1
|
Sun C, Liu H, Guo Y, Fu X, Zhu X, Liu H, Tang N, Chen Z, Liu Y, Liu X. Comparative chloroplast genome analysis of five widespread species ( Zanthoxylum L.) and development of molecular markers for their discrimination. Front Genet 2024; 15:1495891. [PMID: 39777261 PMCID: PMC11703814 DOI: 10.3389/fgene.2024.1495891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025] Open
Abstract
Background Zanthoxylum L., an important genus in the Rutaceae family, has great edible and medical values. However, the high degree of morphological similarity among Zanthoxylum species and the lack of sufficient chloroplast (cp) genomic resources have greatly impeded germplasm identification and phylogenetic analyses of Zanthoxylum. Methods Here we assembled cp genomes of five widespread species (Zanthoxylum bungeanum, Z. armatum, Z. nitidum, Z. ailanthoides and Z. piasezkii) in China as a case study, comparative analysis of these assembled cp genomes. Results Each of them, ranging from 157,231 to 158,728 bp, has a quadripartite structure. Except for one extra gene in Z. piasezkii, 132 genes were identified in each species, including 87 encode protein genes, 37 transfer ribose nucleic acid (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Substantial variation was observed among these five cp genome sequences in the IR/SC boundary regions. Variation in insertions and deletions were observed in the cp genomes of the five species over three different intervals, and a large number of single-nucleotide polymorphism variants were detected in the rps3-rpl22-rps19 region. Phylogenetic analysis of complete cp genome sequences revealed the evolutionary relationships among 23 Zanthoxylum species (29 samples). Conclusion Comparative analysis revealed that rps3-rpl22-rps19 is a highly variable divergent region in Zanthoxylum that could be developed as candidate markers for phylogenetic studies and species identification. This study identified a pair of molecular markers from hypervariable regions that can be used to distinguish between the five Zanthoxylum species and validated their utility. Overall, the results of this study provide new insights into the genetic breeding, germplasm exploration, and phylogeny of Zanthoxylum species.
Collapse
Affiliation(s)
- Chong Sun
- College of Horticulture and Gardening/Spicy Crops Research Institute, Yangtze University, Jingzhou, Hubei, China
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
| | - Huamin Liu
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yuan Guo
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xueqian Fu
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xinxin Zhu
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Han Liu
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Ning Tang
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
| | - Zexiong Chen
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yiqing Liu
- College of Horticulture and Gardening/Spicy Crops Research Institute, Yangtze University, Jingzhou, Hubei, China
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xia Liu
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing, China
| |
Collapse
|
2
|
Shen X, Zong W, Li Y, Liu X, Zhuge F, Zhou Q, Zhou S, Jiang D. Evolution of Cherries ( Prunus Subgenus Cerasus) Based on Chloroplast Genomes. Int J Mol Sci 2023; 24:15612. [PMID: 37958595 PMCID: PMC10650623 DOI: 10.3390/ijms242115612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus individuals, along with 36 additional genomes from the NCBI database, resulting in a total of 90 genomes for comparative analysis. The chloroplast genomes of subg. Cerasus exhibited varying sizes and consisted of 129 genes, including protein-coding, transfer RNA, and ribosomIal RNA genes. Genomic variation was investigated through InDels and SNPs, showcasing distribution patterns and impact levels. A comparative analysis of chloroplast genome boundaries highlighted variations in inverted repeat (IR) regions among Cerasus and other Prunus species. Phylogeny based on whole-chloroplast genome sequences supported the division of Prunus into three subgenera, I subg. Padus, II subg. Prunus and III subg. Cerasus. The subg. Cerasus was subdivided into seven lineages (IIIa to IIIg), which matched roughly to taxonomic sections. The subg. Padus first diverged 51.42 Mya, followed by the separation of subg. Cerasus from subg. Prunus 39.27 Mya. The subg. Cerasus started diversification at 15.01 Mya, coinciding with geological and climatic changes, including the uplift of the Qinghai-Tibet Plateau and global cooling. The Himalayans were the refuge of cherries, from which a few species reached Europe through westward migration and another species reached North America through northeastward migration. The mainstage of cherry evolution was on the Qing-Tibet Plateau and later East China and Japan as well. These findings strengthen our understanding of the evolution of cherry and provide valuable insights into the conservation and sustainable utilization of cherry's genetic resources.
Collapse
Affiliation(s)
- Xin Shen
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Wenjin Zong
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Yingang Li
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Xinhong Liu
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Fei Zhuge
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Qi Zhou
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Shiliang Zhou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dongyue Jiang
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| |
Collapse
|
3
|
Wu JQ, Wang Y, Sun P, Sun ZS, Shen JS. The complete chloroplast genome of Prunus phaeosticta (Hance) Maxim. (Rosaceae) and its phylogenetic implications. Mitochondrial DNA B Resour 2023; 8:136-140. [PMID: 36685644 PMCID: PMC9848267 DOI: 10.1080/23802359.2022.2163841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The complete chloroplast (cp) genome of Prunus phaeosticta (Hance) Maxim. has been characterized by reference-based assembly using Illumina paired-end data. The circular complete cp genome is 158,752 bp in length, comprising a large single-copy (LSC) region of 87,085 bp, a small single-copy (SSC) region of 18,923 bp, and a pair of inverted repeats (IRs) of 26,372 bp.A total of 129 functional genes were identified, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. The phylogenetic analysis showed that P. phaeosticta displayed a kinship to Prunus zippeliana.
Collapse
Affiliation(s)
- Jia-Qi Wu
- Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Yi Wang
- Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Ping Sun
- Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Zhong-Shuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Jian-Sheng Shen
- Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China,CONTACT Jian-Sheng Shen Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China
| |
Collapse
|
4
|
Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Six Almond Species (Prunus spp. L.). Sci Rep 2020; 10:10137. [PMID: 32576920 PMCID: PMC7311419 DOI: 10.1038/s41598-020-67264-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/12/2020] [Indexed: 11/08/2022] Open
Abstract
As a source of genetic variation, almond germplasm resources are of great significance in breeding. To better reveal the mutation characteristics and evolution patterns of the almond chloroplast (cp) genome, the complete cp genomes from six almond species were analyzed. The lengths of the chloroplast genome of the six almond species ranged from 157,783 bp to 158,073 bp. For repeat sequence analysis, 53 pairs of repeats (30 bp or longer) were identified. A total of 117 SSR loci were observed, including 96 polymorphic SSR loci. Nine highly variable regions with a nucleotide variability (Pi) higher than 0.08, including rps16, rps16-psbK, atpF-atpH, rpoB, ycf3-rps4, rps4-ndhJ, accD-psaI and rps7-orf42 (two highly variable regions) were located. Based on the chloroplast genome evolution analysis, three species (P. tenella, P. pedunculata and P. triloba) and wild cherry (P. tomentosa) were grouped into clade I. Clade II consisted of two species (P. mongolica and P. tangutica) and wild peach (P. davidiana). Clade III included the common almond (P. dulcis), cultivated peach (P. persica) and GanSu peach (P. kansuensis). This result expands the researchers' vision of almond plant diversity and promotes an understanding of the evolutionary relationship among almond species. In brief, this study provides abundant resources for the study of the almond chloroplast genome, and has an important reference value for study of the evolution and species identification of almond.
Collapse
|
5
|
Zhao X, Yan M, Ding Y, Huo Y, Yuan Z. Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium 'Summit'. PeerJ 2019; 7:e8210. [PMID: 31879574 PMCID: PMC6927351 DOI: 10.7717/peerj.8210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear. METHODS In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium 'Summit' from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. RESULTS The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium 'Summit' was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and 'Summit' cherry. A total of 73 simple sequence repeats (SSRs) were identified in 'Summit' cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.
Collapse
Affiliation(s)
- Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ming Yan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yu Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yan Huo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| |
Collapse
|
6
|
Chen X, Zong X, Liu Q, Tong B, Xu L, Zhang L, Hong P. Complete chloroplast genome of Prunus canescens: an endemic shrub in China. Mitochondrial DNA B Resour 2019; 4:2381-2382. [PMID: 33365554 PMCID: PMC7687575 DOI: 10.1080/23802359.2019.1624641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Prunus canescens is an endemic cherry species in China, which is distributed in Shaanxi, Gansu, Hubei, and Sichuan provinces of China. The chloroplast (cp) genome of P. canescens is 157,890 bp in size containing 125 unique genes, including 8 rRNA genes, 37 tRNA genes, and 80 protein-coding genes (PCGs). Phylogenetic analysis exhibited that P. canescens is most related to P. pseudocerasus.
Collapse
Affiliation(s)
- Xin Chen
- Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Taian, Shandong, P. R. China
| | - Xiaojuan Zong
- Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Taian, Shandong, P. R. China
| | - Qingzhong Liu
- Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Taian, Shandong, P. R. China
| | - Boqiang Tong
- Shandong Forest Germplasm Resources Center, Jinan, Shandong, P. R. China
| | - Li Xu
- Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Taian, Shandong, P. R. China
| | - Lisi Zhang
- Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Taian, Shandong, P. R. China
| | - Po Hong
- Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Taian, Shandong, P. R. China
| |
Collapse
|
7
|
Characterization of the complete chloroplast genome of longstalk almond (Prunus pedunculata (Pall.) Maxim.), an important sand-fixation shrub plant endemic to northern China. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1039-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|