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Liu X, Luo J, Chen H, Li T, Qu T, Tang M, Fu Z. Comparative analysis of complete chloroplast genomes of Synotis species (Asteraceae, Senecioneae) for identification and phylogenetic analysis. BMC Genomics 2024; 25:769. [PMID: 39112930 PMCID: PMC11308156 DOI: 10.1186/s12864-024-10663-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The Synotis (C. B. Clarke) C. Jeffrey & Y. L. Chen is an ecologically important genus of the tribe Senecioneae, family Asteraceae. Because most species of the genus bear similar morphology, traditional morphological identification methods are very difficult to discriminate them. Therefore, it is essential to develop a reliable and effective identification method for Synotis species. In this study, the complete chloroplast (cp.) genomes of four Synotis species, S. cavaleriei (H.Lév.) C. Jeffrey & Y.L. Chen, S. duclouxii (Dunn) C. Jeffrey & Y.L. Chen, S. nagensium (C.B. Clarke) C. Jeffrey & Y.L. Chen and S. erythropappa (Bureau & Franch.) C. Jeffrey & Y. L. Chen had been sequenced using next-generation sequencing technology and reported here. RESULTS These four cp. genomes exhibited a typical quadripartite structure and contained the large single-copy regions (LSC, 83,288 to 83,399 bp), the small single-copy regions (SSC, 18,262 to 18,287 bp), and the inverted repeat regions (IR, 24,837 to 24,842 bp). Each of the four cp. genomes encoded 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (ycf1 and rps19). The highly variable regions (trnC-GCA-petN, ccsA-psaC, trnE-UUC-rpoB, ycf1, ccsA and petN) may be used as potential molecular barcodes. The complete cp. genomes sequence of Synotis could be used as the potentially effective super-barcode to accurately identify Synotis species. Phylogenetic analysis demonstrated that the four Synotis species were clustered into a monophyletic group, and they were closed to the Senecio, Crassocephalum and Dendrosenecio in tribe Senecioneae. CONCLUSIONS This study will be useful for further species identification, evolution, genetic diversity and phylogenetic studies within this genus Synotis and the tribe Senecioneae.
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Affiliation(s)
- Xiaofeng Liu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), Ministry of Education, Chengdu, 610066, China
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Junjia Luo
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Hui Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Tingyu Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Tianmeng Qu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Ming Tang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Zhixi Fu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), Ministry of Education, Chengdu, 610066, China.
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China.
- Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, 610101, China.
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Lee SR, Oh A, Son DC. Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species. Sci Rep 2024; 14:15352. [PMID: 38961172 PMCID: PMC11222452 DOI: 10.1038/s41598-024-66102-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental and medicinal purposes. Despite its economic importance, Euphorbia's taxonomy has long been challenged by the intricate nature of morphological traits exhibiting high levels of convergence. While molecular markers are essential for phylogenetic studies, their availability for Euphorbia has been limited. To address this gap, we conducted comparative analyses focusing on the chloroplast (CP) genomes of nine Euphorbia species, incorporating three newly sequenced and annotated accessions. In addition, phylogenetic informativeness and nucleotide diversity were computed to identify candidate markers for phylogenetic analyses among closely related taxa in the genus. Our investigation revealed relatively conserved sizes and structures of CP genomes across the studied species, with notable interspecific variations observed primarily in non-coding regions and IR/SC borders. By leveraging phylogenetic informativeness and nucleotide diversity, we identified rpoB gene as the optimal candidate for species delimitation and shallow-level phylogenetic inference within the genus. Through this comprehensive analysis of CP genomes across multiple taxa, our study sheds light on the evolutionary dynamics and taxonomic intricacies of Euphorbia, offering valuable insights into its CP genome evolution and taxonomy.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, 61452, Republic of Korea.
| | - Ami Oh
- Department of Biology Education, College of Education, Chosun University, Gwangju, 61452, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, 11186, Republic of Korea.
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Zhang L, Yi C, Xia X, Jiang Z, Du L, Yang S, Yang X. Solanum aculeatissimum and Solanum torvum chloroplast genome sequences: a comparative analysis with other Solanum chloroplast genomes. BMC Genomics 2024; 25:412. [PMID: 38671394 PMCID: PMC11046870 DOI: 10.1186/s12864-024-10190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/05/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Solanum aculeatissimum and Solanum torvum belong to the Solanum species, and they are essential plants known for their high resistance to diseases and adverse conditions. They are frequently used as rootstocks for grafting and are often crossbred with other Solanum species to leverage their resistance traits. However, the phylogenetic relationship between S. aculeatissimum and S. torvum within the Solanum genus remains unclear. Therefore, this paper aims to sequence the complete chloroplast genomes of S. aculeatissimum and S. torvum and analyze them in comparison with 29 other previously published chloroplast genomes of Solanum species. RESULTS We observed that the chloroplast genomes of S. aculeatissimum and S. torvum possess typical tetrameric structures, consisting of one Large Single Copy (LSC) region, two reverse-symmetric Inverted Repeats (IRs), and one Small Single Copy (SSC) region. The total length of these chloroplast genomes ranged from 154,942 to 156,004 bp, with minimal variation. The highest GC content was found in the IR region, while the lowest was in the SSC region. Regarding gene content, the total number of chloroplast genes and CDS genes remained relatively consistent, ranging from 128 to 134 and 83 to 91, respectively. Nevertheless, there was notable variability in the number of tRNA genes and rRNAs. Relative synonymous codon usage (RSCU) analysis revealed that both S. aculeatissimum and S. torvum preferred codons that utilized A and U bases. Analysis of the IR boundary regions indicated that contraction and expansion primarily occurred at the junction between SSC and IR regions. Nucleotide polymorphism analysis and structural variation analysis demonstrated that chloroplast variation in Solanum species mainly occurred in the LSC and SSC regions. Repeat sequence analysis revealed that A/T was the most frequent base pair in simple repeat sequences (SSR), while Palindromic and Forward repeats were more common in long sequence repeats (LSR), with Reverse and Complement repeats being less frequent. Phylogenetic analysis indicated that S. aculeatissimum and S. torvum belonged to the same meristem and were more closely related to Cultivated Eggplant. CONCLUSION These findings enhance our comprehension of chloroplast genomes within the Solanum genus, offering valuable insights for plant classification, evolutionary studies, and potential molecular markers for species identification.
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Affiliation(s)
- Longhao Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Chengqi Yi
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Xin Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Lihui Du
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Shixin Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China.
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He L, Xu S, Cheng X, Huang H, Dai H, Wang X, Ding Z, Xu M, Gu H, Yan N, Wang C. Chloroplast genomes in seven Lagerstroemia species provide new insights into molecular evolution of photosynthesis genes. Front Genet 2024; 15:1378403. [PMID: 38628576 PMCID: PMC11019025 DOI: 10.3389/fgene.2024.1378403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Lagerstroemia indica is an important commercial tree known for the ornamental value. In this study, the complete chloroplast genome sequence of Lagerstroemia indica "Pink Velour" (Lagerstroemia "Pink Velour") was 152,174 bp in length with a GC content of 39.50%. It contained 85 protein coding genes (PCGs), 37 tRNAs, and 8 rRNA genes. 207 simple sequence repeats (SSRs) and 31 codons with relative synonymous codon (RSCU)value > 1 were detected. Phylogenetic analysis divided 10 Lagerstroemia species into evolutionary branches of clade A and clade B. We conducted a comparative analysis of Lagerstroemia "Pink Velours" complete chloroplast genome with the genomes of six closely related Lagerstroemia species from different origins. The structural features of all seven species were similar, except for the deletion of ycf1 nucleobases at the JSA boundary. The large single-copy (LSC) and the small single-copy (SSC) had a higher sequence divergence than the IR region, and 8 genes that were highly divergent (trnK-UUU, petN, psbF, psbJ, ndhE, ndhD, ndhI, ycf1) had been identified and could be used as molecular markers in future studies. High nucleotide diversity was present in genes belonging to the photosynthesis category. Mutation of single nucleic acid was mainly influenced by codon usage. The value percentage of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) in 6 Lagerstroemia species revealed that more photosynthesis genes have Ka or Ks only in Lagerstroemia fauriei, Lagerstroemia limii, and Lagerstroemia subcostata. These advances will facilitate the breeding of closely related Lagerstroemia species and deepen understanding on climatic adaptation of Lagerstroemia plants.
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Affiliation(s)
- Ling He
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Sujuan Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinnian Cheng
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Hanlin Huang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Hongyu Dai
- College of Medicine, Southeast University, Nanjing, China
| | - Xin Wang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Zhiyang Ding
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Ming Xu
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Haoran Gu
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Na Yan
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Chunyan Wang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
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Kim TH, Ha YH, Setoguchi H, Choi K, Kim SC, Kim HJ. First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae). Genes (Basel) 2024; 15:380. [PMID: 38540439 PMCID: PMC10970243 DOI: 10.3390/genes15030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes but not in Corylopsis. Plastid genomes of Corylopsis species (Corylopsis gotoana, Corylopsis pauciflora, and Corylopsis sinensis) were sequenced using next-generation sequencing techniques. Repeats and nucleotide diversity that could be used as DNA markers were also investigated. A phylogenetic investigation was carried out using 79 protein-coding genes to infer the evolutionary relationships within the genus Corylopsis. By including new plastomes, the overall plastid genome structure of Corylopsis was similar. Simple sequence repeats of 73-106 SSRs were identified in the protein-coding genes of the plastid genomes, and 33-40 long repeat sequences were identified in the plastomes. The Pi value of the rpl33_rps18 region, an intergenic spacer, was the highest. Phylogenetic analysis demonstrated that Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. C. pauciflora, C. gotoana, and C. spicata formed a clade distributed in Japan, whereas C. sinensis, C. glandulifera, and C. velutina formed a clade that was distributed in China.
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Affiliation(s)
- Tae-Hee Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Kyung Choi
- Division of Garden and Plant Resources, Korea National Arboretum, Pocheon 11186, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Hyuk-Jin Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
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Zhang L, Meng Y, Wang D, He GH, Zhang JM, Wen J, Nie ZL. Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae). BMC Genomics 2024; 25:247. [PMID: 38443830 PMCID: PMC10916268 DOI: 10.1186/s12864-024-10149-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., and the Southern Hemisphere clade. However, the relationships of the three clades differ greatly between the nuclear and the plastid topologies. There has been limited exploration of the chloroplast phylogenetic relationships within Ampelopsideae, and studies on the chloroplast genome structure of this tribe are only available for a few individuals. In this study, we aimed to investigate the evolutionary characteristics of plastid genomes of the tribe, including their genome structure and evolutionary insights. RESULTS We sequenced, assembled, and annotated plastid genomes of 36 species from the tribe and related taxa in the family. Three main clades were recognized within Ampelopsideae, corresponding to Ampelopsis, Nekemias, and the Southern Hemisphere lineage, respectively, and all with 100% bootstrap supports. The genome sequences and content of the tribe are highly conserved. However, comparative analyses suggested that the plastomes of Nekemias demonstrate a contraction in the large single copy region and an expansion in the inverted repeat region, and possess a high number of forward and palindromic repeat sequences distinct from both Ampelopsis and the Southern Hemisphere taxa. CONCLUSIONS Our results highlighted plastome variations in genome length, expansion or contraction of the inverted repeat region, codon usage bias, and repeat sequences, are corresponding to the three lineages of the tribe, which probably faced with different environmental selection pressures and evolutionary history. This study provides valuable insights into understanding the evolutionary patterns of plastid genomes within the Ampelopsideae of Vitaceae.
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Affiliation(s)
- Lei Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Ying Meng
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Da Wang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Guan-Hao He
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun-Ming Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Ze-Long Nie
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China.
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He GH, Zhang L, Meng Y, Wen J, Nie ZL. The complete chloroplast genome of Nekemias hypoglauca (Hance) J. Wen & Z. L. Nie 2014 (Family: Vitaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:272-276. [PMID: 38352189 PMCID: PMC10863506 DOI: 10.1080/23802359.2024.2316071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/04/2024] [Indexed: 02/16/2024] Open
Abstract
Nekemias is a perennial woody vine with nine species that had been originally placed in Ampelopsis. These species of Nekemias are economically and medically important. Limited information is available on the genomic characteristics of the chloroplasts of this genus. Nekemias hypoglauca (Hance) J. Wen & Z. L. Nie 2014 contains 131 unique genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The complete chloroplast sequence contains 162,976 bp. The large single-copy region contains 89,291 bp; the small single-copy region contains 19,063 bp, and a pair of inverted repeat sequences is composed of 27,311 bp. There are 84 simple sequence repeat (SSR) loci in the complete chloroplast genome of N. hypoglauca, with mononucleotide, dinucleotide, trinucleotide, tetranucleotide and hexanucleotide SSRs of 58, 9, 6, 10 and 1, respectively. A total of 337 repeats were identified, including 172 forward repeats, three reverse repeats and 163 palindromic repeats. A phylogenetic analysis based on the complete genome data of the chloroplasts of 10 plant species indicated the monophyly of Nekemias and determined the phylogenetic relationships of N. hypoglauca in Nekemias. This study provides a reference for further studies on the taxonomy, identification, origin and evolution of N. hypoglauca and Nekemias.
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Affiliation(s)
- Guan-Hao He
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Lei Zhang
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
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Wang Y, Hu B, Peng J, Zhou Q. The complete chloroplast genome of Sinosenecio globigerus (C. C. Chang) B. Nordenstam (Asteraceae). Mitochondrial DNA B Resour 2024; 9:204-208. [PMID: 38288251 PMCID: PMC10823894 DOI: 10.1080/23802359.2024.2309262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/18/2024] [Indexed: 01/31/2024] Open
Abstract
The genus Sinosenecio B. Nordenstam is a group of perennial or sometimes annual or biennial herbs in the family Asteraceae. Here, we have successfully assembled and characterized the complete chloroplast (cp) genome of S. globigerus, which shows a typical quadratic structure with an overall GC content of 37.4%, comprising a pair of inverted repeat regions (IRs) of 24,848 bp, a large single-copy region (LSC) of 83,379 bp and a small single-copy region (SSC) of 18,180 bp. 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes and eight rRNA genes. Further nucleotide diversity analysis indicated that three genomic regions (accD-psaI, trnK-rps16, and ycf1) exhibited sufficient variability and thus could be recommended as valuable barcodes for the delimitation and identification of Sinosenecio species. Phylogenetic reconstruction presented clear interspecific relationships within Sinosenecio, which were supported to some extent by cytology, morphology and geographic distributions. Our study will provide valuable and high-quality genetic information to further elucidate the diversified mechanisms in Sinosenecio.
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Affiliation(s)
- Yi Wang
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Bin Hu
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Jingyi Peng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Qiang Zhou
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
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Liu H, Liu X, Sun C, Li HL, Li ZX, Guo Y, Fu XQ, Liao QH, Zhang WL, Liu YQ. Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis 'Hongyang'. Genes (Basel) 2023; 14:2136. [PMID: 38136958 PMCID: PMC10743354 DOI: 10.3390/genes14122136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Actinidia chinensis '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 A. chinensis 'Hongyang' cultivated in China was sequenced using de novo technology in this study. A. chinensis '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 A. chinensis 'Hongyang' were biased towards the use of codons containing A/U, and the non-protein coding regions in the A. chinensis '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 Actinidia plants, with small expansions and contractions of the boundaries. Furthermore, phylogenetic tree indicated that A. chinensis 'Hongyang' was the closest relative to A. indochinensis. This research provides a useful basis for future genetic and evolutionary studies of A. chinensis 'Hongyang', and enriches the biological information of Actinidia species.
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Affiliation(s)
- Han Liu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404000, China
| | - Xia Liu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Chong Sun
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou 434023, China;
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Zhe-Xin Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Yuan Guo
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Xue-Qian Fu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Qin-Hong Liao
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Wen-Lin Zhang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (H.L.); (C.S.); (H.-L.L.); (Z.-X.L.); (Y.G.); (X.-Q.F.); (Q.-H.L.); (W.-L.Z.)
| | - Yi-Qing Liu
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou 434023, China;
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Mao J, Lu J, Liu S, Liu Y, Lin Z, Xue Q. Genome-Wide Analysis of Family I84 Protease Inhibitor Genes in Three Bivalves Reveals Important Information About the Protein Family's Evolution. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:729-748. [PMID: 37578572 DOI: 10.1007/s10126-023-10236-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Abstract
Family I84 serine protease inhibitors are believed to be mollusk specific proteins involved in host defense. The molecular evolution of the family, however, remains to be understood. In this study, the genes of Family I84 protease inhibitors in 3 bivalves, Crassostrea gigas, Crassostrea virginica and Tegillarca granosa, were analyzed at the genomic level. A total of 66 Family I84 genes (22 in C. gigas, 28 in C. virginica and 16 in T. granosa) were identified from the 3 species. They distributed unevenly in the genomes involving 4 chromosomes in C. gigas and 5 chromosomes in C. virginica and T. granosa and some genes were tandemly duplicated. Most genes had 3 exons with 12 genes having 4 exons and 1 gene having 2 exons. All genes but 1 from C. gigas and 1 from T. granosa encoded peptides with a signal sequence at the N-terminus, and the properties of the predicted mature molecules were similar. Four conserved motifs were identified in the 66 amino acid sequences. Collinear analysis revealed higher collinearity between the 2 oyster species in general genes and in Family I84 genes. Phylogenetic analysis of the 66 genes with those previously reported from 3 other bivalves and 1 gastropod showed that Family I84 protease inhibitor genes from the same species tended to be grouped together in terminal branches of the constructed Maximum likelihood tree, but most internal nodes were poorly supported by the bootstrap values. In addition, differences in expression patterns between the genes of a same species were observed in the developmental stages and tissues of C. gigas and T. granosa. Moreover, the co-expression of genes within Family I84 and Family I84 genes with non-Family I84 were also detected in C. gigas and T. granosa. These results suggested that Family I84 protease inhibitor genes evolved by active duplications and structural and functional diversifications after the speciation of related mollusks, and the diversified protease inhibitor family was likely multifunctional.
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Affiliation(s)
- Jinxia Mao
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang Province, 315100, China
- Ninghai Institute of Mariculture Breeding and Seed Industry , Zhejiang Wanli University, Ninghai, Zhejiang Province, 315604, China
| | - Jiali Lu
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang Province, 315100, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Sheng Liu
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang Province, 315100, China
- Ninghai Institute of Mariculture Breeding and Seed Industry , Zhejiang Wanli University, Ninghai, Zhejiang Province, 315604, China
| | - Youli Liu
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang Province, 315100, China
- Ninghai Institute of Mariculture Breeding and Seed Industry , Zhejiang Wanli University, Ninghai, Zhejiang Province, 315604, China
| | - Zhihua Lin
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang Province, 315100, China
- Ninghai Institute of Mariculture Breeding and Seed Industry , Zhejiang Wanli University, Ninghai, Zhejiang Province, 315604, China
| | - Qinggang Xue
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang Province, 315100, China.
- Ninghai Institute of Mariculture Breeding and Seed Industry , Zhejiang Wanli University, Ninghai, Zhejiang Province, 315604, China.
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11
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Yang T, Wu Z, Tie J, Qin R, Wang J, Liu H. A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus Chrysosplenium. Int J Mol Sci 2023; 24:14735. [PMID: 37834185 PMCID: PMC10572340 DOI: 10.3390/ijms241914735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Chrysosplenium, a perennial herb in the family Saxifragaceae, prefers to grow in low light and moist environments and is divided into two sections of Alternifolia and Oppositifolia based on phyllotaxy. Although there has been some progress in the phylogeny of Chrysosplenium over the years, the phylogenetic position of some species is still controversial. In this study, we assembled chloroplast genomes (cp genomes) of 34 Chrysosplenium species and performed comparative genomic and phylogenetic analyses in combination with other cp genomes of previously known Chrysosplenium species, for a total of 44 Chrysosplenium species. The comparative analyses revealed that cp genomes of Chrysosplenium species were more conserved in terms of genome structure, gene content and arrangement, SSRs, and codon preference, but differ in genome size and SC/IR boundaries. Phylogenetic analysis showed that cp genomes effectively improved the phylogenetic support and resolution of Chrysosplenium species and strongly supported Chrysosplenium species as a monophyletic taxon and divided into three branches. The results also showed that the sections of Alternifolia and Oppositifolia were not monophyletic with each other, and that C. microspermum was not clustered with other Chrysosplenium species with alternate leaves, but with C. sedakowii into separate branches. In addition, we identified 10 mutational hotspot regions that could serve as potential DNA barcodes for Chrysosplenium species identification. In contrast to Peltoboykinia, the clpP and ycf2 genes of Chrysosplenium were subjected to positive selection and had multiple significant positive selection sites. We further detected a significant positive selection site on the petG gene between the two sections of Chrysosplenium. These evolutionary characteristics may be related to the growth environment of Chrysosplenium species. This study enriches the cp genomes of Chrysosplenium species and provides a reference for future studies on its evolution and origin.
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Affiliation(s)
- Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China;
| | - Jun Tie
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
- College of Computer Science, South-Central Minzu University, Wuhan 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
| | - Jiangqing Wang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
- College of Computer Science, South-Central Minzu University, Wuhan 430074, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China; (T.Y.); (J.T.); (R.Q.)
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12
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Xu XM, Wei Z, Sun JZ, Zhao QF, Lu Y, Wang ZL, Zhu SX. Phylogeny of Leontopodium (Asteraceae) in China-with a reference to plastid genome and nuclear ribosomal DNA. FRONTIERS IN PLANT SCIENCE 2023; 14:1163065. [PMID: 37583593 PMCID: PMC10425225 DOI: 10.3389/fpls.2023.1163065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
The infrageneric taxonomy system, species delimitation, and interspecies systematic relationships of Leontopodium remain controversial and complex. However, only a few studies have focused on the molecular phylogeny of this genus. In this study, the characteristics of 43 chloroplast genomes of Leontopodium and its closely related genera were analyzed. Phylogenetic relationships were inferred based on chloroplast genomes and nuclear ribosomal DNA (nrDNA). Finally, together with the morphological characteristics, the relationships within Leontopodium were identified and discussed. The results showed that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved in terms of gene number, gene order, and GC content. The most remarkable differences among the three genera were the length of the complete chloroplast genome, large single-copy region, small single-copy region, and inverted repeat region. In addition, the chloroplast genome structure of Leontopodium exhibited high consistency and was obviously different from that of Filago and Gamochaeta in some regions, such as matk, trnK (UUU)-rps16, petN-psbM, and trnE (UUC)-rpoB. All the phylogenetic trees indicated that Leontopodium was monophyletic. Except for the subgeneric level, our molecular phylogenetic results were inconsistent with the previous taxonomic system, which was based on morphological characteristics. Nevertheless, we found that the characteristics of the leaf base, stem types, and carpopodium base were phylogenetically correlated and may have potential value in the taxonomic study of Leontopodium. In the phylogenetic trees inferred using complete chloroplast genomes, the subgen. Leontopodium was divided into two clades (Clades 1 and 2), with most species in Clade 1 having herbaceous stems, amplexicaul, or sheathed leaves, and constricted carpopodium; most species in Clade 2 had woody stems, not amplexicaul and sheathed leaves, and not constricted carpopodium.
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Affiliation(s)
| | | | | | | | | | | | - Shi-Xin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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13
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Zhang D, Tu J, Ding X, Guan W, Gong L, Qiu X, Huang Z, Su H. Analysis of the chloroplast genome and phylogenetic evolution of Bidens pilosa. BMC Genomics 2023; 24:113. [PMID: 36918765 PMCID: PMC10015693 DOI: 10.1186/s12864-023-09195-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Chloroplast genomes for 3 Bidens plants endemic to China (Bidens bipinnata Linn., Bidens pilosa Linn., and Bidens alba var. radiata) have been sequenced, assembled and annotated in this study to distinguish their molecular characterization and phylogenetic relationships. The chloroplast genomes are in typical quadripartite structure with two inverted repeat regions separating a large single copy region and a small single copy region, and ranged from 151,599 to 154,478 bp in length. Similar number of SSRs and long repeats were found in Bidens, wherein mononucleotide repeats (A/T), forward and palindromic repeats were the most in abundance. Gene loss of clpP and psbD, IR expansion and contraction were detected in these Bidens plants. It seems that ndhE, ndhF, ndhG, and rpl32 from the Bidens plants were under positive selection while the majority of chloroplast genes were under purifying selection. Phylogenetic analysis revealed that 3 Bidens plants clustered together and further formed molophyletic clade with other Bidens species, indicating Bidens plants might be under radiation adaptive selection to the changing environment world-widely. Moreover, mutation hotspot analysis and in silico PCR analysis indicated that inter-genic regions of ndhD-ccsA, ndhI-ndhG, ndhF-rpl32, trnL_UAG-rpl32, ndhE-psaC, matK-rps16, rps2-atpI, cemA-petA, petN-psbM were candidate markers of molecular identification for Bidens plants. This study may provide useful information for genetic diversity analysis and molecular identification for Bidens species.
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Affiliation(s)
- Danchun Zhang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, 510006, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Jiajun Tu
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, 510006, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Xiaoxia Ding
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, 510006, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Wan Guan
- Luqiao Hospital, Taizhou Enze Medical Center (Group), Taizhou, 318050, Zhejiang, China
| | - Lu Gong
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, 510006, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.,Luqiao Hospital, Taizhou Enze Medical Center (Group), Taizhou, 318050, Zhejiang, China
| | - Xiaohui Qiu
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, 510006, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.,Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, 510000, China
| | - Zhihai Huang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, 510006, China. .,Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, 510000, China.
| | - He Su
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong, 510006, China. .,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China. .,Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, 510000, China.
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14
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Jin G, Li W, Song F, Yang L, Wen Z, Feng Y. Comparative analysis of complete Artemisia subgenus Seriphidium (Asteraceae: Anthemideae) chloroplast genomes: insights into structural divergence and phylogenetic relationships. BMC PLANT BIOLOGY 2023; 23:136. [PMID: 36899296 PMCID: PMC9999589 DOI: 10.1186/s12870-023-04113-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Artemisia subg. Seriphidium, one of the most species-diverse groups within Artemisia, grows mainly in arid or semi-arid regions in temperate climates. Some members have considerable medicinal, ecological, and economic value. Previous studies on this subgenus have been limited by a dearth of genetic information and inadequate sampling, hampering our understanding of their phylogenetics and evolutionary history. We therefore sequenced and compared the chloroplast genomes of this subgenus, and evaluated their phylogenetic relationships. RESULTS We newly sequenced 18 chloroplast genomes of 16 subg. Seriphidium species and compared them with one previously published taxon. The chloroplast genomes, at 150,586-151,256 bp in length, comprised 133 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and one pseudogene, with GC content of 37.40-37.46%. Comparative analysis showed that genomic structures and gene order were relatively conserved, with only some variation in IR borders. A total of 2203 repeats (1385 SSRs and 818 LDRs) and 8 highly variable loci (trnK - rps16, trnE - ropB, trnT, ndhC - trnV, ndhF, rpl32 - trnL, ndhG - ndhI and ycf1) were detected in subg. Seriphidium chloroplast genomes. Phylogenetic analysis of the whole chloroplast genomes based on maximum likelihood and Bayesian inference analyses resolved subg. Seriphidium as polyphyletic, and segregated into two main clades, with the monospecific sect. Minchunensa embedded within sect. Seriphidium, suggesting that the whole chloroplast genomes can be used as molecular markers to infer the interspecific relationship of subg. Seriphidium taxa. CONCLUSION Our findings reveal inconsistencies between the molecular phylogeny and traditional taxonomy of the subg. Seriphidium and provide new insights into the evolutionary development of this complex taxon. Meanwhile, the whole chloroplast genomes with sufficiently polymorphic can be used as superbarcodes to resolve interspecific relationships in subg. Seriphidium.
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Affiliation(s)
- Guangzhao Jin
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
| | - Wenjun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lei Yang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
| | - Zhibin Wen
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
| | - Ying Feng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- The Herbarium of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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15
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Jiang D, Cai X, Gong M, Xia M, Xing H, Dong S, Tian S, Li J, Lin J, Liu Y, Li HL. Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae). BMC Genomics 2023; 24:30. [PMID: 36653780 PMCID: PMC9848714 DOI: 10.1186/s12864-023-09115-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100-150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse. RESULTS We conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986-88,200 bp), a small single copy (SSC, 15,498-15,891 bp) and a pair of inverted repeats (IRs, 29,765-29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis. CONCLUSIONS This study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.
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Affiliation(s)
- Dongzhu Jiang
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.410654.20000 0000 8880 6009College of Horticulture and Gardening, Yangtze University, Jingzhou, 433200 China
| | - Xiaodong Cai
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Min Gong
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.411581.80000 0004 1790 0881College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, 404100 China
| | - Maoqin Xia
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Haitao Xing
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Shanshan Dong
- grid.9227.e0000000119573309Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004 China
| | - Shuming Tian
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.411581.80000 0004 1790 0881College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, 404100 China
| | - Jialin Li
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Junyao Lin
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Yiqing Liu
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.410654.20000 0000 8880 6009College of Horticulture and Gardening, Yangtze University, Jingzhou, 433200 China
| | - Hong-Lei Li
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
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16
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Han S, Ding H, Bi D, Zhang S, Yi R, Gao J, Yang J, Ye Y, Wu L, Kan X. Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales. PLANTS (BASEL, SWITZERLAND) 2022; 11:3544. [PMID: 36559654 PMCID: PMC9787361 DOI: 10.3390/plants11243544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
As representative of the early-divergent groups of angiosperms, Saxifragales is extremely divergent in morphology, comprising 15 families. Within this order, our previous case studies observed significant structural diversities among the plastomes of several lineages, suggesting a possible role in elucidating their deep phylogenetic relationships. Here, we collected 208 available plastomes from 11 constituent families to explore the evolutionary patterns among Saxifragales. With thorough comparisons, the losses of two genes and three introns were found in several groups. Notably, 432 indel events have been observed from the introns of all 17 plastomic intron-containing genes, which could well play an important role in family barcoding. Moreover, numerous heterogeneities and strong intrafamilial phylogenetic implications were revealed in pttRNA (plastomic tRNA) structures, and the unique structural patterns were also determined for five families. Most importantly, based on the well-supported phylogenetic trees, evident phylogenetic signals were detected in combinations with the identified pttRNAs features and intron indels, demonstrating abundant lineage-specific characteristics for Saxifragales. Collectively, the results reported here could not only provide a deeper understanding into the evolutionary patterns of Saxifragales, but also provide a case study for exploring the plastome evolution at a high taxonomic level of angiosperms.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jinming Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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