The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica)

There are 22 species in thePhalarisgenera that distribute almost all over the temperate regions of the world. Among them, reed canary grass (Phalaris arundinacea, tetraploid and hexaploid) and hardinggrass (P. aquatica, tetraploid) have been long cultivated as forage grass and have received attention as bio-energy materials in recent years. We aimed to facilitate inter-species/ploidies comparisons, and to illuminate the degree of sequence variation within existing gene pools, chloroplast (cp) genomes of threePhalariscytotypes (P. aquatica/4x,P.arundinacea/4xand P.arundinacea/6x) were sequenced and assembled. The result indicated that certain sequence variations existed between the cp genomes ofP. arundinaceaandP. aquatica.Several hotspot regions (atpI similar to atpH,trnT-UGU similar to ndhJ,rbcL similar to psaI, andndhF similar to rpl32) were found, and variable genes (infA,psaI,psbK, etc.) were detected. SNPs (single nucleotide polymorphisms) and/or indels (insertions and deletions) were confirmed by the high Ka/Ks and Pi value. Furthermore, distribution and presence of cp simple sequence repeats (cpSSRs) were identified in the threePhalariscp genomes, although little difference was found between hexaploid and tetraploidP. arundinacea, and no rearrangement was detected among the threePhalariscp genomes. The evolutionary relationship and divergent time among these species were discussed. The RNA-seq revealed several differentially expressed genes (DEGs), among which psaA, psaB, and psbB related to leaf color were further verified by leaf color differences.