Chlamydomonas Sp. ICE-L (Chlamydomonas Sp. ICE-L) Multi-omics Analysis And Adaptive Evolution Mechanism Research

Green algae are ancient photosynthetic groups of green plants.Chlamydomonas sp.ICE-L is a unicellular green alga thrived in Antarctic sea ice,and it is the main contributor to primary productivity in sea ice ecosystems.Antarctic sea ice is one of the extreme environments on earth.Chlamydomonas sp.ICE-L is encased in the brine channels,where it tolerates extreme low temperatures,high salinity,and seasonal low light conditions.When sea ice thaws during the summer,populations of Chlamydomonas sp.ICE-L are released into the seawater,where they experience elevated intensities of UV-B radiation owing to the seasonal thinning of the ozone layer over Antarctica.The genetic,biochemical,and physiological data have partially revealed morphological and/or physiological adaptations of Chlamydomonas sp.ICE-L.With the advancement of high-throughput sequencing technology,the complete genomes of green algae have been increasingly sequenced,and provide us the opportunities to investigate the evolution of green algae and their molecular adaptations to extreme environments.Photosynthesis is a crucial energy transformation process of plant,and environmental stress will induce the inhibition of photosynthesis.Chloroplast is the photosynthetic reaction center,and chloroplast genome encodes many important subunits of photosynthetic systems.In this study,we first sequenced the chloroplast genome of Chlamydomonas sp.ICE-L,and performed evolutionary analyses with 12 published chlorophytan chloroplast genome.We identified 29 positively selected sites in atp A,atp B,psa B,psb C and rbc L genes.Our results revealed that the positive selection exclusively targeted chloroplast photosynthetic protein-coding genes,indicating that the positive Darwinian selection operates on the chloroplast protein-coding genes following functional-specific patterns.We further identified convergent amino acid substitutions in the three positively selected genes(atp B,psa B and rbc L),providing clues of parallel molecular adaptations of chloroplast photosynthetic genes of green algae to extreme environments.Convergent evolution is the process by which phenotypic similarities evolve independently among organisms lived in similar environments.Phenotypic convergence are associated with the same amino acid substitutions at the molecular level.Convergent evolution in animals was well studied at the genomic level.However,documented examples of convergent evolution in plants are limited.We conducted transcriptome sequencing of two Antarctic psychrophilic green algae(Chlamydomonas sp.ICE-L and Tetrabaena socialis),and performed positive selection analyses with available chlorophytan genome and transcriptome data.Our results revealed considerable shared positively selected genes between Chlamydomonas sp.ICE-L and Tetrabaena socialis,indicating two psychrophilic algae experienced similar selective pressures.We further used the Convergence at Conservative Sites(CCS)approach to detect convergent amino acid substitutions.Our analyses identified significant evidence of molecular convergence.In order to alleviate the possible false positive detection,we used a stringent criterion that the convergent amino acid substitutions in positively selected gene are a conservative signature of adaptive evolution.Finally,we identified 54 genes with conservative signature of adaptive evolution,and enrichment analyses showed these genes were associated with photosynthetic machinery,multiple antioxidant systems,and several crucial translation elements.Our results revealed that the possession of more stable photosynthetic apparatus and multiple protective mechanisms of Chlamydomonas sp.ICE-L and Tetrabaena socialis might arise via parallel molecular evolution,providing new clues of parallel adaptive evolution in Antarctic psychrophilic green alga.The genome-wide studies of plant mainly focus on model plants and crops,and the genome data of green algae is limited.We used the combination of Pac Bio sequencing,Illumina sequencing,10× Genomics,and high-throughput chromosome conformation capture(Hi-C)and assembled a high-quality genome sequence of Chlamydomonas sp.ICE-L(541.86 Mb,scaffold N50: 19.23Mb).The genome of Chlamydomonas sp.ICE-L is the largest compared to other chlorophytes,and 19,870 protein-coding genes were identified,which is the largest gene number among published chlorophytan genomes.63.78% of the Chlamydomonas sp.ICE-L genome assembly lengths were identified as repeat regions,and the content of repetitive elements of Chlamydomonas sp.ICE-L was the highest among the published chlorophytan genomes.Transposable elements(TEs)accounted for 40.67% of the Chlamydomonas sp.ICE-L genome assembly.We found the retrotransposons proliferation in the genome and no evidence of whole genome duplication,indicating retrotransposon proliferation contributed to the genome size expansion of Chlamydomonas sp.ICE-L.Comparative genomic analyses identified massively expanded gene families involved in unsaturated fatty acid biosynthesis,DNA repair,ionic homeostasis,osmotic homeostasis,and reactive oxygen species detoxification.We also found that Chlamydomonas sp.ICE-L might have acquired ice binding proteins(IBPs)via horizontal gene transfer,and the IBPs played crucial roles in its survival under freezing stress.Moreover,a series of differential expression analyses were performed to investigate the gene expression patterns and stress-responsive genes under stress conditions.Our results showed that some of these expanded genes also experienced significant up-regulation or high expression in Chlamydomonas sp.ICE-L under abiotic stress conditions.In summary,this study provides insights into the molecular adaptations of Chlamydomonas sp.ICE-L to the Antarctic extreme environments based on the chloroplast genome,transcriptome and whole genome data.Our results showed that the photosynthetic genes of Chlamydomonas sp.ICE-L experience adaptive evolution and revealed the parallel molecular adaptations to the cold environment.Our study demonstrated the genome evolution of Chlamydomonas sp.ICE-L under Antarctic extreme environments and advanced the understanding genetic mechanisms for the adaptations of green algae to polar environments.