Genomic Analysis And Genetic Application Of The Natural Intraspecific Diversity Of Schizosaccharomyces Pombe

The fission yeast Schizosaccharomyces pombe is an ideal unicellular model organism,which plays an important role in the biological studies owing to the well developed molecular genetic tools.Actually,most researchers have only focused on one well developed lab strain to study the biological mechanisms.With the emergence and popularity of next generation sequencing,many researchers have started to pay attention to the population genomics and evolution of S.pombe.Previously,Jeffares et al.have acquired 161 natrual isolates of S.pombe and explored the population structure through polymorphic sites of nuclear genome.However,their results revealed weak population structure of S.pombe.Our lab is also interested in the evolutionary history of fission yeast,here we tried to further explore the population structure of this model organism through mitochondrial genomes.In this study,we have acquired 38 isolates from different culture collection centers.All these 38 strains were used to construct whole genome re-sequencing libraries based on Tn5 transposase mediated tagmentation and afterwards performed next generation sequencing on illumine Hiseq platform.Here,we used previously-published S.pombe DNA sequence data from 161 natural isolates as well as sequencing data of 38 strains obtained in this study to produce de novo assembles of the mitochondrial genomes among 199 S.pombe isolates.We have obtained 69 types of mitochondrial genomes.We have constructed phylogenetic tree based on the concatenated mitochondrial genes and population structure through polymorphic sites located on non-intronic mitochondrial sequences.The results from both methods indicate that S.pomcan be divided into two well-separated lineages with the reference strain located clade named as REF clade and the other clade named as NONREF clade.The diversity of REF clade is low and the variation of the branch lengths is very small.The NONREF clade contains many highly similar mitochondrial genomes.Apart from these mitochondrial genomes,the diversity of others in NONREF clade is much higher compared to the REF clade.In order to further detect the population structure of S.pombe,we have constructed nine phylogenetic trees by the nucleotide sequences of nine introns.The result is similar with the tree based on the mitochondrial genes.The isolates from each clade are almost clustered together.In addition,the phylogenetic tree constructed by the K-region,which is a low recombination region of the nuclear genome,also supports the conclusion that S.pombe strains can be divided into two clear lineages.Finally,we have estimated the split time between two lineages of S.pombe on the basis of the mutation rates documented by the previous studies.We considered the split time were at about 40 million generations ago.Our intra-specific comparison of S.pombe mitochondrial genomes will facilitate future population genomic studies of this useful model organism.In addition to the evolutionary history of S.pombe,we are also interested in the genetics application in this model organism.Mapping and discovery of mutations in S.pombe can facilitate the understanding of gene functions that contribute to the biological processes.Although there are many well developed genetic tools in S.pombe,actually almost all these tools can only be applied to the standard laboratory strain.It is also difficult or impossible to identify many novel mutations based on standard genetic methods.The bulk segregant analysis combined with high-throughput sequencing can effectively locate regions of the genes associated with your interested traits.Here we have developed a mapping strain,which can help us to identify the genomic regions containing genetic loci affecting the trait of interest.With the development of the mapping strain and the utilization of bulk segregant analysis can further exploit genetic tools and promote the genetic application of S.pombe.