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Analysis of the Complete Chloroplast Genome of a Medicinal Plant, Dianthus superbus var. longicalyncinus, from a Comparative Genomics Perspective.

Raman G, Park S - PLoS ONE (2015)

Bottom Line: In this study, D. superbus was compared to its closely related family of Caryophyllaceae chloroplast (cp) genomes such as Lychnis chalcedonica and Spinacia oleracea.When the cp genome of Dianthus was compared with 31 other angiosperm lineages, the infA gene was found to have been lost in most members of rosids, solanales of asterids and Lychnis of Caryophyllales, whereas rpl23 gene loss or pseudogization had occurred exclusively in Caryophyllales.The results presented herein will contribute to studies of the evolution, molecular biology and genetic engineering of the medicinal and ornamental plant, D. superbus var. longicalycinus.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea.

ABSTRACT
Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicinal plant that is also used for ornamental purposes. In this study, D. superbus was compared to its closely related family of Caryophyllaceae chloroplast (cp) genomes such as Lychnis chalcedonica and Spinacia oleracea. D. superbus had the longest large single copy (LSC) region (82,805 bp), with some variations in the inverted repeat region A (IRA)/LSC regions. The IRs underwent both expansion and constriction during evolution of the Caryophyllaceae family; however, intense variations were not identified. The pseudogene ribosomal protein subunit S19 (rps19) was identified at the IRA/LSC junction, but was not present in the cp genome of other Caryophyllaceae family members. The translation initiation factor IF-1 (infA) and ribosomal protein subunit L23 (rpl23) genes were absent from the Dianthus cp genome. When the cp genome of Dianthus was compared with 31 other angiosperm lineages, the infA gene was found to have been lost in most members of rosids, solanales of asterids and Lychnis of Caryophyllales, whereas rpl23 gene loss or pseudogization had occurred exclusively in Caryophyllales. Nevertheless, the cp genome of Dianthus and Spinacia has two introns in the proteolytic subunit of ATP-dependent protease (clpP) gene, but Lychnis has lost introns from the clpP gene. Furthermore, phylogenetic analysis of individual protein-coding genes infA and rpl23 revealed that gene loss or pseudogenization occurred independently in the cp genome of Dianthus. Molecular phylogenetic analysis also demonstrated a sister relationship between Dianthus and Lychnis based on 78 protein-coding sequences. The results presented herein will contribute to studies of the evolution, molecular biology and genetic engineering of the medicinal and ornamental plant, D. superbus var. longicalycinus.

No MeSH data available.


Related in: MedlinePlus

Molecular phylogenetic tree analysis of cp protein-coding gene infA of 32 Angiosperms.The tree was constructed by maximum likelihood (ML) analysis using the RaxML program and the GTR+I nucleotide model. The stability of each tree node was tested by bootstrap analysis with 1000 replicates. Nelumbo was set as the outgroup.
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pone.0141329.g004: Molecular phylogenetic tree analysis of cp protein-coding gene infA of 32 Angiosperms.The tree was constructed by maximum likelihood (ML) analysis using the RaxML program and the GTR+I nucleotide model. The stability of each tree node was tested by bootstrap analysis with 1000 replicates. Nelumbo was set as the outgroup.

Mentions: The chloroplast genes infA and rpl23 of Dianthus were analyzed with 31 other angiosperms. Both infA and rpl23 were found to be pseudogenes in the cp genome of Dianthus. Among 32 angiosperms (including Dianthus), the infA gene was found to be a pseudogene or entirely missing from Dianthus and Lychnis of the Caryophyllales family, as well as Brassicales, Cucurbitales, Fabales, Malpighiales, Malvales, Myrtales and Sapindales of Rosids and Solanales of Asterids (Fig 4 and S2 Fig). Comparative analysis of the ribosomal protein gene, rpl23, in 32 angiosperms revealed that it was a pseudogene or lost gene exclusively in members of the Caryophyllales family such as Dianthus, Lychnis and Spinacia (Fig 5 and S3 Fig).


Analysis of the Complete Chloroplast Genome of a Medicinal Plant, Dianthus superbus var. longicalyncinus, from a Comparative Genomics Perspective.

Raman G, Park S - PLoS ONE (2015)

Molecular phylogenetic tree analysis of cp protein-coding gene infA of 32 Angiosperms.The tree was constructed by maximum likelihood (ML) analysis using the RaxML program and the GTR+I nucleotide model. The stability of each tree node was tested by bootstrap analysis with 1000 replicates. Nelumbo was set as the outgroup.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4626046&req=5

pone.0141329.g004: Molecular phylogenetic tree analysis of cp protein-coding gene infA of 32 Angiosperms.The tree was constructed by maximum likelihood (ML) analysis using the RaxML program and the GTR+I nucleotide model. The stability of each tree node was tested by bootstrap analysis with 1000 replicates. Nelumbo was set as the outgroup.
Mentions: The chloroplast genes infA and rpl23 of Dianthus were analyzed with 31 other angiosperms. Both infA and rpl23 were found to be pseudogenes in the cp genome of Dianthus. Among 32 angiosperms (including Dianthus), the infA gene was found to be a pseudogene or entirely missing from Dianthus and Lychnis of the Caryophyllales family, as well as Brassicales, Cucurbitales, Fabales, Malpighiales, Malvales, Myrtales and Sapindales of Rosids and Solanales of Asterids (Fig 4 and S2 Fig). Comparative analysis of the ribosomal protein gene, rpl23, in 32 angiosperms revealed that it was a pseudogene or lost gene exclusively in members of the Caryophyllales family such as Dianthus, Lychnis and Spinacia (Fig 5 and S3 Fig).

Bottom Line: In this study, D. superbus was compared to its closely related family of Caryophyllaceae chloroplast (cp) genomes such as Lychnis chalcedonica and Spinacia oleracea.When the cp genome of Dianthus was compared with 31 other angiosperm lineages, the infA gene was found to have been lost in most members of rosids, solanales of asterids and Lychnis of Caryophyllales, whereas rpl23 gene loss or pseudogization had occurred exclusively in Caryophyllales.The results presented herein will contribute to studies of the evolution, molecular biology and genetic engineering of the medicinal and ornamental plant, D. superbus var. longicalycinus.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea.

ABSTRACT
Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicinal plant that is also used for ornamental purposes. In this study, D. superbus was compared to its closely related family of Caryophyllaceae chloroplast (cp) genomes such as Lychnis chalcedonica and Spinacia oleracea. D. superbus had the longest large single copy (LSC) region (82,805 bp), with some variations in the inverted repeat region A (IRA)/LSC regions. The IRs underwent both expansion and constriction during evolution of the Caryophyllaceae family; however, intense variations were not identified. The pseudogene ribosomal protein subunit S19 (rps19) was identified at the IRA/LSC junction, but was not present in the cp genome of other Caryophyllaceae family members. The translation initiation factor IF-1 (infA) and ribosomal protein subunit L23 (rpl23) genes were absent from the Dianthus cp genome. When the cp genome of Dianthus was compared with 31 other angiosperm lineages, the infA gene was found to have been lost in most members of rosids, solanales of asterids and Lychnis of Caryophyllales, whereas rpl23 gene loss or pseudogization had occurred exclusively in Caryophyllales. Nevertheless, the cp genome of Dianthus and Spinacia has two introns in the proteolytic subunit of ATP-dependent protease (clpP) gene, but Lychnis has lost introns from the clpP gene. Furthermore, phylogenetic analysis of individual protein-coding genes infA and rpl23 revealed that gene loss or pseudogenization occurred independently in the cp genome of Dianthus. Molecular phylogenetic analysis also demonstrated a sister relationship between Dianthus and Lychnis based on 78 protein-coding sequences. The results presented herein will contribute to studies of the evolution, molecular biology and genetic engineering of the medicinal and ornamental plant, D. superbus var. longicalycinus.

No MeSH data available.


Related in: MedlinePlus