Comparative And Phylogenetic Analyses Of Chloroplast Genomes In Poaceae Family

Chloropalst is the most important organelle to green plants and it has a small and simple genome with conserved structure and orthologous genes.Chloroplast genome is widely used in comparative genomics and phylogenetic ananlyses for the reason of a great of value for reveraling evolutionary relationships between plant species.This study is a complex comparative research for the 34 chloroplast genomes in different subfamilies of Poaceae family combined with genomics,bioinformatics and experiments.The maily results are as follows:1.For the investigation of the major characters of chloroplast genomes in Poaceae:Length and GC content were found significantly different between subfamilies.GC content was significantly different in the three different structural regions of a cp genome.Variation in length of IR region was great and might be a core factor to whole chloroplast genome length variation.The structure and gene order of chlorplast genomes in Poaceae family were very conserved.Expansion and contraction in IR boundary happened commonly and caused small fragments variation.A large inversion which was specific in Poaceae cp genomes was detected in the LSC region compared with outgroup species Typha and Tobacco.2.For micirosattlite sequence analysis:SSRs were not uniformly distributed in cp genomes of Poaceae and A/T riched motifs were the most amout.NO.of SSRs were significantly different between subfamlies.Negative correlation was detected between SSR density and GC content.To make full use of SSR information mined massively in Poaceae in this research,universal SSR primers were designed anmong Poaceae family and each subfamiliy,species specific SSR primers were also desgined additionally.Further in silico PCR analysis with universal SSR primers found that length variation were consistent with the relationships revealed by phylogenetic analyses.3.Phylogenetic analyses:By using different data from cp genome and different methods(MP,ML,BI),the results made clear of the relationships between subfaimilses and spesies.Bambusoideae and Pooideae were more closed to Ehrhartoideae.Phylogenetic tree from the whole cp genome sequence was consistant with tree of 80 cp genes,which indicated that the important value of the whole genome data for phylogentic analysess.Phylogenetic tree from the IR data indicated that Ehrhartoideae and Pooideae may share similar evolutionary process in IR region.4.Hotspot sites among Poaceae cp genomes were identified and evaluated.A perl script for high-throughput extracting part of sequences with range infromation was developed and proved to be useful.More than 30 candidate regions were found useful for further phylogenetic analyses or DNA barcoding selection of Poaceae family or subfamlies.Optimized universal primers based multiple sequence alignment of 5 candidate regions were developed and tested with 10 species from different subfamilies and proved to be universal in Poaceae.