 61%of Mo 17 genome sequences could be aligned to the B73 genome in one-to-one syntonic blocks,and 51%to the PH207 genome.There were 9,867,466 SNPs,630,711 Insertions and 791,735 Deletions detected in the B73 and Mo17 aligned syntonic blocks.A total of 25Mb PAV sequences were also identified in B73 and Mo17 genomes.The longest PAV cluster of the B73 genome was a 2.9Mb region from chromosome 6,and the longest one of Mo17 was a 2.5Mb region also from chromosome 6.Most PAV genes in B73,Mo17 and PH207genomes could be detected in at least one of the wild relatives,indicating that most of these PAV genes might have already existed in their direct ancestors.Using fractionation bias estimation with sorghum as a reference,we found that the sub-genome organizations of B73 and Mo 17 were nearly identical.Moreover,two peaks in the distribution of synonymous substitution rates(Ks)were detected:the one corresponding to a group of genes might derive from recent genetic exchanges(Ks<0.0028),and another representing most of those remaining genes might diverge from the conmmon ancestors of maize.Approximately 7,000 genes were identified to be evolutionary constrained(Ka/Ks<0.1).In contrast,relatively few genes(<1,000)were detected to be under positive selection(Ka/Ks>1).