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Götz J, Leinemann L, Gailing O, Hardtke A, Caré O. Development of a highly polymorphic chloroplast SSR set in Abies grandis with transferability to other conifer species-A promising toolkit for gene flow investigations. Ecol Evol 2024; 14:e11593. [PMID: 38903146 PMCID: PMC11188588 DOI: 10.1002/ece3.11593] [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: 02/23/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
The genus Abies is widely distributed across the world and is of high importance for forestry. Since chloroplasts are usually uniparentally inherited, they are an important tool for specific scientific issues like gene flow, parentage, migration and, in general, evolutionary analysis. Established genetic markers for organelles in conifers are rather limited to RFLP markers, which are more labour and time intensive, compared with SSR markers. Using QUIAGEN CLC Workbench 23.03, we aligned two chloroplast genomes from different Abies species (NCBI accessions: NC_039581, NC_042778, NC_039582, NC_042410, NC_035067, NC_062889, NC_042775, NC_057314, NC_041464, MH706706, MH047653 and MH510244) to identify potential SSR candidates. Further selection and development of forward and reverse primers was performed using the NCBI Primer Blast Server application. In this article, we introduce a remarkably polymorphic SSR marker set for various Abies species, which can be useful for other conifer genera, such as Cedrus, Pinus, Pseudotsuga or Picea. In total, 17 cpSSRs showed reliable amplification and polymorphisms in A. grandis with a total of 68 haplotypes detected. All 17 cpSSRs amplified in the tested Abies spp. In the other tested species, except for Taxus baccata, at least one primer was polymorphic.
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Affiliation(s)
| | - Ludger Leinemann
- ISOGEN GmbH & Co KGGöttingenGermany
- Buesgen Institute, Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences and Forest EcologyUniversity of GöttingenGöttingenGermany
| | - Oliver Gailing
- Buesgen Institute, Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences and Forest EcologyUniversity of GöttingenGöttingenGermany
| | - André Hardtke
- Department of Forest Genetic Resources, Breeding and Testing of Forest Reproductive MaterialNorthwest German Forest Research Institute (NW‐FVA)Hann. MündenGermany
| | - Oliver Caré
- ISOGEN GmbH & Co KGGöttingenGermany
- Buesgen Institute, Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences and Forest EcologyUniversity of GöttingenGöttingenGermany
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Shao YZ, Wang Z, Liu WJ, Zhao PF, Wu S. Complete chloroplast genome features and phylogenetic analysis of Abies ernestii var. salouenensis (Bordères and Gaussen) W. C. Cheng and L. K. Fu from southwest China. Mitochondrial DNA B Resour 2023; 8:550-556. [PMID: 37197650 PMCID: PMC10184594 DOI: 10.1080/23802359.2023.2209384] [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: 01/04/2023] [Accepted: 04/26/2023] [Indexed: 05/19/2023] Open
Abstract
Abies ernestii var. salouenensis (Bordères & Gaussen) W. C. Cheng & L. K. Fu is endemic to southwest China, including the southeastern Tibetan Plateau and the northwestern Yunnan Province. The taxonomic relationships between A. ernestii var. salouenensis and two other closely related fir species (A. chensiensis Tiegh. and A. ernestii Rehd.) still need to be determined. Here, we report for the first time the whole chloroplast genome of A. ernestii var. salouenensis. Its genome is 121,759 bp long and is characterized by a circular structure with 68 peptide-encoding genes, 16 tRNAs, six ORFs, and four rRNAs. We also identified 70 microsatellite repeat sequences and 14 tandem repeat sequences in the chloroplast genome of A. ernestii var. salouenensis. Comparative genome analysis indicated considerable variation in ycf1 and ycf2. Phylogenetic analysis supported the monophyly of A. ernestii var. salouenensis, A. chensiensis Tiegh., and A. ernestii Rehd. The relationships among them should be surveyed using more samples at the species level. This study will facilitate taxonomic studies and the development of suitable chloroplast markers for fir species.
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Affiliation(s)
- Yi-Zhen Shao
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Zhao Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Wen-Jun Liu
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Peng-Fei Zhao
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
- CONTACT Peng-Fei Zhao College of Life Science, Henan Agriculture University, Zhengzhou, China
| | - Si Wu
- School of Life Sciences, Zhengzhou Normal University, Zhengzhou, China
- Si Wu School of Life Sciences, Zhengzhou Normal University, Zhengzhou, China
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Shao YZ, Shi ZY, Wang Z, Wang W, Chen Y, Wen Q. The complete chloroplast genome of Abies ernestii Rehder (Pinaceae) and its phylogenetic implications. Mitochondrial DNA B Resour 2022; 7:1497-1503. [PMID: 35989878 PMCID: PMC9387311 DOI: 10.1080/23802359.2022.2109435] [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: 11/28/2022] Open
Abstract
Abies ernestii Rehder is endemic to the montane regions of Southwest China. Till now, phylogenetic relationships between A. ernestii and other closely related species remain unclear. In this study, we first characterized the complete chloroplast (cp) genome of A. ernestii. The whole cp genome was 121,841 bp in size, including one hundred and thirteen genes. Results of comparative cp genome revealed that only ycf1 and ycf2 was characterized by a considerable variation. Our phylogenetic analyses supported the monophyly of the genus Abies and revealed a clear separation between A. ernestii and A. chensiensis Tiegh. This study highlights the significance of using cp genomes to examine species boundaries among closely related fir species.
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Affiliation(s)
- Yi-Zhen Shao
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Zhi-Yuan Shi
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Zhao Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Wei Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Yun Chen
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Qian Wen
- College of Resources and Environmental Sciences, Henan Agriculture University, Zhengzhou, China
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Dong NL, Wang W, Wang Z, Zhang YY, Shao YZ, Sun HZ. Characterization of the complete plastid genome of Abies forrestii (Pinaceae) from southwest China. Mitochondrial DNA B Resour 2021; 6:2772-2774. [PMID: 34471700 PMCID: PMC8405101 DOI: 10.1080/23802359.2021.1969699] [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: 07/12/2021] [Accepted: 08/10/2021] [Indexed: 11/21/2022] Open
Abstract
Abies forrestii is endemic to southwest China and ecologically important as a major component of the cold temperate forests. This study was the first report complete chloroplast (cp) genome of A. forrestii. The complete chloroplast genome was 120,022 bp in size. In total, 114 genes were identified, including 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene. Thirteen genes contain introns. In phylogenetic analysis, A. forrestii was found to be closely related with A. nukiangensis, A. fanjingshanensis and A. delavayi subsp. fansipanensis. Our study will provide potential genetic resources for further evolutionary studies of this ecologically important species.
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Affiliation(s)
- Na-Lin Dong
- College of Landscape Architecture and Art, Henan Agriculture University, Zhengzhou, China
| | - Wei Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Zhao Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Yuan-Yuan Zhang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Yi-Zhen Shao
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Hong-Ze Sun
- Department of Biology, Beijing Dayu School, Beijing, China
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Li Y, Dong Y, Liu Y, Yu X, Yang M, Huang Y. Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae. FRONTIERS IN PLANT SCIENCE 2020; 11:593984. [PMID: 33643327 PMCID: PMC7905392 DOI: 10.3389/fpls.2020.593984] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/28/2020] [Indexed: 05/06/2023]
Abstract
In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860-157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826-86,299bp) and a small single-copy region (SSC) (18,319-18,536bp), separated by a pair of sequences (IRA and IRB; 26,341-26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130-131 genes, including 85-86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26-37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10-12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.
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Affiliation(s)
- Yongtan Li
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yan Dong
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yichao Liu
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
- Institute of Landscaping, Hebei Academic of Forestry and Grassland, Shijiazhuang, China
| | - Xiaoyue Yu
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
- *Correspondence: Minsheng Yang,
| | - Yinran Huang
- Institute of Landscaping, Hebei Academic of Forestry and Grassland, Shijiazhuang, China
- Yinran Huang,
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