Comparative Analysis of the Complete Chloroplast Genome of Mainland <i>Aster spathulifolius</i> and Other <i>Aster</i> Species
<i>Aster spathulifolius</i>, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland <i>A. spathulifolius</i> and compared it w...
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MDPI AG
2020-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/9/5/568 |
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| author | Swati Tyagi Jae-A Jung Jung Sun Kim So Youn Won |
| author_facet | Swati Tyagi Jae-A Jung Jung Sun Kim So Youn Won |
| author_sort | Swati Tyagi |
| collection | DOAJ |
| description | <i>Aster spathulifolius</i>, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland <i>A. spathulifolius</i> and compared it with those of the island type and other <i>Aster</i> species. The chloroplast genome of mainland <i>A. spathulifolius</i> is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two <i>A. spathulifolius</i> lines and the other <i>Aster</i> species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All <i>Aster</i> species clustered into a monophyletic group, but the chloroplast genome of mainland <i>A. spathulifolius</i> was more similar to the other <i>Aster</i> species than to that of the island <i>A. spathulifolius</i>. The <i>accD</i> and <i>ndhF</i> genes were detected to be under positive selection within the <i>Aster</i> lineage compared to other related taxa. The complete chloroplast genome of mainland <i>A. spathulifolius</i> presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the <i>Aster</i> genus and the Asteraceae. |
| first_indexed | 2024-03-10T20:09:09Z |
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| language | English |
| last_indexed | 2024-03-10T20:09:09Z |
| publishDate | 2020-04-01 |
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| series | Plants |
| spelling | doaj.art-14086f11ff28413682c69cd790657ec32023-11-19T23:02:39ZengMDPI AGPlants2223-77472020-04-019556810.3390/plants9050568Comparative Analysis of the Complete Chloroplast Genome of Mainland <i>Aster spathulifolius</i> and Other <i>Aster</i> SpeciesSwati Tyagi0Jae-A Jung1Jung Sun Kim2So Youn Won3Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, KoreaFloriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, KoreaGenomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, KoreaGenomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea<i>Aster spathulifolius</i>, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland <i>A. spathulifolius</i> and compared it with those of the island type and other <i>Aster</i> species. The chloroplast genome of mainland <i>A. spathulifolius</i> is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two <i>A. spathulifolius</i> lines and the other <i>Aster</i> species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All <i>Aster</i> species clustered into a monophyletic group, but the chloroplast genome of mainland <i>A. spathulifolius</i> was more similar to the other <i>Aster</i> species than to that of the island <i>A. spathulifolius</i>. The <i>accD</i> and <i>ndhF</i> genes were detected to be under positive selection within the <i>Aster</i> lineage compared to other related taxa. The complete chloroplast genome of mainland <i>A. spathulifolius</i> presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the <i>Aster</i> genus and the Asteraceae.https://www.mdpi.com/2223-7747/9/5/568<i>Aster</i>Asteraceaechloroplast genomephylogenetic analysiscodon usageintron loss |
| spellingShingle | Swati Tyagi Jae-A Jung Jung Sun Kim So Youn Won Comparative Analysis of the Complete Chloroplast Genome of Mainland <i>Aster spathulifolius</i> and Other <i>Aster</i> Species Plants <i>Aster</i> Asteraceae chloroplast genome phylogenetic analysis codon usage intron loss |
| title | Comparative Analysis of the Complete Chloroplast Genome of Mainland <i>Aster spathulifolius</i> and Other <i>Aster</i> Species |
| title_full | Comparative Analysis of the Complete Chloroplast Genome of Mainland <i>Aster spathulifolius</i> and Other <i>Aster</i> Species |
| title_fullStr | Comparative Analysis of the Complete Chloroplast Genome of Mainland <i>Aster spathulifolius</i> and Other <i>Aster</i> Species |
| title_full_unstemmed | Comparative Analysis of the Complete Chloroplast Genome of Mainland <i>Aster spathulifolius</i> and Other <i>Aster</i> Species |
| title_short | Comparative Analysis of the Complete Chloroplast Genome of Mainland <i>Aster spathulifolius</i> and Other <i>Aster</i> Species |
| title_sort | comparative analysis of the complete chloroplast genome of mainland i aster spathulifolius i and other i aster i species |
| topic | <i>Aster</i> Asteraceae chloroplast genome phylogenetic analysis codon usage intron loss |
| url | https://www.mdpi.com/2223-7747/9/5/568 |
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