Development And Application Of Genome Assembly Improvement Tool Based On Synteny

It has great practical significance to improve the quality of insect genome assemblies,which is conducive for better development and utilization of insect genome resources and provides data support for insect researches and pest control.However,there are some problems such as unbalanced development and uneven assembly quality in insect genomics.By December 2020,only 82 out of 625 insect genomes submitted to the NCBI are assembled to chromosome level.Lacking high-quality genomic data brings challenges to the depth of data mining and effective utilization.Here,a genomic optimization software was developed to improve genome assembly based on synteny between two closely related species and applied to genome of brown planthopper(BPH).The optimized BPH genome was re-annotated,a gene co-expression network was constructed by combining RNA-seq data,and the hub genes with high connectivity in the network were identified.The mainly results are as follows:1.Development of synteny-based genome quality improvement toolsiGAS(Improving Genome Assembly based on Synteny)was developed to improve genome assembly by reordering scaffolds based on synteny between two closely related species.To test the performance of iGAS,16 animal and plant genomes were optimized,and N50 s,NA50s and mis-assemblies were calculated and compared with other software Ra GOO and Chromosomer.The results showed that when taking chromosome-level genomes of closely related species as reference,the N50 s and NA50 s of the genomes after iGAS improvement could be increased by 22 times and3.57 times,and the numbers of the mis-assemblies were lowest among the three software.When taking the non-chromosome level genomes of closely related species as reference,iGAS is also superior to Ra GOO and Chromosomer in N50,NA50 and mis-assembly.For the convenience of users,an online analysis platform was built(http://insect-genome.com/software/iGAS/home.html)for providing helpful technology support for genome assemblies optimization.2.Co-expression network analysis and hub gene identification in BPHThe previous version of the BPH genome assembly was based on NGS reads.In order to improve the assembly quality of BPH,it was optimized by iGAS using the small brown planthopper genome as reference.The improved genome was re-annotated,and the BPH gene co-expression network was constructed using WGCNA by combining 72 RNA-seq data.A total of 323 hub genes closely related to important biological functions were predicted in 18 modules.Among all 9,874 genes in modules,674 genes are homologous to reported insect RNAi target genes,accounting for 6.83%of the total genes;Among the 323 predicted hub genes,24 hub genes were homologous to RNAi target genes,accounting for 7.43%.The identification of hub genes in BPH gene co-expression network is hopeful to play an important role in pest control in the future as screening potential BPH RNAi target genes as a method.