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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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Related in: MedlinePlus

Visualization of alignment of the eight woody bamboo chloroplast genome sequences.VISTA-based identity plots showing sequence identity between six sequenced chloroplast genomes and the two published chloroplast genomes of Bambuseae, with Dendrocalamus latiflorus as a reference. Thick black lines show the inverted repeats (IRs) regions and red line indicates the divergent hotspot region in the chloroplast genome. Genome regions are color coded as protein coding, rRNA coding, tRNA coding or conserved noncoding sequences.
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pone-0020596-g002: Visualization of alignment of the eight woody bamboo chloroplast genome sequences.VISTA-based identity plots showing sequence identity between six sequenced chloroplast genomes and the two published chloroplast genomes of Bambuseae, with Dendrocalamus latiflorus as a reference. Thick black lines show the inverted repeats (IRs) regions and red line indicates the divergent hotspot region in the chloroplast genome. Genome regions are color coded as protein coding, rRNA coding, tRNA coding or conserved noncoding sequences.

Mentions: The genetic divergence is very low among cp genomes of Bambusoideae. After alignment of our six cp genomes and two other published cp genomes in Bambuseae, Bambusa oldhamii (FJ970915) and D. latiflorus [25], we plotted sequence identity using VISTA [38] with D. latiflorus as a reference (Figure 2). The whole aligned sequences show high similarities with only a few regions' sequence identities falling below 90%, suggesting that bamboo cp genomes are rather conservative. As expected, the IRs and coding regions are more conserved than single copy and noncoding regions, respectively. The rpoC2 gene is an exception, with lower sequence identity due to various indels, as also found in other grasses [31], [33]. One divergent hotspot region associated with a tRNA cluster in LSC (trnS(UGA)-trnC(GCA)) region was identified (Figure 2), and this divergent hotspot has also been described in other grass cp genomes [30], [33]. The average genetic divergence of the eight bamboo species, estimated by p-distance, was only 0.009. The p-distance between Arundinarieae and Bambuseae, however, was 0.014, a much larger divergence than that within tribes (0.002 for Arundinarieae and 0.003 for Bambuseae). These values indicate that the majority of the extremely low sequence divergence in Bambusoideae mainly prevails between tribes, and that sequence divergence in Bambuseae is slightly larger than that in Arundinarieae.


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)

Visualization of alignment of the eight woody bamboo chloroplast genome sequences.VISTA-based identity plots showing sequence identity between six sequenced chloroplast genomes and the two published chloroplast genomes of Bambuseae, with Dendrocalamus latiflorus as a reference. Thick black lines show the inverted repeats (IRs) regions and red line indicates the divergent hotspot region in the chloroplast genome. Genome regions are color coded as protein coding, rRNA coding, tRNA coding or conserved noncoding sequences.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020596-g002: Visualization of alignment of the eight woody bamboo chloroplast genome sequences.VISTA-based identity plots showing sequence identity between six sequenced chloroplast genomes and the two published chloroplast genomes of Bambuseae, with Dendrocalamus latiflorus as a reference. Thick black lines show the inverted repeats (IRs) regions and red line indicates the divergent hotspot region in the chloroplast genome. Genome regions are color coded as protein coding, rRNA coding, tRNA coding or conserved noncoding sequences.
Mentions: The genetic divergence is very low among cp genomes of Bambusoideae. After alignment of our six cp genomes and two other published cp genomes in Bambuseae, Bambusa oldhamii (FJ970915) and D. latiflorus [25], we plotted sequence identity using VISTA [38] with D. latiflorus as a reference (Figure 2). The whole aligned sequences show high similarities with only a few regions' sequence identities falling below 90%, suggesting that bamboo cp genomes are rather conservative. As expected, the IRs and coding regions are more conserved than single copy and noncoding regions, respectively. The rpoC2 gene is an exception, with lower sequence identity due to various indels, as also found in other grasses [31], [33]. One divergent hotspot region associated with a tRNA cluster in LSC (trnS(UGA)-trnC(GCA)) region was identified (Figure 2), and this divergent hotspot has also been described in other grass cp genomes [30], [33]. The average genetic divergence of the eight bamboo species, estimated by p-distance, was only 0.009. The p-distance between Arundinarieae and Bambuseae, however, was 0.014, a much larger divergence than that within tribes (0.002 for Arundinarieae and 0.003 for Bambuseae). These values indicate that the majority of the extremely low sequence divergence in Bambusoideae mainly prevails between tribes, and that sequence divergence in Bambuseae is slightly larger than that in Arundinarieae.

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