Comparative Genomics Of Echinochloa Chloroplast And Phylogenetic Analysis

The genus Echinochloa,belonging to the Gramineae family,is widely distributed around the world,including numerous agricultural vicious weeds and also some domesticated species,cultivated in Asia and other places.The similar morphological characteristics of Echinochloa species make the taxonomy in this genus controversial,and the evolutionary relationship among Echinochloa species is still not clear enough.In this study,using the high-throughput genome sequencing data,we assembled and annotated the complete chloroplast genomes of multiple Echinochloa species or varieties,and illustrated the basic characteristics of the chloroplast genomes of Echinochloa genus.In addition,we systematically compared the genomic differences among the chloroplast genomes at species and variety level,and reconstructed the phylogenetic relationship of Echinochloa genus.Meanwhile,based on the chloroplast genomic variations in a large-scale barnyard grass collection sampled globally,we uncovered the complex evolutionary history of Echinochloa species or varietie.The major results are as follows:1.We assembled the chloroplast genomes of 9 Echinochloa species/varieties and finally obtained a total of 22 complete chloroplast genomes.The chloroplast genome size of Echinochloa ranged from 139,592 to 139,902 bp,and the average GC content was about 38.6%,which was similar to the chloroplast genome size of other C4 plants in the Gramineae.The chloroplast genomes in Echinochloa were highly conserved,with tiny differences among species.Each of the Echinochloa chloroplast genomes contained 112 or 113 genes,in which 23 genes have two copies.The codon preference of Echinochloa chloroplast genomes was weak,with most of the preferred codons ending with A/U,and the codon preference was mainly affected by mutations rather than selection.2.According to the phylogenetic tree constructed based on the full-length chloroplast sequences and SNPs,the Echinochloa plants could be generally divided into 6 branches:(1)hexaploid E.colona and cultivated E.frumentacea branch;(2)tetraploid E.oryzicola,E.stagnina and hexaploid E.crus-galli var.crus-galli branch;(3)diploid E.haploclada branch;(4)tetraploid E.walteri branch;(5)tetraploid E.oryzicola var.hainanensis branch;(6)hexaploid E.crus-galli mixed group branch.3.The phylogeny based on 607 accessions of Echinochloa revealed that part of E.crus-galli var.crus-galli from the Yangtze River Basin had a "nuclear-cytoplasmic conflict" phenomenon.To be detailed,the nuclear genomes of these accessions were clustered together with hexaploid E.crus-galli,while the chloroplast genomes were close to the genomes of tetraploid E.oryzicola.Itmay be explained by the hybridization between E.oryzicola and E.crus-galli var.crus-galli located sympatricly at the same ecological niche(Yangtze River Basin,China),and following recurrent back-crossing with E.crus-galli var.crus-galli.The processes finally resulted in the formation of a special population with nuclear genomes of E.crus-galli var.crus-galli but chloroplast genomes of E.oryzicola,which was revealed by two independent branches of E.crus-galli var.crus-galli in the phylogenetic tree.