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High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae).

Zhang YJ, Ma PF, Li DZ - PLoS ONE (2011)

Bottom Line: Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae.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.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China.

ABSTRACT

Background: Bambusoideae 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 findings: Here 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/significance: The 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.

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Maximum parsimony phylogram of 24 Poaceae accessions as determined from different data partitions.A) 74 Protein coding genes. B) Large single copy (LSC) region. C) Small single copy (SSC) region. Numbers above nodes are maximum parsimony bootstrap/maximum likelihood bootstrap support values and only one number is shown if the two values are equal. Numbers below nodes are Bayesian inference posterior probability. The inset box in the lower right indicates topological difference form maximum likelihood and Bayesian analysis.
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pone-0020596-g006: Maximum parsimony phylogram of 24 Poaceae accessions as determined from different data partitions.A) 74 Protein coding genes. B) Large single copy (LSC) region. C) Small single copy (SSC) region. Numbers above nodes are maximum parsimony bootstrap/maximum likelihood bootstrap support values and only one number is shown if the two values are equal. Numbers below nodes are Bayesian inference posterior probability. The inset box in the lower right indicates topological difference form maximum likelihood and Bayesian analysis.

Mentions: Four data partitions (whole cp genomes, protein coding genes, the LSC region and the SSC region) (Table 2) from 24 grass cp genomes were used to construct phylogenetic trees. The SSC region had the highest percentage of parsimony informative characters (PIs) with 13.83%. However, this data partition contained the fewest PIs as the aligned sequence length was only 13,524 bp. Furthermore, SSC regions of bamboo cp genomes contained a small inversion located in the rpl32-trnL (UAG) intergenic spacer (Table S4) that had great influence on the branching order of I. longiauritus, P. edulis and P. nigra var. henonis (Figure S1). This inversion was considered to be of homoplasious character because of its random distribution in Bambuseae and Arundinarieae. However, the influence of the small inversion on a phylogenetic tree based on complete cp genome sequences was almost negligible. Therefore, in subsequent analysis we excluded this inversion from the data partition of SSC region. Phylogenetic trees with BS values and posterior probabilities (PP) based on the four data partitions are presented in Figures 5 and 6. The Bayesian, MP and maximum likelihood (ML) analyses yielded similar trees in each data partition and phylogenetic trees of the four data partitions were largely congruent with each other. The topological differences occurred mainly within Ehrhartoideae. Within this subfamily, three cultivated varieties of Oryza sativa could form a monophyletic group only when using the data partition of protein coding genes, whereas no BS or PP showed significant support for this monophyletic relationship (Figure 6A). The best resolution in phylogenetic relationships was achieved using full cp genome sequences, thus we discuss the phylogenetic relationships mainly based on Figure 5.


High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae).

Zhang YJ, Ma PF, Li DZ - PLoS ONE (2011)

Maximum parsimony phylogram of 24 Poaceae accessions as determined from different data partitions.A) 74 Protein coding genes. B) Large single copy (LSC) region. C) Small single copy (SSC) region. Numbers above nodes are maximum parsimony bootstrap/maximum likelihood bootstrap support values and only one number is shown if the two values are equal. Numbers below nodes are Bayesian inference posterior probability. The inset box in the lower right indicates topological difference form maximum likelihood and Bayesian analysis.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105084&req=5

pone-0020596-g006: Maximum parsimony phylogram of 24 Poaceae accessions as determined from different data partitions.A) 74 Protein coding genes. B) Large single copy (LSC) region. C) Small single copy (SSC) region. Numbers above nodes are maximum parsimony bootstrap/maximum likelihood bootstrap support values and only one number is shown if the two values are equal. Numbers below nodes are Bayesian inference posterior probability. The inset box in the lower right indicates topological difference form maximum likelihood and Bayesian analysis.
Mentions: Four data partitions (whole cp genomes, protein coding genes, the LSC region and the SSC region) (Table 2) from 24 grass cp genomes were used to construct phylogenetic trees. The SSC region had the highest percentage of parsimony informative characters (PIs) with 13.83%. However, this data partition contained the fewest PIs as the aligned sequence length was only 13,524 bp. Furthermore, SSC regions of bamboo cp genomes contained a small inversion located in the rpl32-trnL (UAG) intergenic spacer (Table S4) that had great influence on the branching order of I. longiauritus, P. edulis and P. nigra var. henonis (Figure S1). This inversion was considered to be of homoplasious character because of its random distribution in Bambuseae and Arundinarieae. However, the influence of the small inversion on a phylogenetic tree based on complete cp genome sequences was almost negligible. Therefore, in subsequent analysis we excluded this inversion from the data partition of SSC region. Phylogenetic trees with BS values and posterior probabilities (PP) based on the four data partitions are presented in Figures 5 and 6. The Bayesian, MP and maximum likelihood (ML) analyses yielded similar trees in each data partition and phylogenetic trees of the four data partitions were largely congruent with each other. The topological differences occurred mainly within Ehrhartoideae. Within this subfamily, three cultivated varieties of Oryza sativa could form a monophyletic group only when using the data partition of protein coding genes, whereas no BS or PP showed significant support for this monophyletic relationship (Figure 6A). The best resolution in phylogenetic relationships was achieved using full cp genome sequences, thus we discuss the phylogenetic relationships mainly based on Figure 5.

Bottom Line: Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae.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.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China.

ABSTRACT

Background: Bambusoideae 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 findings: Here 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/significance: The 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.

Show MeSH
Related in: MedlinePlus