High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

Abstract

BackgroundBambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies.Methodology/Principal FindingsHere we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae.Conclusions/SignificanceThe cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly.

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

“…The analyzed grasses were divided into two sister groups, the BEP clade (Bambusoideae, Ehrhartoideae and Pooideae) and the Panicoideae clade, consistent with stated phylogeny and classification of grass subfamilies in early studies [20][21][22] . The tree supported the idea that the closest relationship exists between Brachypodium and bamboo, agreeing with the result from the analysis of chloroplast genome sequences 3 . The dN/dS value (the ratio of the rate of nonsynonymous substitution to the rate of synonymous substitution) of the bamboo lineage was the highest among the compared species, suggesting strong selection pressure on bamboo genes.…”

“…Bamboo has a rather striking life history, characterized by a prolonged vegetative phase lasting decades before flowering, thereby inhibiting genetic improvement. Recent genomic studies in bamboo have included genome-wide full-length cDNA sequencing 2 , chloroplast genome sequencing 3 , identification of syntenic genes between bamboo and other grasses 4 and phylogenetic analysis of Bambusoideae subspecies 5 . Fifty-nine simple sequence repeat markers from rice and sugarcane were used in the genetic diversity analyses of 23 bamboo species 6 , and 2 species-specific sequence-characterized amplified region markers were developed in the identification of different bamboo species 7 .…”

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

“…In the Z. latifolia cp genome, the gene pairs atpB-atpE, psbC-psbD, and ndhC-ndhK had 4-, 53-, and 10-bp overlapping regions, respectively. The junctions between IR and SSC regions usually vary among chloroplast genomes of higher plants (Zhang et al, 2011;Xu et al, 2012;Wang et al, 2013). In the Z. latifolia cp genome, the distance of rps19 from the LSC/IR junction was 42 bp, while ndhH gene regions extended into the IR region in the junctions between IR and SSC.…”

“…Repeat sequences may play an important role in chloroplast genome rearrangement and the generation of divergent regions via illegitimate recombination and slipped-strand mispairing (Timme et al, 2007;Zhang et al, 2011;Xu et al, 2012;Wang et al, 2013). One of the IR regions was omitted to avoid redundancy in the detection of repeats in the Z. latifolia cp genome.…”

The complete chloroplast genome sequence and phylogenetic analysis of Chuanminshen (Chuanminshenviolaceum Sheh et Shan)

“…3a). The number of tandem repeats in Chuanminshen cp genome was equivalent to that of crofton weed (Nie et al 2012) and slightly more than bamboo (Zhang et al 2011) whereas the longest tandem repeat size was shorter than the crofton weed with 85 bp and bamboo with 65 bp. To investigate the dispersed repeats in Chuanminshen cp genome, we adjusted the setting parameters of the REPuter described above.…”