| The potato is a solanaceous plant that originated in the Andes Mountains of South America[1],and plays an important role in ensuring world food security as the world’s fourth largest food crop[2].Potato tubers are important commodity organs for storing starch,with high nutritional value and commercial value,but the current research on the regulatory mechanism of potato block development is not fully understood,and Solanum etuberosum（ETB）,as an external taxon of natural potatoes,is of great significance for studying the evolution of potato blocks.At present,most of the research uses ETB to carry out somatic cell hybridization with potatoes to study potato disease resistance in depth,but the lack of complete genomic information greatly limits the evolution analysis of potato tubers based on it and the localization of disease resistance genes.The aim of this study is to analyze the characteristics of the genome and understand the structure and function of genes by assembling high-quality ETB genomes.In this study,the protocol of ETB genome assembly was constructed by means of various types of data such as second-generation sequencing,third-generation sequencing and Hi-C sequencing,and the assembled ETB genome was compared with the potato and tomato genomes,and the evolution of potato regulatory genes was preliminarily analyzed from the perspective of evolution.1.The final successful assembly of the ETB genome sequence is about 684.6 Mb,and the assembly of the genome contigs N50 reaches 3.9 Mb,of which 98.2%of the sequence is anchored to 12 chromosomes.A total of 37,658 genes and 40,457transcripts were obtained by annotating gene structures by means of transcript prediction,homologous protein prediction,and de novo prediction.2.Using the above genomic data,this study inferred the phylogenetic relationship of ETBs,indicating that ETBs are sister taxa of the common ancestor of potatoes and tomatoes,and the divergence time of the two is about 8.37 million years ago;in ETBs,221 gene families shrink and 935 gene families expand;Gene ontology（GO）enrichment analysis shows that these gene families are mainly involved in redox and some metabolic processes,and may not be directly related to the potato-free characteristics of ETBs.3.Through genomic collinear analysis,a total of 11,015 orthologic genes were identified between ETBs,potatoes and tomatoes,and of the 23 genes reported by previous generations related to potato block development,19 were present in all three species.Combining transcriptome data from three species and previous reports,it is preliminarily suggested that potato chunk formation may be the result of a combination of variations in gene structure and expression levels.By using the accuracy of the second-generation data combined with the advantages of reading length of the third-generation data,this study completed the genome assembly and gene structure annotation of the ETB,which made up for the gap in the ETB genome data.On this basis,the analysis of comparative genomics revealed the phylogenetic relationship between ETB and potato and tomato,and preliminarily analyzed the changes of the reported potato regulatory genes in three species,which provided a data basis for further study of the evolution history of potato potato blocks by comparative genome methods. |
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