Echinochloa Chloroplast Genome Sequencing And Development Of Molecular Markers

The genus Echinochloa (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus Echinochloa. In this study, we completed the entire chloroplast genomes of two Echinochloa species(Echinochloa oryzicola and Echinochloa crus-galli) based on high-throughput sequencing data using their fresh green leaves. In addition, we estimated the divergence time of the genus Echinochloa and developed a new chloroplast molecular marker psbA, which are meaningful for the whole genome study of Echinochloa. The major results are as follows:1. The chloroplast genome of E. oryzicola STB03is139,891base pairs in length, and the length of its LSC, SSC and IRs are82,108bp,13,205bp and22,289bp, respectively. The chloroplast genome of E. crus-galli BTS02is139,800base pairs in length, and the length of its LSC, SSC and IRs are82,047bp,12,517bp and22,618bp, respectively. The two Echinochloa chloroplast genomes have79indels and466substitutions, and contain131protein-coding genes, including112single-copy genes which are in the LSC/SSC and19double-copy genes which are in the IRs.2. We estimated the divergence time of the genus Echinochloa based on the chloroplast genomes. The divergence between the genus Echinochloa and Panicum occurred about21.6million years ago, whereas the divergence between E. oryzicola and E. crus-galli chloroplast genes occurred about3.3million years ago.3. Based on the differences of trnT-L sequences in the Echinochloa chloroplast genomes, we used the marker trna-b1to identify E. oryzicola. The481materials were divided into225E. oryzicola and256other species of Echinochloa.4. In order to identify the other species of Echinochloa, we developed a new chloroplast molecular marker psbA based on the differences between the two Echinochloa chloroplast genomes, using three kown Echinochloa species as controls. The new marker can divide the245Echinochloa materials into4clusters, including E. crus-galli var. crus-galli and so on.