Transcriptome Sequencing And Environmental Adaptation Analysis Of ULVA

As a widely distributed species in the world,Ulva is an attractive model species for the study of plant growth,development and environmental adaptation evolution owing to its ecological characteristics of resistance to abiotic stresses such as high temperature,high salinity and high permeability.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Therefore,it is of great significance to study the adaptive mechanism of Ulva species for revealing their ecological function.Currently,the Ulva mutabilis genome is the only genome that has been sequenced.In order to better understand the evolutionary mechanism of environmental adaptation of Ulva,we first sequenced and analyzed the transcriptome of three Ulva species,Ulva compressa,Ulva linza and Ulva prolifera.Combined with the published genome sequences of Ulva mutabilis and transcriptome sequence of Ulva lactuca and Ulva endozoica,we analyzed the adaptive evolution mechanism of six species of Ulva species based on positive selection theory with single cellular green algae Chlamydomonas reinhardtii and Volvox carteri as a outgroup.The analysis results showed that using Reciprocal Best Hits(RBH)of the protein sequences of eight species,HMMER model prediction and sequence length filtering,a total of 3107 homologous proteins were found among the eight species,which were used for positive selection analysis.Then based on the orthofinder software,a total of2530 single-copy homologous genes among eight species were identified.These homologous genes were aligned,conserved sites were extracted and concatenated into sequences,and the MEGA software was used to build the species tree using the maximum likelihood method under the JC model.And the result showed that a total of two branches in topology,which six species of Ulva flocked together and C.reinhardtii and V.carteri formed another branch.Using the PAML tool,we systematically analyzed the homologous genes of Ulva species including the branch model,site model and branch-site model.The results showed that the selection pressure of Ulva was much greater than that of the outgroup species.In addition,a total of 465 and 334 positive selection genes in Ulva were identified by site model and branch-site model,and functional annotation enrichment analysis showed that these genes were involved in multiple biological processes such as photosynthesis,fatty acid synthesis,stress resistance,signal transduction.Lastly,U.compressa was selected to perform transcriptome sequencing and expression pattern analysis under six environmental stresses.349 and 230 positive selection genes in Ulva under site model and branch-site model were differentially expressed and a total of 37 genes in two models were differentially expressed in all six stress condition,including molecular partner,initiation factor,peptide methionine sulfoxide reductase,cytochrome P450,and ribosomal protein genes.In addition,many positive selection genes in the two models were associated with stress tolerance,signal transduction,photosynthesis which play an important role in the environmental adaptability of Ulva.