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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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Repeat analyses.BE, B. emeiensis; FR, F. rimosivaginus; AP, A. purpurea; IL, I. longiauritus; PE, P. edulis; PN, P. nigra var. henonis. (A) Histogram showing the number of repeats in the six woody bamboo chloroplast genomes. (B) Summary of shared repeats among six bamboos. tRNA- or gene-similar repeats are excluded. (C) Composition of the 228 repeats from six bamboos. (D) Location of the 228 repeats from six bamboos. Repeats that occurred in two regions were counted in both. (E) Histogram showing the number of four repeat types in each bamboo chloroplast genome.
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pone-0020596-g003: Repeat analyses.BE, B. emeiensis; FR, F. rimosivaginus; AP, A. purpurea; IL, I. longiauritus; PE, P. edulis; PN, P. nigra var. henonis. (A) Histogram showing the number of repeats in the six woody bamboo chloroplast genomes. (B) Summary of shared repeats among six bamboos. tRNA- or gene-similar repeats are excluded. (C) Composition of the 228 repeats from six bamboos. (D) Location of the 228 repeats from six bamboos. Repeats that occurred in two regions were counted in both. (E) Histogram showing the number of four repeat types in each bamboo chloroplast genome.

Mentions: We divided repeats into three categories: dispersed, tandem and palindromic repeats. For all repeat types, the minimal cut-off identity between two copies was set to 90%. The minimal copy size investigated were 30 bp for dispersed, 15 bp for tandem and 20 bp for palindromic repeats, respectively. In all, 228 repeats were detected in six bamboo cp genomes (Table S3) using REPuter [39]. Manual verification of these identified repeats revealed that some repeats were associated with two tRNA (e.g. trnfM(CAU)) copies, or gene duplication (e.g. psaA/psaB), and these repeats may simply be due to similarity of gene functions and thus we classified them into another type—tRNA or gene similarity repeats (same procedure as was used in [40]). Tandem repeats, accounting for 39.9% of total repeats, are the most common of the four types (Figure 3C). The majority of repeats are located in noncoding regions (Figure 3D), while some are found in genes such as infA, rpoC2, rps18 and rps3. 82.7% of repeats range in size between 15 bp and 40 bp (Figure 3A), although the defined smallest size is 20 bp and 30 bp for palindromic and dispersed repeats, respectively. The longest repeat is a dispersed repeat of 132 bp in B. emeiensis. Except for a 65 bp tandem repeat in P. nigra var. henonis, all other tandem repeats are 45 bp or shorter, while palindromic repeats occur in a narrower size range from 20 to 25 bp. Numbers of the four repeat types are similar among these six cp genomes (Figure 3E) and their overall distribution in the cp genome is highly conserved. Thus we investigated the repeats shared between species using strict criteria. Repeats that had identical lengths, and which were located in homologous regions were defined as shared repeats. Under these criteria there were 14 repeats shared by all six bamboo species and 8 repeats shared by the five woody temperate bamboos (excluding shared repeats with B. emeiensis) (Figure 3B). B. emeiensis had the most unique repeats (20), while P. edulis showed no unique repeats.


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)

Repeat analyses.BE, B. emeiensis; FR, F. rimosivaginus; AP, A. purpurea; IL, I. longiauritus; PE, P. edulis; PN, P. nigra var. henonis. (A) Histogram showing the number of repeats in the six woody bamboo chloroplast genomes. (B) Summary of shared repeats among six bamboos. tRNA- or gene-similar repeats are excluded. (C) Composition of the 228 repeats from six bamboos. (D) Location of the 228 repeats from six bamboos. Repeats that occurred in two regions were counted in both. (E) Histogram showing the number of four repeat types in each bamboo chloroplast genome.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3105084&req=5

pone-0020596-g003: Repeat analyses.BE, B. emeiensis; FR, F. rimosivaginus; AP, A. purpurea; IL, I. longiauritus; PE, P. edulis; PN, P. nigra var. henonis. (A) Histogram showing the number of repeats in the six woody bamboo chloroplast genomes. (B) Summary of shared repeats among six bamboos. tRNA- or gene-similar repeats are excluded. (C) Composition of the 228 repeats from six bamboos. (D) Location of the 228 repeats from six bamboos. Repeats that occurred in two regions were counted in both. (E) Histogram showing the number of four repeat types in each bamboo chloroplast genome.
Mentions: We divided repeats into three categories: dispersed, tandem and palindromic repeats. For all repeat types, the minimal cut-off identity between two copies was set to 90%. The minimal copy size investigated were 30 bp for dispersed, 15 bp for tandem and 20 bp for palindromic repeats, respectively. In all, 228 repeats were detected in six bamboo cp genomes (Table S3) using REPuter [39]. Manual verification of these identified repeats revealed that some repeats were associated with two tRNA (e.g. trnfM(CAU)) copies, or gene duplication (e.g. psaA/psaB), and these repeats may simply be due to similarity of gene functions and thus we classified them into another type—tRNA or gene similarity repeats (same procedure as was used in [40]). Tandem repeats, accounting for 39.9% of total repeats, are the most common of the four types (Figure 3C). The majority of repeats are located in noncoding regions (Figure 3D), while some are found in genes such as infA, rpoC2, rps18 and rps3. 82.7% of repeats range in size between 15 bp and 40 bp (Figure 3A), although the defined smallest size is 20 bp and 30 bp for palindromic and dispersed repeats, respectively. The longest repeat is a dispersed repeat of 132 bp in B. emeiensis. Except for a 65 bp tandem repeat in P. nigra var. henonis, all other tandem repeats are 45 bp or shorter, while palindromic repeats occur in a narrower size range from 20 to 25 bp. Numbers of the four repeat types are similar among these six cp genomes (Figure 3E) and their overall distribution in the cp genome is highly conserved. Thus we investigated the repeats shared between species using strict criteria. Repeats that had identical lengths, and which were located in homologous regions were defined as shared repeats. Under these criteria there were 14 repeats shared by all six bamboo species and 8 repeats shared by the five woody temperate bamboos (excluding shared repeats with B. emeiensis) (Figure 3B). B. emeiensis had the most unique repeats (20), while P. edulis showed no unique repeats.

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