Horizontal Gene Transfer And Evolution In Chromalveolata

HGT is the direct communication of genetic material between organisms or organelles across genetic distance and reproductive isolation.The mechanism of horizontal gene transfer and its contribution to adaptive evolution and diversity is one of the 125 most challenging scientific issues raised by the Science journal.Identification and validation of HGT events in Eukaryotes is much more challenging than that in Prokaryotes.Chromalveolata,derived from the Secondary endosymbiosis between heterotrophic organisms with heterotrophic and photosynthetic organisms,is one of the six domains of eukaryotic organisms including some well-known oceanic algae terms such as diatoms,dinoflagellates and brown algae.Both large scale EGTs and sporadic HGTs play important roles during the formation and diversification of Chromalveolata,which thus is an excellent experimental field for eukaryotic gene transfer research.In this study,the whole genome sequences of five large groups of Chromalveolata(Cryptophytes,Rhizarians,Alveolates,Stramenopiles,and Haptophytes,the CRASH group)were used as the research object to identify the sporadic HGT and large scale EGT events and to evaluate the main contribution of exogenous genes in the CRASH group.Firstly,sporadic HGT of CRASH was analyzed.With the Refseq database as background,a strict bioinformatics screening process was established based on sequence similarity and phylogeny and subsequently certified by the assessment of genome contamination and the flanking gene homology.0.16-1.44%of all the 23 studied genomes were detected as HGTs with highly confidence respectively,which is consistent with the "1%HGT principle" of eukaryotic genome.This study carefully inferred the distribution of HGT gene contributors based on the clustering characteristics of phylogeny,and inferred the possibility of prokaryotic-to-eukaryotic gene transfer based on the sharing phenotype and behavior between prokaryotic donors and eukaryotic recipients.We performed functional prediction for HGT genes,and found they played roles in many important and representative metabolic pathways for species in CRASH(e.g.the alginate pathway for kelps).According to the distribution of HGTs in gene families of public database such as SEED,KEGG,EGGNOG,IPR2GO,we inferred that HGT drove the evolutionary divergence of the CRASH group and has a profound impact on the formation of the evolutionary pattern of the current CRASH group.Otherwise this study tested several important theoretical hypotheses for horizontal gene transfer events between eukaryotes and prokaryotes.Although the HGTs represented adaptive evolution towards eukaryotic genes,it still differed from CRASH core genes in CDS length,intron counts,CG ratio,codon usage preference,maintaining some characteristic marks of prokaryotic genes.These results answer the long-existing doubts in horizontal gene transfer theory across eukaryotic taxon.This study determined the screening criteria for high confidence HGT genes,established the bioinformatics process for HGT research,and independently developed the HGT tree screening tool NestedIN.The results expand the applicable taxon of HGT theories,and are an important breakthrough and sublimation in the field of HGT research,which provides novel ideas and perspective for HGT research on a large genetic scale.Identification and validation of large-scale EGT genes is another achievement of this study.We set CRASH as the experimental group and the model species of other taxon of life tree as the control groups.We constructed a matrix using the identities between each two species members based on their genome sequence identity.We found the imprints of primary endosymbiosis and secondary endosymbiosis across the whole matrix.Both the red algae and green algae were found to be potential secondary endosymbiont ancestors of CRASH.We investigated the best BLAST hit proteins of the experimental group in the control groups and found strong signals in both red algae and green algae in the control group.We constructed 15,726 gene families using all protein sequences and perform the primary component analysis(PCA)for all species in the CRASH and control groups according to their gene distribution information in 15,726 gene families.The clear clustering boundaries between eukaryotic and prokaryotic organisms were found,as well as between photosynthetic and nonphotosynthetic.Interestingly,the clustering relationship between CRASH species and green algae was stronger than that between CRASH species and red algae.To achieve the higher resolution of EGT resources the maximum likelihood tree was constructed for 5197 gene families involved in EGT events,generating the final 2720 Green genes,763 Red genes and 1687 RNG genes with high confidence.By comparing the differentiation distances of these genes and their homologous genes(dS and gene identity),we concluded that the engulfment of the green algal by the ancestors of CRASH was earlier than that in red algal.Only a small proportion(<15%)of either green or red algal derived proteins in extant CASH lineages provide robust evidence of being targeted to the plastid.Functional comparative analyses of CRASH genes with green and red ancestry reveal major contributions from the green algal endosymbiont to nucleotide,amino acid,and glycan metabolism,in addition to photosynthetic electron transport,that greatly outweigh contributions from the red algal partner.At last,we compared gene expression profiles between host core genes and HGTs that have shared Gene Ontology(GO)/Kyoto Encyclopedia of Genes and Genomes(KEGG)/Pfam terms,as well as Green and Red in EGT genes by analyzing 600 transcriptomes collected extensively in the CRASH group.Compared with CRASH core genes,HGTs generally show lower expression levels.Moreover,HGT genes display higher expression dispersal and higher expression specificity compared with CRASH core genes.These results indicate that HGTs might be implicated in functions that are important in specific conditions such as response to environmental stressors.Given these results,the expectation is that over time,selection on CRASH lineages will lead to the adaptation of HGT-derived genes to their domestic tRNA pools and regulatory machineries via alterations in GC content,intron length,and codon usage.Global analysis of gene expression shows red genes are more highly expressed under the tested conditions than those of green origin.On the other hand,they all play an important role in the core metabolic pathway of CRASH and have abundant expression.