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Complete chloroplast genome sequence of Omani lime (Citrus aurantiifolia) and comparative analysis within the rosids.

Su HJ, Hogenhout SA, Al-Sadi AM, Kuo CH - PLoS ONE (2014)

Bottom Line: The complete C. aurantiifolia chloroplast genome is 159,893 bp in length; the organization and gene content are similar to most of the rosids lineages characterized to date.These markers can be utilized to better understand the origin of cultivated Citrus.A comparison among 72 species belonging to 10 families of representative rosids lineages also provides new insights into their chloroplast genome evolution.

View Article: PubMed Central - PubMed

Affiliation: Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.

ABSTRACT
The genus Citrus contains many economically important fruits that are grown worldwide for their high nutritional and medicinal value. Due to frequent hybridizations among species and cultivars, the exact number of natural species and the taxonomic relationships within this genus are unclear. To compare the differences between the Citrus chloroplast genomes and to develop useful genetic markers, we used a reference-assisted approach to assemble the complete chloroplast genome of Omani lime (C. aurantiifolia). The complete C. aurantiifolia chloroplast genome is 159,893 bp in length; the organization and gene content are similar to most of the rosids lineages characterized to date. Through comparison with the sweet orange (C. sinensis) chloroplast genome, we identified three intergenic regions and 94 simple sequence repeats (SSRs) that are potentially informative markers with resolution for interspecific relationships. These markers can be utilized to better understand the origin of cultivated Citrus. A comparison among 72 species belonging to 10 families of representative rosids lineages also provides new insights into their chloroplast genome evolution.

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Maximum likelihood phylogeny of the representative rosids lineages.The common grape vine (Vitis vinifera) is included as the outgroup to root the tree. The concatenated alignment includes 62 conserved chloroplast genome genes and 54,689 aligned nucleotide sites. Nodes received <70% bootstrap support are indicated by gray arrows. The putative events of gene losses are inferred based on the most parsimonious scenario.
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pone-0113049-g002: Maximum likelihood phylogeny of the representative rosids lineages.The common grape vine (Vitis vinifera) is included as the outgroup to root the tree. The concatenated alignment includes 62 conserved chloroplast genome genes and 54,689 aligned nucleotide sites. Nodes received <70% bootstrap support are indicated by gray arrows. The putative events of gene losses are inferred based on the most parsimonious scenario.

Mentions: A maximum likelihood phylogenetic analysis of 72 representative rosids lineages was conducted based on a concatenated alignment of four rRNA and 58 protein-coding genes with 54,689 sites (Figure 2). Citrus represents Sapindales and is sister to the clade containing Malvales and Brassicales. These relationships are congruent with the previous reports [10], [41]–[43]. Based on this phylogeny and the gene content, we inferred the gene loss events during the cp genome evolution in rosids.


Complete chloroplast genome sequence of Omani lime (Citrus aurantiifolia) and comparative analysis within the rosids.

Su HJ, Hogenhout SA, Al-Sadi AM, Kuo CH - PLoS ONE (2014)

Maximum likelihood phylogeny of the representative rosids lineages.The common grape vine (Vitis vinifera) is included as the outgroup to root the tree. The concatenated alignment includes 62 conserved chloroplast genome genes and 54,689 aligned nucleotide sites. Nodes received <70% bootstrap support are indicated by gray arrows. The putative events of gene losses are inferred based on the most parsimonious scenario.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232571&req=5

pone-0113049-g002: Maximum likelihood phylogeny of the representative rosids lineages.The common grape vine (Vitis vinifera) is included as the outgroup to root the tree. The concatenated alignment includes 62 conserved chloroplast genome genes and 54,689 aligned nucleotide sites. Nodes received <70% bootstrap support are indicated by gray arrows. The putative events of gene losses are inferred based on the most parsimonious scenario.
Mentions: A maximum likelihood phylogenetic analysis of 72 representative rosids lineages was conducted based on a concatenated alignment of four rRNA and 58 protein-coding genes with 54,689 sites (Figure 2). Citrus represents Sapindales and is sister to the clade containing Malvales and Brassicales. These relationships are congruent with the previous reports [10], [41]–[43]. Based on this phylogeny and the gene content, we inferred the gene loss events during the cp genome evolution in rosids.

Bottom Line: The complete C. aurantiifolia chloroplast genome is 159,893 bp in length; the organization and gene content are similar to most of the rosids lineages characterized to date.These markers can be utilized to better understand the origin of cultivated Citrus.A comparison among 72 species belonging to 10 families of representative rosids lineages also provides new insights into their chloroplast genome evolution.

View Article: PubMed Central - PubMed

Affiliation: Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.

ABSTRACT
The genus Citrus contains many economically important fruits that are grown worldwide for their high nutritional and medicinal value. Due to frequent hybridizations among species and cultivars, the exact number of natural species and the taxonomic relationships within this genus are unclear. To compare the differences between the Citrus chloroplast genomes and to develop useful genetic markers, we used a reference-assisted approach to assemble the complete chloroplast genome of Omani lime (C. aurantiifolia). The complete C. aurantiifolia chloroplast genome is 159,893 bp in length; the organization and gene content are similar to most of the rosids lineages characterized to date. Through comparison with the sweet orange (C. sinensis) chloroplast genome, we identified three intergenic regions and 94 simple sequence repeats (SSRs) that are potentially informative markers with resolution for interspecific relationships. These markers can be utilized to better understand the origin of cultivated Citrus. A comparison among 72 species belonging to 10 families of representative rosids lineages also provides new insights into their chloroplast genome evolution.

Show MeSH
Related in: MedlinePlus