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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

Gene map of the six woody bamboo chloroplast genomes.Genes shown outside the outer circle are transcribed clockwise and those inside are transcribed counterclockwise. Genes belonging to different functional groups are color coded. Dashed area in the inner circle indicates the GC content of the chloroplast genome.
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pone-0020596-g001: Gene map of the six woody bamboo chloroplast genomes.Genes shown outside the outer circle are transcribed clockwise and those inside are transcribed counterclockwise. Genes belonging to different functional groups are color coded. Dashed area in the inner circle indicates the GC content of the chloroplast genome.

Mentions: The determined nucleotide sequences of six cp genomes ranged from 139,493 bp in B. emeiensis to 139,839 bp in P. nigra var. henonis (Table 1). All six cp genomes showed a typical quadripartite structure, consisting of a pair of IRs (21,792–21,863 bp) separated by the LSC (82,988–83,273 bp) and SSC (12,718–12,901 bp) regions (Table 1). They encode an identical set of 131 genes with the same gene order and gene clusters, of which 112 are unique and 19 are duplicated in the IR regions (Figure 1). The 112 unique genes include 4 ribosomal RNAs, 31 transfer RNAs and 77 protein-coding genes. Fifteen distinct genes (rps16, atpF, rpl16, rpl2, ndhB, rps12, ndhA, petB, petD, trnK(UUU), trnG(UCC), trnL(UAA), trnV(UAC), trnI(GAU), trnA(UGC)) contain one intron and only one gene (ycf3) contains two. The cp genomes consist of 50.4% to 50.7% coding regions, and the overall GC content is 38.9% for all species except for A. purpurea (38.8%). Altogether, these six cp genomes are highly conserved in each aspect of genome features, such as gene content and gene order, intron and GC content.


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)

Gene map of the six woody bamboo chloroplast genomes.Genes shown outside the outer circle are transcribed clockwise and those inside are transcribed counterclockwise. Genes belonging to different functional groups are color coded. Dashed area in the inner circle indicates the GC content of the chloroplast genome.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020596-g001: Gene map of the six woody bamboo chloroplast genomes.Genes shown outside the outer circle are transcribed clockwise and those inside are transcribed counterclockwise. Genes belonging to different functional groups are color coded. Dashed area in the inner circle indicates the GC content of the chloroplast genome.
Mentions: The determined nucleotide sequences of six cp genomes ranged from 139,493 bp in B. emeiensis to 139,839 bp in P. nigra var. henonis (Table 1). All six cp genomes showed a typical quadripartite structure, consisting of a pair of IRs (21,792–21,863 bp) separated by the LSC (82,988–83,273 bp) and SSC (12,718–12,901 bp) regions (Table 1). They encode an identical set of 131 genes with the same gene order and gene clusters, of which 112 are unique and 19 are duplicated in the IR regions (Figure 1). The 112 unique genes include 4 ribosomal RNAs, 31 transfer RNAs and 77 protein-coding genes. Fifteen distinct genes (rps16, atpF, rpl16, rpl2, ndhB, rps12, ndhA, petB, petD, trnK(UUU), trnG(UCC), trnL(UAA), trnV(UAC), trnI(GAU), trnA(UGC)) contain one intron and only one gene (ycf3) contains two. The cp genomes consist of 50.4% to 50.7% coding regions, and the overall GC content is 38.9% for all species except for A. purpurea (38.8%). Altogether, these six cp genomes are highly conserved in each aspect of genome features, such as gene content and gene order, intron and GC content.

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