DOI:10.3390/plants9060748

Xiong Yi;Xiong Yanli;Jia Shangang;Ma Xiao

发表期刊：Plants

链接:https://www.mdpi.com/2223-7747/9/6/748/htm

Abstract：

Background:There are 22 species in the Phalaris genera 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 three Phalaris cytotypes (P. aquatica/4x, P. arundinacea/ 4x and P. arundinacea/6x) were sequenced and assembled.

Results:The result indicated that certain sequence variations existed between the cp genomes of P. arundinacea and P. aquatica. Several hotspot regions (atpI~atpH, trnT-UGU~ndhJ, rbcL~psaI, and ndhF~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 three Phalaris cp genomes, although little difference was found between hexaploid and tetraploid P. arundinacea, and no rearrangement was detected among the three Phalaris cp 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.

Conclusions:The cp genomes of two Phalaris species P. aquatica and P. arundinacea (including tetraploid and hexaploid) werefirstly sequenced and annotated in this study, which was beneficial to the evolutionary study of Phalaris genus. Though gene content were highly conserved and no arrangement among those three Phalaris cp genomes, some hotspot regions and variable genes were identified. Furthermore, the divergence time and evolutionary relationship among these three Phalaris cp genomes along with other Gramineae species was discussed. The DEGs obtained by RNA-seq might be one of the explanations for the differences in leaf color among those three accessions.