Precise Genome Sequence And Its Methylation Characterization In Jatropha Curcas

Jatropha curcas L.is a diploid woody economic plant of the dicotyledon Euphorbiaceae.It has biological characteristics such as perennial,drought tolerance,salt tolerance and barren tolerance.Jatropha is a well-known diesel tree,its seed kernel oil content reaches 40%-60%,so the seeds can be processed into biodiesel,and Jatropha can also be used as a greening tree.Although there are reports on the sketch of the Jatropha curcas genome,there is still a lack of a fine genome map with a coverage of more than90%.Moreover,there is no report about the whole genome methylation research.Therefore,it is of great theoretical and practical significance to analyze the methylation information of the Jatropha curcas genome and its population.In this study,the third-generation genome sequencing technology was used to carry out the whole genome sequencing and annotation of Jatropha curcas.At the same time,a new simplified re-sequencing analysis technology was used to analyze the types and levels of methylation sites in the Jatropha curcas population,and to compare the three methylation site patterns in the Jatropha curcas population(m CCGG full methylation,m CCGG Hemimethylation,Cm CGG full methylation)and the differences.The main results are as follows:The leaf,flower and fruit materials of Jatropha curcas strain HN001-31-1 collected from Hainan Island were selected.Using the third generation Nanopore sequencing technology,the sequencing depth was 284 times,and the high-quality genome sequence of Jatropha curcas was obtained.The total size reaches 357.3Mb,assembled on only 50 contigs,the N50 length reaches 26 Mb,and the GC content is 34.72%.It is currently the most complete map of the Jatropha curcas genome.The annotation results show that 315,421 duplicate sequences of the Jatropha curcas genome were identified,accounting for 56.1% of the genome size.Among the known sequences,the number of LTR is the highest,mainly including Copia and Gypsy.Using egg-mapper annotation to 21,284 encoding protein genes.Analysis of the methylation differences between the flower,leaf and fruit organs of the Jatropha curcas HN001-31-1 strain showed that the number of methylation sites in the fruit was the most,while the flower organs were the least.The average methylation level is:flower 59.93%,leaf 56.32%,fruit 58.98%,the overall overall average methylation level is58.41%.The annotation results show that 315,421 duplicate sequences of the Jatropha curcas genome were identified,accounting for 56.1% of the genome size.Among the known repeated sequences,the number of LTR is the highest.It mainly contains two major categories: Copia and Gypsy;21,284 protein coding genes are obtained by egg-mapper annotation.Analysis of the methylation differences between the flower,leaf and fruit organs of the Jatropha curcas HN001-31-1 strain showed that the number of methylation sites in the fruit was the highest,while the flower organs were the least.The average methylation level is: flower 59.93%,leaf 56.32%,fruit 58.98%,the overall average methylation level is58.41%.Simplified resequencing using AFSM to detect population methylation results showed that: in the Jatropha curcas population,a total of 537,231 CCGG methylation sites were obtained,of which 10,085 were in the hybrid parents,with an average value of 5042.50,and 527,146 in the hybrid progeny F1,With an average value of 263,573.In addition,according to the classification statistics of the three methylation modes,there are 69,068 m CCGG fully methylated sites,125,828 Cm CGG fully methylated sites,and 342,335 m CCGG semi-methylated sites,thus obtaining hemimethylation Types account for the highest proportion.The GO enrichment of genes related to the two types of methylation sites of m CCGG and Cm CGG in the full methylation model shows that m CCGG full methylation is mainly concentrated in nuclear acid binding transcription factor activity,response to stimulus,cellular process,regulation of biological process,cellular component,catalytic activity binding.The three samples of Cm CGG full methylation mode are all enriched in organelle,catalytic activity,binding,and biological processes such as cellular process and metabolic process.However,their common feature is the significant enrichment of catalytic activity and protein binding.In addition,the genes involved in the changes of the methylation sites of the three models were screened according to the entropy value,and it was found that they shared a common gene CAT.This experiment is also the first time to analyze the population methylation of Jatropha curcas using AFSM technology.It is hoped that this article can provide a reference for the subsequent research on the methylation of Jatropha curcas population.