The chloroplast genome characteristics, comparative genomics and gene resource mining of Celtis sinensis (Persoon, 1805)
Celtis is a large genus in Cannabaceae family, with more than 70 species in the world. However, the intraspecific variabilities of morphological features make it difficult for some species to be distinguished based on their morphological characteristics. To supply the chloroplast (cp) genome resourc...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2022-04-01
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| Series: | Mitochondrial DNA. Part B. Resources |
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| Online Access: | http://dx.doi.org/10.1080/23802359.2022.2067013 |
| _version_ | 1797638623294652416 |
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| author | Jing Fan Yan Chen MingHua Luo Zi Liang Xiang Nong |
| author_facet | Jing Fan Yan Chen MingHua Luo Zi Liang Xiang Nong |
| author_sort | Jing Fan |
| collection | DOAJ |
| description | Celtis is a large genus in Cannabaceae family, with more than 70 species in the world. However, the intraspecific variabilities of morphological features make it difficult for some species to be distinguished based on their morphological characteristics. To supply the chloroplast (cp) genome resources of Celtis for species identification, the plastome of Celtis sinensis Persoon 1805 was newly sequenced and comparative genomics was analyzed. The chloroplast genome was 159,085 bp in length and had a quadripartite structure consisting of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. A total of 133 genes were annotated, including 88 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Among the protein-coding genes, the frequency of the leucine codon is the highest and that of the cysteine codon is the lowest. Comparative genomic analysis showed that the IRS region was more conservative than the LSC and SSC regions, with most sequence variations located in the intergenic spacer rather than the protein-coding region. Moreover, sixteen highly divergent hotspots were identified. The ML phylogenetic tree showed that all involved Celtis species were clustered together, and the plastome reported in this paper has high enough resolution to distinguish C. sinensis (Pers.) from other Celtis plants. This study provides useful genetic resources for the identification of C. sinensis (Pers.) and is also of great significance for the phylogeny study of Celtis plants in the future. |
| first_indexed | 2024-03-11T13:05:16Z |
| format | Article |
| id | doaj.art-1f53cc9442e74b17a7a0208a4a2766af |
| institution | Directory Open Access Journal |
| issn | 2380-2359 |
| language | English |
| last_indexed | 2024-03-11T13:05:16Z |
| publishDate | 2022-04-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Mitochondrial DNA. Part B. Resources |
| spelling | doaj.art-1f53cc9442e74b17a7a0208a4a2766af2023-11-03T14:36:03ZengTaylor & Francis GroupMitochondrial DNA. Part B. Resources2380-23592022-04-017469870410.1080/23802359.2022.20670132067013The chloroplast genome characteristics, comparative genomics and gene resource mining of Celtis sinensis (Persoon, 1805)Jing Fan0Yan Chen1MingHua Luo2Zi Liang3Xiang Nong4College of Life Sciences, Leshan Normal UniversityEcological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal UniversitySchool of Life Science and Biotechnology, Mianyang Normal UniversityCollege of Life Sciences, Leshan Normal UniversityCollege of Life Sciences, Leshan Normal UniversityCeltis is a large genus in Cannabaceae family, with more than 70 species in the world. However, the intraspecific variabilities of morphological features make it difficult for some species to be distinguished based on their morphological characteristics. To supply the chloroplast (cp) genome resources of Celtis for species identification, the plastome of Celtis sinensis Persoon 1805 was newly sequenced and comparative genomics was analyzed. The chloroplast genome was 159,085 bp in length and had a quadripartite structure consisting of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. A total of 133 genes were annotated, including 88 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Among the protein-coding genes, the frequency of the leucine codon is the highest and that of the cysteine codon is the lowest. Comparative genomic analysis showed that the IRS region was more conservative than the LSC and SSC regions, with most sequence variations located in the intergenic spacer rather than the protein-coding region. Moreover, sixteen highly divergent hotspots were identified. The ML phylogenetic tree showed that all involved Celtis species were clustered together, and the plastome reported in this paper has high enough resolution to distinguish C. sinensis (Pers.) from other Celtis plants. This study provides useful genetic resources for the identification of C. sinensis (Pers.) and is also of great significance for the phylogeny study of Celtis plants in the future.http://dx.doi.org/10.1080/23802359.2022.2067013celtis sinensis persoonchloroplast genomecomparative analysisplastome |
| spellingShingle | Jing Fan Yan Chen MingHua Luo Zi Liang Xiang Nong The chloroplast genome characteristics, comparative genomics and gene resource mining of Celtis sinensis (Persoon, 1805) Mitochondrial DNA. Part B. Resources celtis sinensis persoon chloroplast genome comparative analysis plastome |
| title | The chloroplast genome characteristics, comparative genomics and gene resource mining of Celtis sinensis (Persoon, 1805) |
| title_full | The chloroplast genome characteristics, comparative genomics and gene resource mining of Celtis sinensis (Persoon, 1805) |
| title_fullStr | The chloroplast genome characteristics, comparative genomics and gene resource mining of Celtis sinensis (Persoon, 1805) |
| title_full_unstemmed | The chloroplast genome characteristics, comparative genomics and gene resource mining of Celtis sinensis (Persoon, 1805) |
| title_short | The chloroplast genome characteristics, comparative genomics and gene resource mining of Celtis sinensis (Persoon, 1805) |
| title_sort | chloroplast genome characteristics comparative genomics and gene resource mining of celtis sinensis persoon 1805 |
| topic | celtis sinensis persoon chloroplast genome comparative analysis plastome |
| url | http://dx.doi.org/10.1080/23802359.2022.2067013 |
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