Transposable Elements In Rhus Gall Aphids With Particular Repertoire In Schlechtendalia Chinensis Genome

Transposable elements(TEs),also known as jumping genes,are widely spread in the genomes of insects and play a significant role in genomic evolution.TEs can multiply and translocate from one place to another within the genome.TEs are grouped into two classes based on their transposition mechanism,i.e.,Class I and Class II.The abundance and evolution of TEs have been reported in all life forms from bacteria to higher plants and animals,including insects.There are many reports about the widespread of TEs in insects’ genomes,but there was a lack of information about the TEs in the genome of Rhus gall aphids.In this study,we sequenced the genomes of Rhus gall aphids by the high throughput sequencing methods,and characterized the landscape of Mariner TEs in their genomes,and reported horizontal transfer events in Rhus gall aphids and other insects,and also provided a detailed analysis of TEs repertoire in Schlechtendalia chinensis genome.The detailed results are in the following three phases.First,we characterized Mariner transposable elements in the genome of seven species of Rhus gall aphids obtained by the shotgun genome skimming methods.Mariner family is the most widely spread elements of Class II TEs in the genomes of arthropods and insects,and has a significant role in genomic evolution.We searched the genomes of seven Rhus gall aphid species from six major genera for the prevalence of aphids Mariner-like elements(MLEs).In total,one hundred twenty-one MLEs were identified in the genomes of the seven investigated species,which reflected the invasion of MLEs in Rhus gall aphids.The sequences sizes of MLEs ranged from 1,000 to 1440 bp,and the structural analysis revealed that only five copies were potentially active with intact open reading frame(ORF)and terminal inverted repeats(TIRs).Phylogenetic analysis indicated that all the MLE sequences belonged to four subfamilies,i.e.,Mauritiana,Drosophila,Vertumana,and Irritans,of which the two subfamilies Drosophila and Vertumana were reported in aphids for the first time.This study reported and revealed the diversity and distribution of Mariner TEs in Rhus gall aphid genomes.The current results will expand our understanding of the diversity and evolution of transposable elements in aphid genomes,which would be helpful as genetic markers,and may play an important role in genomic evolution and adaptation of aphids.Second,we analyzed the events of the horizontal transfer of transposable elements(HTT)between Rhus gall aphids and other insects.Like all other nuclear genes,TEs also inherit vertically from parents to offspring;however,TEs can be transmitted among different organisms through a phenomenon known as horizontal transfer(HT).The event of HTT is not well understood,but most certainly,it is related to the mobile nature of TEs.We analyzed all the detected Mariner-like elements(MLEs)in seven Rhus gall aphid species for the possible HT events.MLEs having low nucleotide divergence with the MLEs of distantly related insect species were considered for the HT analysis.Based on the above analysis that all the 121 sequences belonged to five lineages,we selected one representative sequence from each group for the further phylogenetic analysis.We identified at least five different events of HT between MLEs of Rhus gall aphids and other insects from five different orders,i.e.,Hymenoptera,Lepidoptera,Diptera,Coleoptera,and Neuroptera.We also found multiple HTT events among the MLEs of insects from the five orders.HTT is a common phenomenon in TEs and helps them spread among different genomes,while there was no previous report on HT events involving the Rhus gall aphids.Our current study closed the knowledge gap of HTT and reported the events between Rhus gall aphids and other insects for the first time.We believe that this study about HTT events will help further understand the evolution and spread of transposable elements in the genomes of Rhus gall aphids.Third,we sequenced the whole genome of the Rhus gall aphid Schlechtendalia chinensis by the third-generation high throughput sequencing method,and extensively analyzed the TEs content in the whole genome level.Using signature and homology-based strategies,a total of 308,196 TEs was identified in the genome of S.chinensis.Among the whole data set,the full-length TEs consists of 7,601 elements,including LTR-RTs,non-LTR-RTs,and DNA transposons,accounting for approximately 7% of the whole genome.Among the LTR-RTs,Gypsy and Pao have a more significant number of full-length copies,while LINE has more full-length copies in non-LTR-RTs.While in DNA transposons,h AT and Tc1/Mariner superfamilies of DIRs were the most abundant,and Maverick superfamily was the most abundant in subclass II.Overall,Repeat Masker masked about 26.04% of the S.chinensis genome,with LTR-RTs,non-LTR-RTs,and DNA transposons occupying 4.47,5.12,and16.45%,respectively.The RT-TEs were grouped into ten superfamilies and one unknown group,while DNA transposons were grouped into two subclasses,twenty superfamilies and one unknown group.We reliably annotated the TE fraction of the whole genome of S.chinensis.We also found that many TEs from different families were transcriptionally active in the S.chinensis genome.Furthermore,different types of transposase-derived protein were also found in the S.chinensis genome.We also provide insight into functional genes’ TEsrelated insertional inactivation and exogenization.We considered that the presence of TE fragments in the introns of functional genes could impact the activity of functional genes.A large number of TE fragments in introns could lead to the indirect inactivation of functional genes.In conclusion,we identified and reported the diversity of Mariner transposons in the seven species of Rhus gall aphids for the first time.We also uncovered the information about HTT events of TEs between Rhus gall aphids and other insects from five different orders,and reported at least five independent HTT events between them.Finally,we presented the landscape,diversity and classification of TEs in the chromosome level genome assembly of S.chinensis,which could be used as a reference for comparative studies between galling and non-galling aphids.These will also be beneficial in understanding the role of TEs in the genomic evolution of their hosts.