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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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The number of noncoding regions with different sizes between the plastid genomes of Tilia mandshurica and Gossypium hirsutum.The black bar indicates the regions are larger in T. mandshurica, while the gray bar indicates the regions are larger in G. hirsutum.
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pone.0142705.g002: The number of noncoding regions with different sizes between the plastid genomes of Tilia mandshurica and Gossypium hirsutum.The black bar indicates the regions are larger in T. mandshurica, while the gray bar indicates the regions are larger in G. hirsutum.

Mentions: In terms of genome size, the plastid genome of Tilia (162,653–162,796 bp) is slightly larger than those of Gossypium (159,039–160,433 bp) and Theobroma (160,604 bp). We selected T. mandshurica and G. hirsutum as representative species to investigate the trend toward increased genome size in Tilia. The whole plastid genome of T. mandshurica is 2495 bp larger than that of G. hirsutum, and all three regions LSC, SSC and IR of T. mandshurica are larger with LSC (2311 bp) accounting for most variation in genome size (Table 2). Among the 78 common unique protein-coding genes between these two genomes there are 11 genes with difference in length. Four genes (atpI, ccsA, rbcL, and ycf1) are larger in T. mandshurica while seven genes (accD, matK, ndhF, petB, rpl22, rpoA, and rpoC2) are larger in G. hirsutum, accounting for 63 bp and 180 bp of the variation in genome size respectively. On the other hand, the majority of noncoding (intergenic and intron) regions (120 of 153) show variations in length. The number of noncoding regions that are larger is similar in T. mandshurica and G. hirsutum (63 versus 47) (Fig 2). Nevertheless, the 9 regions with length difference above 100 bp are all those larger in T. mandshurica than G. hirsutum. These 9 regions are ycf3-trnS-GGA, ndhC-trnV-UAC, trnH-GUG-psbA, trnT-UGU-trnL-UAA, trnR-UCC-atpA, psbZ-trnG-UCC, atpB-rbcL, trnC-GCA-petN, and trnK-UUU-rps16. These length differences are mainly caused by the large insertions in the T. mandshurica (or deletions in G. hirsutum) plastid genome and there are 8 indels (insertions or deletions) in all larger than 100 bp. The total length of these indels is 1990 bp, explaining ~80% of variation in genome size.


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)

The number of noncoding regions with different sizes between the plastid genomes of Tilia mandshurica and Gossypium hirsutum.The black bar indicates the regions are larger in T. mandshurica, while the gray bar indicates the regions are larger in G. hirsutum.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0142705.g002: The number of noncoding regions with different sizes between the plastid genomes of Tilia mandshurica and Gossypium hirsutum.The black bar indicates the regions are larger in T. mandshurica, while the gray bar indicates the regions are larger in G. hirsutum.
Mentions: In terms of genome size, the plastid genome of Tilia (162,653–162,796 bp) is slightly larger than those of Gossypium (159,039–160,433 bp) and Theobroma (160,604 bp). We selected T. mandshurica and G. hirsutum as representative species to investigate the trend toward increased genome size in Tilia. The whole plastid genome of T. mandshurica is 2495 bp larger than that of G. hirsutum, and all three regions LSC, SSC and IR of T. mandshurica are larger with LSC (2311 bp) accounting for most variation in genome size (Table 2). Among the 78 common unique protein-coding genes between these two genomes there are 11 genes with difference in length. Four genes (atpI, ccsA, rbcL, and ycf1) are larger in T. mandshurica while seven genes (accD, matK, ndhF, petB, rpl22, rpoA, and rpoC2) are larger in G. hirsutum, accounting for 63 bp and 180 bp of the variation in genome size respectively. On the other hand, the majority of noncoding (intergenic and intron) regions (120 of 153) show variations in length. The number of noncoding regions that are larger is similar in T. mandshurica and G. hirsutum (63 versus 47) (Fig 2). Nevertheless, the 9 regions with length difference above 100 bp are all those larger in T. mandshurica than G. hirsutum. These 9 regions are ycf3-trnS-GGA, ndhC-trnV-UAC, trnH-GUG-psbA, trnT-UGU-trnL-UAA, trnR-UCC-atpA, psbZ-trnG-UCC, atpB-rbcL, trnC-GCA-petN, and trnK-UUU-rps16. These length differences are mainly caused by the large insertions in the T. mandshurica (or deletions in G. hirsutum) plastid genome and there are 8 indels (insertions or deletions) in all larger than 100 bp. The total length of these indels is 1990 bp, explaining ~80% of variation in genome size.

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