Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety <i>Actinidia chinensis</i> ‘Hongyang’
<i>Actinidia chinensis</i> ‘Hongyang’, also known as red yangtao (red heart kiwifruit), is a vine fruit tree native to China possessing significant nutritional and economic value. However, information on its genetic diversity and phylogeny is still very limited. The first chloroplast (cp...
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MDPI AG
2023-11-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/12/2136 |
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| author | Han Liu Xia Liu Chong Sun Hong-Lei Li Zhe-Xin Li Yuan Guo Xue-Qian Fu Qin-Hong Liao Wen-Lin Zhang Yi-Qing Liu |
| author_facet | Han Liu Xia Liu Chong Sun Hong-Lei Li Zhe-Xin Li Yuan Guo Xue-Qian Fu Qin-Hong Liao Wen-Lin Zhang Yi-Qing Liu |
| author_sort | Han Liu |
| collection | DOAJ |
| description | <i>Actinidia chinensis</i> ‘Hongyang’, also known as red yangtao (red heart kiwifruit), is a vine fruit tree native to China possessing significant nutritional and economic value. However, information on its genetic diversity and phylogeny is still very limited. The first chloroplast (cp) genome of <i>A. chinensis</i> ‘Hongyang’ cultivated in China was sequenced using de novo technology in this study. <i>A. chinensis</i> ‘Hongyang’ possesses a cp genome that spans 156,267 base pairs (bp), exhibiting an overall GC content of 37.20%. There were 132 genes that were annotated, with 85 of them being protein-coding genes, 39 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 49 microsatellite sequences (SSRs) were detected, mainly single nucleotide repeats, mostly consisting of A or T base repeats. Compared with 14 other species, the cp genomes of <i>A. chinensis</i> ‘Hongyang’ were biased towards the use of codons containing A/U, and the non-protein coding regions in the <i>A. chinensis</i> ‘Hongyang’ cpDNA showed greater variation than the coding regions. The nucleotide polymorphism analysis (Pi) yielded nine highly variable region hotspots, most in the large single copy (LSC) region. The cp genome boundary analysis revealed a conservative order of gene arrangement in the inverted repeats (IRs) region of the cp genomes of 15 <i>Actinidia</i> plants, with small expansions and contractions of the boundaries. Furthermore, phylogenetic tree indicated that <i>A. chinensis</i> ‘Hongyang’ was the closest relative to <i>A. indochinensis</i>. This research provides a useful basis for future genetic and evolutionary studies of <i>A. chinensis</i> ‘Hongyang’, and enriches the biological information of <i>Actinidia</i> species. |
| first_indexed | 2024-03-08T20:44:31Z |
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| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-08T20:44:31Z |
| publishDate | 2023-11-01 |
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| spelling | doaj.art-25480e50736a4a3ea663f92083d9be152023-12-22T14:11:03ZengMDPI AGGenes2073-44252023-11-011412213610.3390/genes14122136Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety <i>Actinidia chinensis</i> ‘Hongyang’Han Liu0Xia Liu1Chong Sun2Hong-Lei Li3Zhe-Xin Li4Yuan Guo5Xue-Qian Fu6Qin-Hong Liao7Wen-Lin Zhang8Yi-Qing Liu9College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, ChinaSpice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou 434023, China<i>Actinidia chinensis</i> ‘Hongyang’, also known as red yangtao (red heart kiwifruit), is a vine fruit tree native to China possessing significant nutritional and economic value. However, information on its genetic diversity and phylogeny is still very limited. The first chloroplast (cp) genome of <i>A. chinensis</i> ‘Hongyang’ cultivated in China was sequenced using de novo technology in this study. <i>A. chinensis</i> ‘Hongyang’ possesses a cp genome that spans 156,267 base pairs (bp), exhibiting an overall GC content of 37.20%. There were 132 genes that were annotated, with 85 of them being protein-coding genes, 39 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 49 microsatellite sequences (SSRs) were detected, mainly single nucleotide repeats, mostly consisting of A or T base repeats. Compared with 14 other species, the cp genomes of <i>A. chinensis</i> ‘Hongyang’ were biased towards the use of codons containing A/U, and the non-protein coding regions in the <i>A. chinensis</i> ‘Hongyang’ cpDNA showed greater variation than the coding regions. The nucleotide polymorphism analysis (Pi) yielded nine highly variable region hotspots, most in the large single copy (LSC) region. The cp genome boundary analysis revealed a conservative order of gene arrangement in the inverted repeats (IRs) region of the cp genomes of 15 <i>Actinidia</i> plants, with small expansions and contractions of the boundaries. Furthermore, phylogenetic tree indicated that <i>A. chinensis</i> ‘Hongyang’ was the closest relative to <i>A. indochinensis</i>. This research provides a useful basis for future genetic and evolutionary studies of <i>A. chinensis</i> ‘Hongyang’, and enriches the biological information of <i>Actinidia</i> species.https://www.mdpi.com/2073-4425/14/12/2136comparative analysis<i>A. chinensis</i> ‘Hongyang’chloroplast genomephylogeny |
| spellingShingle | Han Liu Xia Liu Chong Sun Hong-Lei Li Zhe-Xin Li Yuan Guo Xue-Qian Fu Qin-Hong Liao Wen-Lin Zhang Yi-Qing Liu Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety <i>Actinidia chinensis</i> ‘Hongyang’ Genes comparative analysis <i>A. chinensis</i> ‘Hongyang’ chloroplast genome phylogeny |
| title | Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety <i>Actinidia chinensis</i> ‘Hongyang’ |
| title_full | Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety <i>Actinidia chinensis</i> ‘Hongyang’ |
| title_fullStr | Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety <i>Actinidia chinensis</i> ‘Hongyang’ |
| title_full_unstemmed | Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety <i>Actinidia chinensis</i> ‘Hongyang’ |
| title_short | Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety <i>Actinidia chinensis</i> ‘Hongyang’ |
| title_sort | chloroplast genome comparison and phylogenetic analysis of the commercial variety i actinidia chinensis i hongyang |
| topic | comparative analysis <i>A. chinensis</i> ‘Hongyang’ chloroplast genome phylogeny |
| url | https://www.mdpi.com/2073-4425/14/12/2136 |
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