| Two rice leaffolders,C.medinalis and C.exigua,are among the major pests in rice production areas in Southeast Asia,both posing serious threats to rice production.C.medinalis has the habit of long-distance migration and is one of the most important migratory pests in China.C.exigua is closely related to C.medinalis,which occurs and damages rice together with C.medinalis in some rice areas.However,they exhibit obvious differences in living habits,such as migration and overwintering,as well as their pest control strategies.Because the genomic sequences of these two pests have not been reported yet,the genetic mechanism of various habit differences are not well understood.Here,the Illumina and Pac Bio sequencing technology were utilized in genome sequencing of two rice leaffolders,and the Hi-C technology was used to scaffold the draft genome to chromosome level;Based on genome assemblies,two sex chromosomes,Z and W,were identified in both rice leaffolders;The genomic characteristics of the two pests were compared and analyzed;The population structure and genetic differentiation status were inferred using whole genome re-sequencing data of C.medinalis individulas which collected from different geographic area.The results preliminarily revealed the genetic mechanism of the habit differences between two pests,which is of great significance for developing more efficient pest control strategies,and provide a reference for the study of the molecular mechanism of pest migration.(1)Chromosome-level genome analysis of two rice leaffoldersThe genomes of two rice leaffolders,C.medinalis and C.exigua,were sequenced using Illumina and Pac Bio technology.The genomes of two rice leaffolders were both assembled to chromosome level using Hi-C technology.The genome size of C.medinalis and C.exigua were 528.3 Mb and 798.8 Mb,with Scaffold N50 of 16.1 Mb and 25.7 Mb,respectively.According to the results of karyotype analysis,by combining with Hi-C interaction information,C.medinalis genome was assembled to 31 chromosomes with 2,464 scaffolds mounted on them,while 1,413 scaffolds were anchored on 32 chromosomes in C.exigua.The quality assessment showed that BUCSO values of two assemblies were both greater than 96%,indicating high assembly quality.Using an in-house genome annotation pipeline,a total of 15,765 and 14,922protein-coding genes were annotated from C.medinalis and C.exigua,with 39.5% and52% repeat sequences,and 38.5% and 39.1% GC content,respectively.Based on the different copy number of Z and W chromosomes in male and female,sex chromosomes of C.medinalis and C.exigua were identified according to the coverage rate.The results showed that the Z chromosomes of C.medinalis was 22.08 Mb with 592 protein-coding genes;W chromosome was 20.75 Mb with 534 genes,and it is the most intact W sequence reported in lepidoptera insects.The size of Z and W chromosomes in C.exigua were 30.69 Mb and 12.12 Mb,with 527 genes and 294 genes,respectively.In addition,the species-specific segments from the W chromosome of C.medinalis and C.exigua were identified by comparative analysis,with lengths of 388 bp and 453 bp,respectively.Specific primers were designed followed by PCR verification.These species-specific primers can be used as molecular marker of W chromosome,providing reference for the subsequent sex chromosome research of rice leaffolders.(2)Comparative genomic analysis of two rice leaffoldersComparative genomics analysis between two rice leaffolders showed that 64.5%unknown transposons were expanded in the genome of C.exigua,which partly explain the larger genome size compared to C.medinalis genome.Synteny analysis showed that high collinearity exists between the autosomes of two rice leaffolders,while fusion and fission events of the W chromosomes were more frenquently observed.Chromosome32 of C.exigua had few colinear regions with C.medinalis,indicating that more variation or rearrangements occurred on this chromosome.The phylogenetic relationships of 22 lepidopteran species were reconstructed using 91 single-copy genes,revealing the differentiation of two rice leaffolders was about 18.5 million years ago.Gene families and positive selection analysis showed that gene families which are expanded or positive selected in two rice leaffolders were different.In C.medinalis,gene families related to migration,host location and environment adaption were significantly expanded.In contrast,genes associated to insect immune,cold tolerance and resistance to exogenous infection were positively selected in C.exigua.To further reveal the genome features of insect migration,six migratory insects and six nonmigratory insects were selected to conduct comparative genome analysis.The results showed that genes involved in energy metabolism and muscle development have significantly different evolution rate in the two groups of insects,and the number of migration-related genes are significantly different.The results revealed the differences between the two rice leaffolders at genome level and provided a theoretical reference for understanding the genetic mechanism of their environmental adaptability.(3)Population structure and properties of C.medinalis individuals from different countriesTo carry out genome-wide re-sequencing,C.medinalis samples were collected from seven different countries,including China,Vietnam,Laos,Philippines,Myanmar,Thailand,and Bangladesh.A total of 15,105,302 SNPs were detected.By carring out principal component analysis,phylogenetic tree construction and population stratification analysis,it was found that the Lao population have different genomic characteristics compared to all other populations.Compared to C.medinalis from other Indo-China Peninsula countries,most of the Vietnamese population could be clustered alone and has close relationship with population from Hainan of China.These results suggested that C.medinalis individuals from Laos and Vietnam might have formed subpopulations,respectively,and differ a lot with SNPs from other populations.Compared C.medinalis populations from China with that from other countries,results showed the genetic fixation index(Fst)value of 95.8% loci on chromosomes was lower than 0.05,indicating that the genetic differentiation degree of C.medinalis in Domestic and non-Domestic populations was low,of which was closely related to its migratory habit that resulted in frequent gene flow among populations.Whole-genome scanning showed that 96.7% of the loci in the chromosome region were subjected to low frequency selection(Tajima’s D > 0).Of whole genome,52 regions have loci with high nucleotide diversity(pi > 0.009),in which the nucleotide polymorphism on W chromosome was the lowest.A total of 69 protein-coding genes related to adaptive evolution were detected by selective elimination analysis.By simulating the population history of C.medinalis,it was found that the effective population size of C.medinalis has been shrinking in the last 8000 years. |
PDF Full Text Request