Comparative Genomics Analysis And Construction Of Homologous Gene Database In Solanaceae

Solanaceae plants,including tomato,peppers,eggplant,potato,tobacco and other important crops,are one of the most important vegetable groups of dicotyledons.At present,the whole genome of 9 Solanaceae plants has been successfully sequenced,and their genomes are constantly being updated and improved,which provide available data resources for the research on the structural variation and the evolution of Solanaceae plants.Almost all Solanaceae plants have experienced two rounds of whole genome duplication events(WGDs;Polyploidization).In the process of evolution,as chromosomes undergo rearrangement,recombination and polyploidization,their genome structure has also undergone great changes.However,there is still a lack of comprehensive and systematic reports on genome structure changes and polyploid gene identification of Solanaceae plants.In this study,seven representative genomes with high quality were used to compare and analyze the genome structures of the Solanaceae plants.We further revealed the general pattern of genome rearrangement in the process of Solanaceae plant species differentiation,and constructed the first Solanaceae homologous gene database(SolCGD).The main results are summarized below:(1)The syntenic relationships among and within seven genomes of Solanaceae(tomato,potato,eggplant,pepper,husk tomato,wolfberry and tobacco)were comprehensively identified.Phylogenetic relationships and syntenic maps indicated the evolutionary status of each species and the occurrence of WGDs in Solanaceae.The result showed that tobacco first differentiated from the ancestors of Solanaceae at about 29.8 Mya,followed by wolfberry(?29.7Mya),pepper/husk tomato(?25.3Mya),eggplant(?14.5Mya),and potato/tomato(?7.7Mya)in sequence.And we verified the occurrence of two polyploidization events in the evolutionary history of Solanaceae plants.(2)The homologous structure of seven Solanaceae plant genomes at chromosome levels were compared and analyzed,and the ancestral genomes of each phylogenetic node and the common ancestral genomes before species differentiation of Solanaceae plants wer e deduced.Besides,the evolutionary path from ancestor genome to modern genome of 12 chromosomes was clarified,and the phenomenon and pattern of the rearrangement from ancestor genome to each modern genome were determined.It was found that the chromosome structure of potato and tomato are th e most conservative.(3)According to the homologous gene pairs formed by tomato polyploidy events previously determined by our research group,25 sequenced Solanaceae genomes were compared,and 41,413 homologous genes produced by WGD-T events and 18,018 homologous genes produced by WGD-y events were obtained.On this basis,the pan genome of polyploid genes in Solanaceae plants was constructed.(4)The first Solanaceae homologous gene database(SolCGD)was constructed,including the genome information of 26 Solanaceae plants,homologous genes produced by polyploid events in each species,the corresponding functional annotations and protein structure.The database also integrates tools such as sequence alignment,gene browser and primer design,and developed a complete set of gene search modules,download modules and data visualization interfaces,which are used to analyze the structural characteristics,gene function innovation and development research of Solanaceae plant genome.