Sequencing And Analysis Of The Full Genome Of Bangia Fuscopurpurea

Red algae(Rhodophyta)is one of the most ancient algae groups.The fossil evidence of Rhodophyta(Bangiomorpha pubescens)can be traced to 1.2 billion years ago.Rhodophyta,Viridiplantae and Glaucophytes formed the Archaeplastida.The endosymbiosis hypothesis of plastids evolution shows the red algae was born from the first endosymbiosis.Cyanobacteria were swallowed by the host result to become the plastids in Archaeplastida.Meanwhile,red algae also participate in the second endosymbiosis,providing plastids for Chromophyta.Therefore,Rhodophyta playing an important role in the study of algae evolution.Red algae genomic information is quite limited at present,research focused on the simple unicellular algae red alga Cyanidioschyzon merolae(16.5 Mb),Galdieria sulphuraria(13.7Mb),and multicellular red algae Chondrus crispus(105 Mb),Porphyra umbilicalis(87.7 Mb).This thesis has sequenced the genome of Bangia fuscopurpurea from Bangiaceae.By using the k-mer method,the genome size is predicted around 144.5 Mb.Using single molecule sequencing and chromosome conformation capture(3C)technology,we final got the 148.9 Mb genome with 4 chromosomes.The GC content of the genome is 66.80%,N50 is 31.45 Mb.The genome contains a total of 11,949 encoding genes.Among all the sequenced red algae,Bangia's genome is the biggest.However,when compared with green algae and higher plants,this genome also shows the characteristics shared with other red algae which contain fewer genes and introns.After collinearity analysis,Bangia's genome didn't experience the whole genome duplication event,in which we only found 57 tandem repeat gene.When insight into the non-coding sequences of genomes,result shows that the multicellular red algae contain more TE elements,specially the long terminal repeat(LTR)comparing with unicellular algae.We conclusion that TE elements may leading to the bigger genome size in red algae evolution.Comparing the functional genomes of different red algae,there were some new findings:1)We found some specific multi-copy genes in Bangia's genome data,including the anti-stress gene Msr A.There were 6 copies in Bangia genome;2)By comparing the functional genomes of multicellular and unicellular red algae,we found that the NB-ARC family proteins specific appeared in multicellular red algae.These family were involved in the signal transmission during the stress resistance;3)In addition,we analyzed the selected gene families and metabolic pathways,such as the expansion of cytochrome P450 family in red algae,the difference of MVA/MEP pathway between Rhodophyta and Chromophyta;4)The Cyanidiophyceae lack genes involved in polyunsaturated fatty acid synthesis pathway which consistent with their living environment and the genes related with plant hormones in red algae.5)Finally,through the comparative genome analysis of the Archaeplastida,we found the common gene encoding Hsp33 among different algae and it is the unique orthologous of the Archaeplastida.By the analysis of gene family expansion,we found that in the early evolution of the red algae,they experienced a stage of large-scale gene family reduction.In this stage,red algae lost genes related to flagella and autophagy,and acquired a large number of genes during the evolution of multicellular red algae,especially in the branch of Bangia.These genes encoding nucleic acid binding and DNA replication which may be involved in sexual reproduction.