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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.

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Circular gene map of the plastid genome of Tilia mandshurica.Genes drawn within the circle are transcribed clockwise, while those drawn outside are transcribed counterclockwise. Genes are color-coded according to their functional groups.
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pone.0142705.g001: Circular gene map of the plastid genome of Tilia mandshurica.Genes drawn within the circle are transcribed clockwise, while those drawn outside are transcribed counterclockwise. Genes are color-coded according to their functional groups.

Mentions: Illumina 90-bp paired-end sequencing of long-rang PCR amplified plastid DNA generated 5,021,460–13,141,606 clean reads for the four sampled Tilia species, with an average sequencing depth from 282× to 739× (Table 1). Using the combination of de novo and reference-guided assembly, we obtained the complete plastid nucleotide sequences for all four species. The determined nucleotide sequences of the four plastid genomes range narrowly from 162,653 bp in Tilia paucicostata to 162,796 bp in Tilia mandshurica (Table 2). They all have a genome structure resembling those of the vast majority of angiosperms, consisting of a pair of IRs separated by LSC and SSC, and the gene map of T. mandshurica plastid genome is presented in Fig 1 as a representative. The four genomes encode an identical set of 130 genes, of which 113 are unique and 17 are duplicated in the IR regions (Table 2), and the arrangements of these 130 genes in them are totally collinear. The 113 unique genes include 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. They also have an identical GC content of 36.5% that is similar to other angiosperms plastid genomes [23, 24].


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)

Circular gene map of the plastid genome of Tilia mandshurica.Genes drawn within the circle are transcribed clockwise, while those drawn outside are transcribed counterclockwise. Genes are color-coded according to their functional groups.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0142705.g001: Circular gene map of the plastid genome of Tilia mandshurica.Genes drawn within the circle are transcribed clockwise, while those drawn outside are transcribed counterclockwise. Genes are color-coded according to their functional groups.
Mentions: Illumina 90-bp paired-end sequencing of long-rang PCR amplified plastid DNA generated 5,021,460–13,141,606 clean reads for the four sampled Tilia species, with an average sequencing depth from 282× to 739× (Table 1). Using the combination of de novo and reference-guided assembly, we obtained the complete plastid nucleotide sequences for all four species. The determined nucleotide sequences of the four plastid genomes range narrowly from 162,653 bp in Tilia paucicostata to 162,796 bp in Tilia mandshurica (Table 2). They all have a genome structure resembling those of the vast majority of angiosperms, consisting of a pair of IRs separated by LSC and SSC, and the gene map of T. mandshurica plastid genome is presented in Fig 1 as a representative. The four genomes encode an identical set of 130 genes, of which 113 are unique and 17 are duplicated in the IR regions (Table 2), and the arrangements of these 130 genes in them are totally collinear. The 113 unique genes include 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. They also have an identical GC content of 36.5% that is similar to other angiosperms plastid genomes [23, 24].

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