Phylogenetic Analysis Of Triticeae Based On Sequences Of The Whole Chloroplast Genome

Bread wheat(Triticum aestivum L.)is one of most important food crops in the world and the update of wheat germplasm resources is important guarantee to the production of wheat varieties.To study the phylogenetic relationship of Triticeae is very important for riching wheat germplasm resources,revealing the genetic relationship and utilizing the excellent genes of wheat.Meanwhile,as an important part of the plant organelles and photosynthesis organs,chloroplast played an important role in the history of biological evolution.Studies on the structure and sequence of the chloroplast genome of Triticeae are important in revealing the origin of species,the evolutionary process and the genetic relationship between species.In this study,we completed eight chloroplast genomes' DNA extraction,sequencing,splicing and assembly.In addition,genome annotation,physical map building,SSRs and repetitive sequence detection of chloroplast genome were also completed.At last,genome divergence hotpot regions,comparative analyses of genomes,building phylogenetic tree and divergence time estimates were achieved using eight chloroplast genome we assembled and 26 existing chloroplast genome sequences from NCBI.The main results were following:(1)According to analysis the chloroplast genome of Triticum dicoccum and other seven genomes,we found that the size of chloroplast genomes were between 113,449 bp and 136,041 bp,the smallest was Aegilops caudata,and the largest was Triticum araraticum.Triticum aestivum ssp.Tibetanum Shao had 138 genes annotated and Eremopyrum triticeum had 191 genes.The number of SSR markers detected was between 144 and 173,Haynaldia villosa and Triticum zhukovskyi respectively.The number of repeat sequences found was between 29 and 42,Eremopyrum triticeum and Elymus sibiricus respectively.(2)We found 19 genome divergence hotpot regions in 33 chloroplast genomes through the multiple sequence alignment and visual processing with the chloroplast genome of Oryza sativa as the reference sequence.These hotpot regions can be used as potential markers for the reconstruction of systematic development of Triticeae.Furthermore,a comparative genome analysis was carried out on the chloroplast genomes of 31 Triticeae species with the chloroplast genome of Triticum aestivum as the reference sequence.We found some frequent inversions in the chloroplast genomes of Triticeae.The 31 species were classified into four categories,including 16,11,2 and 2 species,based on the degree of genome conservation relative to the Triticum aestivum chloroplast genome.(3)We constructed the phylogenetic tree of Triticeae with Oryza sativa and Brachypodium distachyon for outgroup by multiple sequence alignment,conservative sequence extraction,saturation detection,nucleotide substitution model selection and phylogenetic tree construction.We found that compared with the S genome,the A genome was closely related to the D genome and Triticum timopheevii had a close relationship with Aegilops speltoides.Furthermore,it also suggested that there had closer relationship between Aegilops cylindrica and Aegilops tauschii.Secale cereale was closely related to Triticum-Aegilops complex.In the Hordeun,Hordeum vulgare was has a closer relationship with Hordeum vulgare subsp.Spontaneum(FT462),the wild species of Hordeum vulgare.(4)Using strict molecular clock(SMC)and relaxed molecular clock(RMC),we calculated the divergence time of Triticeae based on the chloroplast genome with the divergence time of Brachypodium distachyon and Oryza sativa for anchor points.In this study,the divergence time between Hordeum vulgare and Triticum aestivum was shortened from 6~15 MYA to about 9.13~9.43 MYA.Secale cereale diverged from Triticum aestivum approximately 3.03~5.96 MYA.The divergence time between Eremopyrum triticeum and Elymus sibiricus is about 4.11~4.19 MYA.Aegilops tauschii diverged from Aegilops cylindrical and Aegilops genliculata approximately 0.24~0.71 MYA and 1.23~3.13 MYA respectively.In addition,the divergence time of Hordeum vulgare subsp.Spontaneum FT462 and Hordeum vulgare was about 0.11~0.46 MYA.Moreover,the A genome diverged from D genome,including D,M,C and S* genome,approximately 1.38~3.81 MYA and the S genome divergenced from A and D genome approximately 2.22~4.98 MYA.