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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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Phylogenetic distribution of exon coding indels in sampled grass accessions.Gene names are given above boxes and sizes of indels (bp) and polarity (‘+’  =  insertion, ‘−’ = deletion) are given below boxes. Polarity of mutations was determined by comparison to outgroup Anomochloa marantoidea. Tree topology was based on maximum parsimony analysis of complete chloroplast genomes.
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pone-0020596-g007: Phylogenetic distribution of exon coding indels in sampled grass accessions.Gene names are given above boxes and sizes of indels (bp) and polarity (‘+’  =  insertion, ‘−’ = deletion) are given below boxes. Polarity of mutations was determined by comparison to outgroup Anomochloa marantoidea. Tree topology was based on maximum parsimony analysis of complete chloroplast genomes.

Mentions: Forty-five possibly informative exon indels were identified and mapped to cp genome-based phylogenetic tree (Figure 7). Of these, 25 indels mapped to monophyletic groups which have been highly supported, and thus may be synapomorphies. The remaining 20 indels may be homoplasies possibly associated with parallel mutations or back mutations during evolutionary history. There is not clear consensus about whether the indels should be used for phylogenetic analyses [48], [49], although most hesitancy against them has been based on studies using one or several DNA fragments. In our study, the 45 indels were located in 21 genes (Table S5), and they were coded and subsequently added to the protein coding gene matrix to perform MP analyses. Including indel characters in the protein coding gene matrix did not change the topology of the strict consensus tree, although it increased three nodal support values (Figure S2). Thus, we inferred that the influence of indels on our phylogenomic analyses on the basis of large data sets could be neglected. Furthermore, genes in the cp genome could contain both synapomorphic and homoplasious indels and the proportion between synapomorphic indels and homoplasious indels varied among different genes (Table S5). For example, half of the indels in the ccsA gene were synapomorphic, but three of four indels were homoplasious characters in rps18 gene. Therefore, small cp genome structural changes such as indels should be carefully used in phylogenetic studies based only on several DNA fragments. Mapping the indels to species whose relationships have been well clarified could first exclude the possible homoplasious indels and thus decrease the influence of such homoplasious characters.


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)

Phylogenetic distribution of exon coding indels in sampled grass accessions.Gene names are given above boxes and sizes of indels (bp) and polarity (‘+’  =  insertion, ‘−’ = deletion) are given below boxes. Polarity of mutations was determined by comparison to outgroup Anomochloa marantoidea. Tree topology was based on maximum parsimony analysis of complete chloroplast genomes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020596-g007: Phylogenetic distribution of exon coding indels in sampled grass accessions.Gene names are given above boxes and sizes of indels (bp) and polarity (‘+’  =  insertion, ‘−’ = deletion) are given below boxes. Polarity of mutations was determined by comparison to outgroup Anomochloa marantoidea. Tree topology was based on maximum parsimony analysis of complete chloroplast genomes.
Mentions: Forty-five possibly informative exon indels were identified and mapped to cp genome-based phylogenetic tree (Figure 7). Of these, 25 indels mapped to monophyletic groups which have been highly supported, and thus may be synapomorphies. The remaining 20 indels may be homoplasies possibly associated with parallel mutations or back mutations during evolutionary history. There is not clear consensus about whether the indels should be used for phylogenetic analyses [48], [49], although most hesitancy against them has been based on studies using one or several DNA fragments. In our study, the 45 indels were located in 21 genes (Table S5), and they were coded and subsequently added to the protein coding gene matrix to perform MP analyses. Including indel characters in the protein coding gene matrix did not change the topology of the strict consensus tree, although it increased three nodal support values (Figure S2). Thus, we inferred that the influence of indels on our phylogenomic analyses on the basis of large data sets could be neglected. Furthermore, genes in the cp genome could contain both synapomorphic and homoplasious indels and the proportion between synapomorphic indels and homoplasious indels varied among different genes (Table S5). For example, half of the indels in the ccsA gene were synapomorphic, but three of four indels were homoplasious characters in rps18 gene. Therefore, small cp genome structural changes such as indels should be carefully used in phylogenetic studies based only on several DNA fragments. Mapping the indels to species whose relationships have been well clarified could first exclude the possible homoplasious indels and thus decrease the influence of such homoplasious characters.

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