Genetic Differentiation And Multi Omics Comparative Analysis Of Kandelia Obovata Populations At Different Latitude

Mangroves are woody plant communities located in the intertidal zone of tropical and subtropical coasts.They not only provide habitat for fish,birds,shellfish and reptiles,but protect coastal areas from waves.At the same time,they can fix carbon and slow down the climate change caused by carbon dioxide.However,a large area of mangroves have been destroyed worldwide,including in China.In order to restore the mangroves,the Chinese government has formulated a series of laws,regulations and action plans to protect the mangrove ecosystems,and strengthened the mangrove protection and management through the establishment of Mangrove Nature Reserve,and constantly planted artificial forests to restore the mangrove ecosystem.Although the protection and restoration of mangroves in our country have begun to make progress and is one of the few countries where the area of mangroves is beginning to show an increasing trend,there is still a large amount of suitable forest land available for afforestation.Kandelia obovata is one of mostly used plantation trees in mangrove with its wide growing range and strong cold tolerance,especially at higher latitudes.At present,the main problem faced in the process of afforestation in China is the low survival rate,especially after experiencing cold spells,the plantation have a large area of death.Previous studies have found that the survival rate of K.obovata in different provenances was different,and their ability to resist cold spells varies,however,the mechanism of regulation is not clear.In order to investigate the differences among K.obovata with different provenances,how they respond to environmental changes,and the regulatory mechanism to cope with environmental stresses such as low temperature,we collected K.obovata embryos from Leizhou,Yunxiao,and Ningde,along the latitudinal gradient in the southeastern coastal region of China.Common garden experiment and interactive transplanting experiment were carried out in the intertidal zone in Leizhou,Yunxiao,and Yueqing.The plant height,crown width and base diameter of K obovata in the test field were measured,and their leaves were performed whole genome re-sequencing(WGRS),whole genome bisulfite sequencing(WGBS),and transcriptome sequencing(RNA-Seq).Combining with phenotype and multi-omics analyses,we found:a)Phenotypically,local adaptation was observed in Ningde and Yunxiao,that is,good growth locally and suppressed growth after transplantation to other latitudes;Leizhou ones grew faster than locally in Leizhou after transplantation northward to Yunxiao,but did not survive after transplantation further northward to Yueqing.The growth conditions of K.obovata that were from different latitudes but planted in the same environment were different.The cold tolerance of K.obovata from Ningde is better than that from Leizhou and Yunxiao.b)Genome sequencing results showed that the populations of Leizhou,Yunxiao and Ningde had already differentiated,with higher frequency of gene exchange within the Yunxiao population and lower genetic diversity within the Ningde population.More effective ecological restoration measures are required to increase the genetic diversity of Ningde population.c)The vast majority(～90%)of the methylation sites were located in transposable elements(TEs)and a small number(～10%)in genes;CG methylation sites were almost exclusively present in genes,and methylation in TEs occurred in CG,CHG and CHH sequence contexts,but CG and CHG methylation was at relatively high levels.d)Differences in DNA methylation exist among K.obovata in Leizhou,Yunxiao and Ningde,with Ningde ones having the lowest methylation level and the lowest number of methylation sites.22,980 differentially methylated cytosines were detected in Ningde K.obovata,of which about 70 percent occurred on CG context and were mostly genetically located.Functional enrichment analysis of differentially methylated genes revealed that DNA methylation may be involved in regulating biological process such as DNA mismatch repair,GTP binding and affecting GTPase activity.e)DNA methylation on CG and CHG sequences in K obovata is more associated with its origin than in the growing environment.In general,CG methylation levels in K.obovata at higher latitudes are generally lower.f)DNA methylation profile of K.obovata would change while the planting environment changed;a large number of cytosines were methylated on CHH sequence context after transplantation from Yunxiao to Yueqing.In K.obovata,DNA methylation is involved in the regulation of several signal transduction processes,including the regulation of Phot1,Phot2,ZTL,AHK2,PLC2,CIPK23,ETR2,CIPK3,and a large number of Rab GTPase genes,to regulate stomatal opening and closing,circadian rhythm,flowering time,stress response,growth and reproduction,and thus enhance the ability to adapt to the local environment.Our study analyzed the K.obovata in Leizhou,Yunxiao and Ningde,including phenotype,genome,DNA methylation profile,and transcriptome,and explored the differences in phenotype,cold tolerance,and genetic diversity,providing scientific recommendations for mangrove plantation and theoretical guidance for ecological restoration of mangroves.In addition,a comparative analysis of DNA methylation differences among populations at different latitudes was conducted,and the regulatory role of DNA methylation in response to environmental changes was also explored,which provided new ideas for improving the ability of K.obovata to survive in cold and adapt to changed environment.