A Preliminary Discussion Ondistribution Of Horizontal Gene Transfers In Aquatic Species

New genes with novel functions can confer evolutionary advantages for all species.They can arise slowly through modification of existing genetic materials,or through horizontal gene transfer(HGT)between different species.In prokaryotes,it is widely acknowledged that HGTs play key roles in fast evolution.In multicellular eukaryotes,however,their generally huge and complex genomes make the analysis procedures extremely nuanced and inefficient.Consequently,our knowledge about HGTs in eukaryotes is still very limited.For aquatic species,their living habitat and some of their own unique features may facilitate HGTs.Therefore,systematic investigation HGTs in aquatic species may be helpful for elucidating mechanisms and common rules of HGTs in eukaryotes,and helpful for people to have a deeper comprehension of the essence of genetic resources.Eukaryotes generally harbor a great quantity of transposable elements(TEs),which have some degree of autonomy,and may consequently lead to different mechanisms of HGT comparing to single copy genes.Therefore,the horizontal transfer of TEs and single copy genes were investigated separately.Horizontal transfer of TEsLitopenaeus vannamei was used as key species,a high throughput transcriptome sequencing assembly was used as key dataset.The transcriptome was conducted similarity search based on multistep local/online blast search,phylogenetic analyses and expression profile analyses,with the aim to identify TE transcripts,their involvements in HGT and possible biological functions.The results are listed below:1.We identified 395 high reliable TE transcripts from 56608 transcripts of L.vannamei,most of which are retrotransposon transcripts.157 of those transcripts showed highest similarity to sequences from non-arthropod organisms,including ray-finned fishes,mollusks and putative parasites;83 of the 157 transcripts could be identified as transcripts of known L.vannamei TE families,corresponding to 16 TE families.2.Of the above 16 TE families,10 have annotated coding regions,therefore the protein sequences of the latter were used for phylogenetic analysis.The results showed that in most cases their closest neighbors are sequences of aquatic species.Besides,even without the query sequence,sequences of other aquatic species are also tend to cluster together,although they are very distant in taxonomy.3.Short read alignments were conducted against two NCBI Bio Projects of L.vannamei: transcriptome of early stages and after stimulation of recombinant VP28.Expression profile analyses revealed that transcripts involved in HGT are likely to play important roles in antiviral immunity.More specificly,those transcripts might act as inhibitors of antiviral immunity.Horizontal transfer of single copy genesTo handle dataset on a larger scale,we developed a TF-IDF based method to identify putative HGTs.Uni Gene sequences of 27 species that covered a wide range of taxa were used as key dataset.We used the novel method to investigate HGTs in such 27 species,and conducted rigorous tests based on traditional similarity search and phylogenetic analysis.The results are listed below:1.Using a proper threshold value,we extracted 20257 conserved gene fragments from 4048 homologous gene groups of 21 species.The lengths of these fragments varied from 3 to 40 nt,with 8 and 11 nt fragments being most abundant.These gene fragments were deemed as words of DNA language.The distribution of these words partially meets Zipf's law;for words that do not meet Zipf's law,their weights are very low due to extremely low TFs or IDFs.To count frequency of words in sequences,we developed a dynamic programming algorithm,and implemented it in Python and C.2.We designed a measurement Dis,which is used to indicate distance between characteristic value of a sequence and mean characteristic value of a collection of sequences in a species.By comparing with different species,we can directly find sequences that are distant to mean characteristic values of its own species,yet close to mean characteristic values of other species.Using this method,we identified 585 putative HGT sequences from 13 species,but most of them come from Schmidtea mediterranea,Schistosoma japonicum,Lottia giganteaand Ixodes scapularis.The putative gene donors were also concentrated,especially Salmosalar,Daniorerio and Anoliscarolinensis.3.Through further rigorous conformations,we identified 63 more reliable HGT sequences,39 of which come from S.mediterranea.These 63 sequences have homologous sequences distributed in a wide range of species,especially in deuterostomes.Yet phylogenetic analyses showed that their closest neighbors are generally aquatic species,which is accordant with results predicated by Dis.The 63 sequences represent a wide range of genes,including those encode ribosomal proteins,cytoskeletal proteins and proteins necessary for energy metabolism,most of them look like to be house-keeping genes.Our results clearly showed that both TEs and single copy genes are more prone to horizontally transfer between aquatic species,especially those with close ecological niche.Aquatic species generally adopt external fertilization,which makes their germ cells and larvae totally exposed to environmental DNA.Perhaps such a weak-link in lifecycle makes aquatic species more prone to receive foreign DNA.The detected single copy genes involved in HGT are universally exist in eukaryotes,indicating such HGTs replaced an existing homologue rather than introducing a new function;unless evolved into a new gene,TEs are generally selfish.Therefore,eukaryote-eukaryote gene transfer may be mostly neutral in term of function.