| Bambusoideae is one of the 12 subfamilies of Poaceae,with world wide distribution.It consists of three tribes,further divided into four lineages.Woody bamboos include temperate woody bamboos,neotropical woody bamboos and palaeotropical woody bamboos,allotetraploid or allohexaploid,which contain a complex evolutionary history.There are a large number of genome size variation events occurred in woody bamboos,which indicated by C value data published.Presumably,it’s related to expansion of transposable elements（TEs）,but lacks of specific analyses.As an important basic unit that can replicate and shift in genome autonomously,TEs have been proven to play an important role in evolution of genome like maize and wheat.Especially the Long terminal repeat retrotransposons（LTR-RTs）,it’s considered to have an vital driving impact in evolution of genome size.This article is based on allohexaploid neotropical woody bamboos Bonia amplexicaulis draft genome,which has been published,further through Nanopore sequencing and Hi-C technology,obtained new chromosome-level reference genome of B.amplexicaulis.Comprehensive comparison and analysis with chromosome-level reference genome of Phyllostachys edulis,leading to deeper insight for the important role of TEs in the genome size variation of woody bamboos.Main conclusions are summarized as follows:1.Reconstruction for evolutionary history with genome size of BambusoideaeBased on the C value data of each lineage of woody bamboos that we have obtained,and nuclear-genome internal transcribed spacer（ITS）sequences obtained based from genome skimming sequencing,and integrated with the results of fossil calibration time in Time Tree website,we reconstructed the evolutionary history of genome size within Bambusoideae finally.What’s more,brownian motion models used for calculated the rates of genome size variation of ancestral branches.We found that allotetraploid temperate woody bamboos branches has a faster rate of genome size expansion than other branches,which combined with the visualization results of the Phytools R package.Contrarily,the allohexaploid palaeotropical woody bamboos branches reveals a shrinking trend.2.Obtain and evaluation for genome of B.amplexicaulisWe implemented Nanopore long-read sequencing and Hi-C technology,obtained chromosome-level genome of B.amplexicaulis.The genome was assembled into 35 chromosomes with N50 of 2.70 Mb and a total length of 850.41 Mb,and 98.93%sequences are anchored to chromosomes.Different evaluations have shown that the quality of assembly obtained by Nanopore sequencing has been improved significantly compared with previous version.The Assembly results satisfied with standards of high-quality genome.3.Annotation and comparison of TEsCompleted de novo annotation and statistical analysis has been finished with EDTA pipeline for two versions of B.amplexicaulisgenome and P.edulis genome.The results indicated that there is a significant distinguish in the total number of transposable elements between B.amplexicaulis and P.edulis.Especially,Gypsy families of LTR-RTs account for 10.05% in genome of B.amplexicaulis,while 27.06% for P.edulis,but difference of proportion with DNA TEs are inapparent circumstances.Simultaneously,the features of TEs along chromosomes in B.amplexicaulis and P.edulis has been described in detail.We also finished the clustering analysis of LTR-RTs families for two bamboos.It shows that the number of LTR-RTs families in the genome of B.amplexicaulis is much smaller than P.edulis.4.Expansion of TEs in genome of woody bamboosIn the non-conserved region,which obtained after the collinearity of the two bamboos,TEs accounts for a large proportion,and the distribution is balanced relatively.It indicated that the expansion of TEs are the main cause of variation of genome size.Estimation and analysis for insertion time of LTR-RTs,revealed different level of LTR-RTs expansion events existed in the similar period of B.amplexicaulis and P.edulis,which shows the explosive expansion of the LTR-RTs in recent,caused the increase of genome size of temperate woody bamboos rapidly represented by P.edulis. |
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