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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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Linear relationship between percentages of parsimony informative characters (PIs) and percentages of variable sites.A) Coding region. B) Noncoding region. The fitted slope from linear regression analysis is shown.
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pone-0020596-g009: Linear relationship between percentages of parsimony informative characters (PIs) and percentages of variable sites.A) Coding region. B) Noncoding region. The fitted slope from linear regression analysis is shown.

Mentions: In Bambusoideae, the proportion of variability in noncoding regions ranged from 1.33% to 8.14% and the mean value was 3.86%, which was twice as much as in the coding regions (1.57% on average). Correlation analysis revealed a significant positive linear relationship between percentages of PIs and percentages of variable sites in coding (R2 = 0.6671, P<0.001) and noncoding (R2 = 0.7258, P<0.001) regions as expected, respectively (Figure 9). Therefore, we choose the twenty most variable noncoding regions as potential molecular markers for our bamboo phylogenetic study. The variations of twenty noncoding regions exceeded 4%, and 14 of them had a percentage of PIs that exceeded 3% (Table S6). The 20 noncoding regions identified in this study are listed here from high to low relative genetic divergence: trnD(GUC)-psbM, ycf4-cemA, trnG(UCC)-trnT(GGU), ndhF-rpl32, rpl32-trnL(UAG), trnK(UUU)-rps16, psbK-psbI, ycf3-trnS(GGA), trnT(UGU)-trnL(UAA), psbZ-trnfM(CAU), rbcL-psaI, psaC-ndhE, trnT(GGU)-trnE(UUC), trnY(GUA)-trnD(GUC), rps15-ndhF, trnL(UAA)-trnF(GAA), trnF(GAA)-ndhJ, rpl16 intron, psaI-ycf4, psaA-ycf3. Five of them are located in SSC region (ndhF-rpl32, rpl32-trnL(UAG), psaC-ndhE, rpl16 intron) and rps15-ndhF is in the IRb-SSC junction. Among these regions, rpl32-trnL(UAG), trnK(UUU)-rps16, trnT(UGU)-trnL(UAA), trnT(GGU)-trnE(UUC), trnY(GUA)-trnD(GUC) and psaA-ycf3 have been used in bamboo phylogenetic studies, and proved to be able to provide relatively more informative characters. However, determining whether the other 14 regions could be applied to bamboo phylogenetic analyses requires further study.


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)

Linear relationship between percentages of parsimony informative characters (PIs) and percentages of variable sites.A) Coding region. B) Noncoding region. The fitted slope from linear regression analysis is shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020596-g009: Linear relationship between percentages of parsimony informative characters (PIs) and percentages of variable sites.A) Coding region. B) Noncoding region. The fitted slope from linear regression analysis is shown.
Mentions: In Bambusoideae, the proportion of variability in noncoding regions ranged from 1.33% to 8.14% and the mean value was 3.86%, which was twice as much as in the coding regions (1.57% on average). Correlation analysis revealed a significant positive linear relationship between percentages of PIs and percentages of variable sites in coding (R2 = 0.6671, P<0.001) and noncoding (R2 = 0.7258, P<0.001) regions as expected, respectively (Figure 9). Therefore, we choose the twenty most variable noncoding regions as potential molecular markers for our bamboo phylogenetic study. The variations of twenty noncoding regions exceeded 4%, and 14 of them had a percentage of PIs that exceeded 3% (Table S6). The 20 noncoding regions identified in this study are listed here from high to low relative genetic divergence: trnD(GUC)-psbM, ycf4-cemA, trnG(UCC)-trnT(GGU), ndhF-rpl32, rpl32-trnL(UAG), trnK(UUU)-rps16, psbK-psbI, ycf3-trnS(GGA), trnT(UGU)-trnL(UAA), psbZ-trnfM(CAU), rbcL-psaI, psaC-ndhE, trnT(GGU)-trnE(UUC), trnY(GUA)-trnD(GUC), rps15-ndhF, trnL(UAA)-trnF(GAA), trnF(GAA)-ndhJ, rpl16 intron, psaI-ycf4, psaA-ycf3. Five of them are located in SSC region (ndhF-rpl32, rpl32-trnL(UAG), psaC-ndhE, rpl16 intron) and rps15-ndhF is in the IRb-SSC junction. Among these regions, rpl32-trnL(UAG), trnK(UUU)-rps16, trnT(UGU)-trnL(UAA), trnT(GGU)-trnE(UUC), trnY(GUA)-trnD(GUC) and psaA-ycf3 have been used in bamboo phylogenetic studies, and proved to be able to provide relatively more informative characters. However, determining whether the other 14 regions could be applied to bamboo phylogenetic analyses requires further study.

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