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Almerekova S, Yermagambetova M, Jumanov S, Abugalieva S, Turuspekov Y. Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan. PLoS One 2024; 19:e0295550. [PMID: 38271463 PMCID: PMC10810545 DOI: 10.1371/journal.pone.0295550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/24/2023] [Indexed: 01/27/2024] Open
Abstract
Juniperus species are shrubs or trees in the family Cupressaceae that play an important role in forest ecosystems. In this study, we report the complete sequences of the plastid (pt) genomes of five Juniperus species collected in Kazakhstan (J. communis, J. sibirica, J. pseudosabina, J. semiglobosa, and J. davurica). The sequences of the pt genomes of the five species were annotated in addition to two full pt genome sequences from J. sabina and J. seravschanica, which we have previously reported. The pt genome sequences of these seven species were compared to the pt genomes of Juniperus species available in the public NCBI database. The total length of the pt genomes of Juniperus species, including previously published pt genome data, ranged from 127,469 bp (J. semiglobosa) to 128,097 bp (J. communis). Each Juniperus plastome consisted of 119 genes, including 82 protein-coding genes, 33 transfer RNA and 4 ribosomal RNA genes. Among the identified genes, 16 contained one or two introns, and 2 tRNA genes were duplicated. A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. A phylogenetic tree of 26 Juniperus species based on the 82 protein-coding genes separated the Juniperus samples into two major clades, corresponding to the Juniperus and Sabina sections. The analysis of pt genome sequences indicated that accD and ycf2 were the two most polymorphic genes. The phylogenetic evaluation of 26 Juniperus species using these two genes confirmed that they can be efficiently used as DNA barcodes for phylogenetic analyses in the genus. The sequenced plastomes of these Juniperus species have provided a large amount of genetic data that will be valuable for future genomic studies of this genus.
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Affiliation(s)
- Shyryn Almerekova
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Moldir Yermagambetova
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Smatulla Jumanov
- Aksu-Zhabagly Nature Reserve, Zhabagly, Turkestan Region, Kazakhstan
| | - Saule Abugalieva
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Yerlan Turuspekov
- Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Uckele KA, Adams RP, Schwarzbach AE, Parchman TL. Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny. Mol Phylogenet Evol 2020; 156:107022. [PMID: 33242585 DOI: 10.1016/j.ympev.2020.107022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 12/22/2022]
Abstract
Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.
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Affiliation(s)
- Kathryn A Uckele
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
| | - Robert P Adams
- Baylor University, Utah Lab, 201 N 5500 W, Hurricane, UT 84790, USA.
| | - Andrea E Schwarzbach
- Department of Health and Biomedical Sciences, University of Texas - Rio Grande Valley, 1 W University Drive, Brownsville, TX 78520, USA.
| | - Thomas L Parchman
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
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Li Y, Zhang C, Zhang M, Li Y, Wang X, Duan Y. The complete chloroplast genome sequence of Keteleeria fortunei (Pinaceae). Mitochondrial DNA B Resour 2019; 4:3157-3158. [PMID: 33365897 PMCID: PMC7706782 DOI: 10.1080/23802359.2019.1667896] [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: 08/06/2019] [Accepted: 08/16/2019] [Indexed: 10/26/2022] Open
Abstract
Here, the complete chloroplast genome of Keteleeria fortunei, a vulnerable species in China, was sequenced by next-generation sequencing platform. Its circular genome was 117,183 bp in length and the GC content was 38.5%. A total of 101 genes were annotated, including 4 rRNA genes, 20 tRNA genes, and 71 protein coding genes. This study would further our understanding of the genomics and the conservation and utilization of K. fortunei.
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Affiliation(s)
- Yuanyuan Li
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Cheng Zhang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Min Zhang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yongfu Li
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xianrong Wang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yifan Duan
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
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