Abstract
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. 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.
Highlights
To fully understand the evolutionary paths of Phalaris species, it is necessary to know the information coded in their nuclear genome and the accompanying organelle genomic sequence [1]
The guanine and cytosine (GC)contents of the cp genomes were 38.52%, 38.52%, and 38.45%, and the percentages of GC nucleotides were unevenly distributed throughout the cp Plants 2020, 9, x FOR PEER REVIEW
We found that the percentage of simple sequence repeats (SSRs) was higher at the large single-copy (LSC) or small single-copy (SSC) region, but lower at the inverted repeat (IR) regions in P. aquatica than those of the others (Figure 5A)
Summary
To fully understand the evolutionary paths of Phalaris species, it is necessary to know the information coded in their nuclear genome and the accompanying organelle genomic (mitochondria and/or chloroplast) sequence [1]. Given that the nuclear genome assembly is costly and difficult, the genome sequences of mitochondria and chloroplast are much smaller and appropriate for genetic information mining. Chloroplast (cp) genome sequences have been proven useful in genetic studies like differential gene detection, polymorphic probe development, and phylogenetic analysis [1]. Plants 2020, 9, 748 relatively independent from the nuclear genome. This makes it good material for the study of plant genealogy geography, systematics, gene and intron losses, and population history, as well as excellent substrates for genetic transformation [1,2,3]. A typical plant cp genome size ranges from 120 kb to
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