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Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes.
PLoS One. 2013; 8(4):e62548.Plos

Abstract

Ardisia is a basal asterid genus well known for its medicinal values and has the potential for development of novel phytopharmaceuticals. In this genus of nearly 500 species, many ornamental species are commonly grown worldwide and some have become invasive species that caused ecological problems. As there is no completed plastid genome (plastome) sequence in related taxa, we sequenced and characterized the plastome of Ardisia polysticta to find plastid markers of potential utility for phylogenetic analyses at low taxonomic levels. The complete A. polysticta plastome is 156,506 bp in length and has gene content and organization typical of most asterids and other angiosperms. We identified seven intergenic regions as potentially informative markers with resolution for interspecific relationships. Additionally, we characterized the diversity of asterid plastomes with respect to GC content, plastome organization, gene content, and repetitive sequences through comparative analyses. The results demonstrated that the genome organizations near the boundaries between inverted repeats (IRs) and single-copy regions (SCs) are polymorphic. The boundary organization found in Ardisia appears to be the most common type among asterids, while six other types are also found in various asterid lineages. In general, the repetitive sequences in genic regions tend to be more conserved, whereas those in noncoding regions are usually lineage-specific. Finally, we inferred the whole-plastome phylogeny with the available asterid sequences. With the improvement in taxon sampling of asterid orders and families, our result highlights the uncertainty of the position of Gentianales within euasterids I.

Authors+Show Affiliations

Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.No affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23638113

Citation

Ku, Chuan, et al. "Complete Plastid Genome Sequence of the Basal Asterid Ardisia Polysticta Miq. and Comparative Analyses of Asterid Plastid Genomes." PloS One, vol. 8, no. 4, 2013, pp. e62548.
Ku C, Hu JM, Kuo CH. Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS ONE. 2013;8(4):e62548.
Ku, C., Hu, J. M., & Kuo, C. H. (2013). Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PloS One, 8(4), e62548. https://doi.org/10.1371/journal.pone.0062548
Ku C, Hu JM, Kuo CH. Complete Plastid Genome Sequence of the Basal Asterid Ardisia Polysticta Miq. and Comparative Analyses of Asterid Plastid Genomes. PLoS ONE. 2013;8(4):e62548. PubMed PMID: 23638113.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. AU - Ku,Chuan, AU - Hu,Jer-Ming, AU - Kuo,Chih-Horng, Y1 - 2013/04/30/ PY - 2013/01/15/received PY - 2013/03/22/accepted PY - 2013/5/3/entrez PY - 2013/5/3/pubmed PY - 2013/12/16/medline SP - e62548 EP - e62548 JF - PloS one JO - PLoS ONE VL - 8 IS - 4 N2 - Ardisia is a basal asterid genus well known for its medicinal values and has the potential for development of novel phytopharmaceuticals. In this genus of nearly 500 species, many ornamental species are commonly grown worldwide and some have become invasive species that caused ecological problems. As there is no completed plastid genome (plastome) sequence in related taxa, we sequenced and characterized the plastome of Ardisia polysticta to find plastid markers of potential utility for phylogenetic analyses at low taxonomic levels. The complete A. polysticta plastome is 156,506 bp in length and has gene content and organization typical of most asterids and other angiosperms. We identified seven intergenic regions as potentially informative markers with resolution for interspecific relationships. Additionally, we characterized the diversity of asterid plastomes with respect to GC content, plastome organization, gene content, and repetitive sequences through comparative analyses. The results demonstrated that the genome organizations near the boundaries between inverted repeats (IRs) and single-copy regions (SCs) are polymorphic. The boundary organization found in Ardisia appears to be the most common type among asterids, while six other types are also found in various asterid lineages. In general, the repetitive sequences in genic regions tend to be more conserved, whereas those in noncoding regions are usually lineage-specific. Finally, we inferred the whole-plastome phylogeny with the available asterid sequences. With the improvement in taxon sampling of asterid orders and families, our result highlights the uncertainty of the position of Gentianales within euasterids I. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/23638113/Complete_plastid_genome_sequence_of_the_basal_asterid_Ardisia_polysticta_Miq__and_comparative_analyses_of_asterid_plastid_genomes_ L2 - http://dx.plos.org/10.1371/journal.pone.0062548 DB - PRIME DP - Unbound Medicine ER -