Abstract
Herbaceous bamboos (Olyreae) are a separate lineage with idiosyncratic traits, e.g., unisexual flowers and annual or seasonal flowering lifestyle, in the grass family. To elucidate the evolution of herbaceous bamboos we produced two complete chloroplast (cp) genomes from two monotypic genera i.e., Froesiochloa and Rehia via the genome-skimming approach. The assembled F. boutelouoides and R. nervata cp genomes were 135,905 and 136,700 base-pair (bp), respectively. Further whole-genome comparative analyses revealed that the cp genes order was perfectly collinear, but the inverted repeats (IRs) borders, i.e., the junctions between IRs and single copy regions, were highly divergent in Olyreae. The IRs expansions/contractions occurred frequently in Olyreae, which have caused gene content and genome size variations, e.g., the copy number reduction of rps19 and trnH(GUG) genes in Froesiochloa. Subsequent nucleotide mutation analyses uncovered a greatly heterogeneous divergence pattern among different cpDNA regions in Olyreae cp genomes. On average, non-coding loci evolved at a rate of circa 1.9 times faster than coding loci, from which 20 rapidly evolving loci were determined as potential genetic markers for further studies on Olyreae. In addition, the phylogenomic analyses from 67 grass plastomes strongly supported the phylogenetic positions of Froesiochloa and Rehia in the Olyreae.
Highlights
Herbaceous bamboos (Olyreae) are a distinct lineage in Bambusoideae (Poaceae), with short and weakly lignified shoots, simple vegetative branching, unisexual flowers, and annual or seasonal flowering patterns [1,2,3,4]
There were 432,450 and 425,590 paired-end reads that were further aligned for F. boutelouoides and R. nervata, respectively (Table 1)
Complete sequencing and comparative analyses in this study revealed that cp genome size of F. boutelouoides (135.9 kb) is similar to that of R. nervata (136.7 kb) (Table 1), showing a typical cp genome size range of bamboos [12]
Summary
Herbaceous bamboos (Olyreae) are a distinct lineage in Bambusoideae (Poaceae), with short and weakly lignified shoots, simple vegetative branching, unisexual flowers, and annual or seasonal flowering patterns [1,2,3,4]. Olyreae consist of circa 22 genera and 124 species, mainly distributed in Central and South America, except for Buergersiochloa bambusoides Pilg. Previous studies on Bambusoideae mainly focused on the woody bamboos, i.e., temperate woody bamboos (Arundinarieae) and tropical woody bamboos. The phylogenetic relationships among genera of Olyreae, as well as within the species-rich genera e.g., Olyra and Pariana, remain elusive and controversial [1,11]. There have been few genomic resources available for herbaceous bamboos [11,12], limiting further comparative genomic studies in this particular grass lineage
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