The Investigation On Formation Of Genome Dynamics In Early Seed Plants

Genomes largely evolve as a result of transposable element recombination activities.Organisms have developed mechanisms to regulate repeat element activities to prevent harmful mutations from affecting stability of the genome.Epigenetic modifications such as DNA methylation play a role in silencing repeats and is therefore an important factor in understanding genome evolution dynamics.Seed plant genomes differ in size and other characteristics,particularly Gnetophytes are an enigmatic lineage of gymnosperms which are unique from other seed plants.We thus sought to analyze transcriptome silencing phenomenon in seed plants with an emphasis on Gnetophyte species particularly Welwitschia mirabillis.Previously,gymnosperm genomes were thought to be similar to Norway spruce conifer(20Gb)in terms of size and ineffective TE removal mechanisms that resulted in repeat accumulation.However,the sequenced Gnetum montanum genome revealed a smaller genome(4.1 Gb)and a high TE excision rate(solo/intact ratio 2.07:1).In order to further compare genome and methylome dynamics to better understand the enigmatic Gnetophyte lineage and ancient seed plants as a whole,we widened the sample size to include another Gnetophyte;W.mirabillis,a monotypic desert perennial.This revealed distinctive features;a 7 Gb genome constituting 68% repetitive elements and high TE elimination rates(solo/intact ratio 3.87:1)consistent with G.montanum findings.There was also evidence of recent burst in TEs.Furthermore,bisulfite sequencing revealed high levels of CG and CHG methylation among tissue types similar to conifer but significantly higher CHH methylation(58%)with distinct variation between leaf and meristemic tissues potentially functioning to maintain the meristem and enforce inheritance of repeat silencing.Notably,growth environment also influenced the rate of methylation with wild grown samples being slightly higher methylated than greenhouse grown.On a whole,our findings further distinguish Gnetophytes from other gymnosperm lineages and adds on to currently known seed plant dynamics.We also illustrate additional aspects of evolution,occurrence,regulation and functions of methylation of W.mirabillis and compare them to known angiosperms and gymnosperms to show the contribution to their divergent genomes and structures.