The Analysis Of Horizontal Gene Transfer In Takakia Lepidozioides Genome

Horizontal gene transfer(HGT),also known as lateral gene transfer,is one of the paths for sharing genetic information among different organisms.Although mutation and recombination through sexual reproduction are the major sources for gaining genetic variation in eukaryotes,horizontally transferred gene could also play an important role in their recipient organisms,as well as affect the evolution of genomic architecture.Bryophytes,comprising liverworts,hornworts and mosses,have a key status in land plant evolution.In addition,bryophytes could form a wide variety of symbiotic associations with bacteria and fungi,especially cyanobacteria.Thus,it is not surprising that bryophytes acquire foreign genes through horizontal transfer from their symbiotic partners.As one of the earliest diverging mosses,Takakia lepidozioides shares some morphological characters with liverworts.With distribution mainly in Tibetan plateau with an average elevation exceeding 4,000 meters,T.lepidozioides may process special adaptive mechanisms.Here,based on the newly sequenced genome of T.lepidozioides and some selected published land plant genomes,horizontally transferred genes in T.lepidozioides were identified by the HGT-inferring pipeline that is newly developed in this study,together with validations by some strict criterions,such as phylogenetic analyses and topology tests.The main results are as follows:1.HGT-inferring pipeline,implemented using python programming language,uses Blastp outputs to get HGT AI,HGT Index,as well as HGT Identity value of each protein query sequences.Then,the identified protein sequences with high similarity are used to build phylogenetic tree using the Maximum likelihood method.This pipeline is primarily intended for this study,but it can be easily used for other studies involving HGT researches.2.There are four HGT events only occurring in T.lepidozioides genome with eight genes.Two HGT gene families come from fungi and the other two from bacteria.These four gene families are all involved in enzyme activities:hydrolase activity(CCG018076,CCG018082;CCG006039,CCG01091 1,CCG018501,CCG019186),oxidoreductase activity(CCG014580),as well as aromatic prenyltransferase activity(CCG010144),respectively.3.Takakia lepidozioides and other 26 land plant genomes all have thirty-four horizontal gene families from bacteria and fungi as well.About 74%(25/34)of these gene families were found among bryophytes,ferns and seed plants.T.lepidozioides,Physcomitrella patens,and Arabidopsis thaliana totally have fifty-nine,fifty-seven,forty-six genes from horizontal transfer,respectively.The copy numbers of these transferring genes usually vary from one to three.In addition,the result of gene annotation shows that horizontally acquired genes in T.lepidozioides tend to code for enzyme activities.4.By comparing the genomes of T.lepidozioides,P.patens,and A.thaliana,we found out that except for the horizontal transfer genes in P.patens containing less introns(P-value=0.04509),the horizontal and non-horizontal transfer genes generally show no significant differences in most genome structures,i.e.the GC content,GC skew,codon usage bias,and number of introns.The character of horizontal transfer genes may become similar to its host oganism during the long history of evolution,which is virtually 450 Ma.Meanwhile,the transcription level of horizontal transfer genes is slightly higher than the non-horizontal transfer genes in T.lepidozioides.5.At least 19%horizontal genes transferred to the ancestors of land plants are lost in special plant clades.However,twenty-five acquired gene families still identified in all main land plant clades.Although many gene duplication events have been observed during the evolutionary history of land plants,there is not any evidence showing the expansion of the transferred gene families.Here we propose a hypothesis:after HGT event,the acquired genes could stay in their recipient and offspring genomes for a long time and other genes may be lost,but it is very difficult for these genes to expand for their copy numbers.This study provides a new insight into the T.lepidozioides genome research,and obtains a deeper understanding of the features(GC content,GC skew,Codon usage bias,the number of introns,and transcription ability)of genes with horizontal transfer in land plants,and the fate of transferred gene during the long history of land plant evolution is also proposed.