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The complete chloroplast genome of Phyllostachys glauca (Bambusoideae), a dominant bamboo species in limestone mountains endemic to China.

ABSTRACT: Phyllostachys glauca is a dominant species in limestone mountains endemic to China. Here, we characterized its complete chloroplast genome. It is a circular DNA molecule of 139,689 bp in length, including a pair of 21,798 bp inverted repeats (IRs), a 12,872 bp small single-copy (SSC) region and an 83221 bp large single-copy (LSC) region. The total GC content of P. glauca chloroplast genome was 38.9%, and it encodes a total of 137 functional genes, including 89 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The phylogenetic analysis shows that P. glauca is highly clustered in the Phyllostachys clade (V), sister to the lineage of P. nigra var. henonis + P. sulphurea.

SUBMITTER: Cao B

PROVIDER: S-EPMC7783095 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description: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.

Dataset Information

The complete chloroplast genome of Phyllostachys glauca (Bambusoideae), a dominant bamboo species in limestone mountains endemic to China.

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