Limits...
Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications.

Cai J, Ma PF, Li HT, Li DZ - PLoS ONE (2015)

Bottom Line: As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low.And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes.Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.

View Article: PubMed Central - PubMed

Affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.

ABSTRACT
Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.

Show MeSH
Maximum likelihood phylogeny of the seven Malvaceae species based on the complete plastid genome sequences.The numbers associated with the nodes are bootstrap support and posterior probability values.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4643919&req=5

pone.0142705.g006: Maximum likelihood phylogeny of the seven Malvaceae species based on the complete plastid genome sequences.The numbers associated with the nodes are bootstrap support and posterior probability values.

Mentions: The data matrix for phylogenetic analyses contained the whole plastid genome with one IR region removed for nine taxa, including six species of Malvaceae and two outgroups from Brassicaceae. The data set comprised of 145,679 nucleotide positions with 3,377 informative sites for the ingroup taxa. However, there were only 20 informative sites for the four Tilia species. Unpartitioned ML analyses resulted in a fully resolved tree with 5 of the 6 nodes supported by 100% bootstrap values (Fig 6). ML analyses partitioned by the three plastid genomic regions (LSC, SSC, and IR) yielded an identical topology with the same 5 nodes 100% supported (data not shown). The remaining one received 81% and 82% bootstrap values from unpartitoned and partitioned analyses, respectively. In Bayesian analysis, the identical topology was obtained with a posterior probability (PP) of 1.0 for all nodes (Fig 6). T. amurensis was sister to the other three sampled Tilia species, and T. mandshurica was then sister to the grouping of T. oliveri and T. paucicostata (Fig 6).


Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications.

Cai J, Ma PF, Li HT, Li DZ - PLoS ONE (2015)

Maximum likelihood phylogeny of the seven Malvaceae species based on the complete plastid genome sequences.The numbers associated with the nodes are bootstrap support and posterior probability values.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4643919&req=5

pone.0142705.g006: Maximum likelihood phylogeny of the seven Malvaceae species based on the complete plastid genome sequences.The numbers associated with the nodes are bootstrap support and posterior probability values.
Mentions: The data matrix for phylogenetic analyses contained the whole plastid genome with one IR region removed for nine taxa, including six species of Malvaceae and two outgroups from Brassicaceae. The data set comprised of 145,679 nucleotide positions with 3,377 informative sites for the ingroup taxa. However, there were only 20 informative sites for the four Tilia species. Unpartitioned ML analyses resulted in a fully resolved tree with 5 of the 6 nodes supported by 100% bootstrap values (Fig 6). ML analyses partitioned by the three plastid genomic regions (LSC, SSC, and IR) yielded an identical topology with the same 5 nodes 100% supported (data not shown). The remaining one received 81% and 82% bootstrap values from unpartitoned and partitioned analyses, respectively. In Bayesian analysis, the identical topology was obtained with a posterior probability (PP) of 1.0 for all nodes (Fig 6). T. amurensis was sister to the other three sampled Tilia species, and T. mandshurica was then sister to the grouping of T. oliveri and T. paucicostata (Fig 6).

Bottom Line: As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low.And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes.Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.

View Article: PubMed Central - PubMed

Affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.

ABSTRACT
Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.

Show MeSH