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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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Percentage of variable characters in homologous regions among chloroplast genomes of Panicoideae, Pooideae and Bambusoideae.A) Coding region. B) Noncoding region. The homologous regions are oriented according to their locations in the chloroplast genome.
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pone-0020596-g008: Percentage of variable characters in homologous regions among chloroplast genomes of Panicoideae, Pooideae and Bambusoideae.A) Coding region. B) Noncoding region. The homologous regions are oriented according to their locations in the chloroplast genome.

Mentions: Rates of molecular evolution are linked to life history in flowering plants [50]. Woody bamboos with rather long generation times have been shown to have evolved relatively slowly in the grass family [51]. Since this low rate of molecular evolution could complicate the phylogenetic study of Bambusoideae, identifying rapidly evolving regions in bamboo cp genomes through comparative genomics is critical. We found that Pooideae accumulated more mutations in their cp genomes than Bambusoideae and Panicoideae (Figure 8) as indicated by percentage of variations (variation %). The number and distribution pattern of variable characters in coding and noncoding regions were rather different among Bambusoideae, Pooideae and Panicoideae. For example, rpl32-trnL(UAG) accumulated more variations than other noncoding regions in Pooideae. However, it was not the most variable region (in terms of variation percentage) in the other two subfamilies. As the evolutionary pattern of each region is different in the three subfamilies, it is more reasonable to select rapidly evolving regions for phylogenetic studies specific to each subfamily.


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)

Percentage of variable characters in homologous regions among chloroplast genomes of Panicoideae, Pooideae and Bambusoideae.A) Coding region. B) Noncoding region. The homologous regions are oriented according to their locations in the chloroplast genome.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020596-g008: Percentage of variable characters in homologous regions among chloroplast genomes of Panicoideae, Pooideae and Bambusoideae.A) Coding region. B) Noncoding region. The homologous regions are oriented according to their locations in the chloroplast genome.
Mentions: Rates of molecular evolution are linked to life history in flowering plants [50]. Woody bamboos with rather long generation times have been shown to have evolved relatively slowly in the grass family [51]. Since this low rate of molecular evolution could complicate the phylogenetic study of Bambusoideae, identifying rapidly evolving regions in bamboo cp genomes through comparative genomics is critical. We found that Pooideae accumulated more mutations in their cp genomes than Bambusoideae and Panicoideae (Figure 8) as indicated by percentage of variations (variation %). The number and distribution pattern of variable characters in coding and noncoding regions were rather different among Bambusoideae, Pooideae and Panicoideae. For example, rpl32-trnL(UAG) accumulated more variations than other noncoding regions in Pooideae. However, it was not the most variable region (in terms of variation percentage) in the other two subfamilies. As the evolutionary pattern of each region is different in the three subfamilies, it is more reasonable to select rapidly evolving regions for phylogenetic studies specific to each subfamily.

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