The Complete Chloroplast Genome Sequence of the <i>Speirantha</i> <i>gardenii</i>: Comparative and Adaptive Evolutionary Analysis
The plant “False Lily of the Valley”, <i>Speirantha gardenii</i> is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete...
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MDPI AG
2020-09-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/10/9/1405 |
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| author | Gurusamy Raman SeonJoo Park |
| author_facet | Gurusamy Raman SeonJoo Park |
| author_sort | Gurusamy Raman |
| collection | DOAJ |
| description | The plant “False Lily of the Valley”, <i>Speirantha gardenii</i> is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of <i>S. gardenii</i> and this is the first report on the chloroplast genome sequence of <i>Speirantha</i>. The complete <i>S. gardenii</i> chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, K<sub>A</sub>/K<sub>S</sub> nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that <i>S</i>. <i>gardenii</i> species has a closer genetic relationship to the <i>Reineckea</i>, <i>Rohdea</i> and <i>Convallaria</i> genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa. |
| first_indexed | 2024-03-10T16:16:57Z |
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| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-10T16:16:57Z |
| publishDate | 2020-09-01 |
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| series | Agronomy |
| spelling | doaj.art-7c364dd34a0d492293f751472924f13e2023-11-20T13:59:49ZengMDPI AGAgronomy2073-43952020-09-01109140510.3390/agronomy10091405The Complete Chloroplast Genome Sequence of the <i>Speirantha</i> <i>gardenii</i>: Comparative and Adaptive Evolutionary AnalysisGurusamy Raman0SeonJoo Park1Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsan-buk, KoreaDepartment of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsan-buk, KoreaThe plant “False Lily of the Valley”, <i>Speirantha gardenii</i> is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of <i>S. gardenii</i> and this is the first report on the chloroplast genome sequence of <i>Speirantha</i>. The complete <i>S. gardenii</i> chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, K<sub>A</sub>/K<sub>S</sub> nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that <i>S</i>. <i>gardenii</i> species has a closer genetic relationship to the <i>Reineckea</i>, <i>Rohdea</i> and <i>Convallaria</i> genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.https://www.mdpi.com/2073-4395/10/9/1405<i>Speirantha gardenii</i>chloroplast genomepositive selectionadaptive evolutionsubstitutionNolinoideae |
| spellingShingle | Gurusamy Raman SeonJoo Park The Complete Chloroplast Genome Sequence of the <i>Speirantha</i> <i>gardenii</i>: Comparative and Adaptive Evolutionary Analysis Agronomy <i>Speirantha gardenii</i> chloroplast genome positive selection adaptive evolution substitution Nolinoideae |
| title | The Complete Chloroplast Genome Sequence of the <i>Speirantha</i> <i>gardenii</i>: Comparative and Adaptive Evolutionary Analysis |
| title_full | The Complete Chloroplast Genome Sequence of the <i>Speirantha</i> <i>gardenii</i>: Comparative and Adaptive Evolutionary Analysis |
| title_fullStr | The Complete Chloroplast Genome Sequence of the <i>Speirantha</i> <i>gardenii</i>: Comparative and Adaptive Evolutionary Analysis |
| title_full_unstemmed | The Complete Chloroplast Genome Sequence of the <i>Speirantha</i> <i>gardenii</i>: Comparative and Adaptive Evolutionary Analysis |
| title_short | The Complete Chloroplast Genome Sequence of the <i>Speirantha</i> <i>gardenii</i>: Comparative and Adaptive Evolutionary Analysis |
| title_sort | complete chloroplast genome sequence of the i speirantha i i gardenii i comparative and adaptive evolutionary analysis |
| topic | <i>Speirantha gardenii</i> chloroplast genome positive selection adaptive evolution substitution Nolinoideae |
| url | https://www.mdpi.com/2073-4395/10/9/1405 |
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