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Li Z, Liu Y, Ma Y. Characterization and phylogenetic analysis of the complete chloroplast genome of Asterothamnus centraliasiaticus Novopokr. (Asteraceae: Asterothamnus). Mitochondrial DNA B Resour 2024; 9:168-172. [PMID: 38274851 PMCID: PMC10810623 DOI: 10.1080/23802359.2024.2306207] [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: 04/05/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Asterothamnus centraliasiaticus Novopokr., a species of perennial deciduous semi-shrub within the family Asteraceae, has excellent medical, economic, ecological and genetic value. In this study, the chloroplast genome of A. centraliasiaticus was first assembled using Illumina HiSeq2500 sequences. The results indicate that the complete cp genome of A. centraliasiaticus is 152,205 bp in length, and comprises a pair of inverted repeat (IR) regions of 25,031 bp each, a large single-copy (LSC) region of 83,956 bp and a small single-copy (SSC) region of 18,187 bp. The GC content of A. centraliasiaticus is 37.3%. A total of 130 genes were successfully annotated containing 85 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The maximum likelihood (ML) phylogenetic analysis based on the complete chloroplast genome data highly supported that A. centraliasiaticus was close to Aster lavandulifolius. These results will provide significant genetic information for the germplasm protection and reasonable development.
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Affiliation(s)
- Zhengsheng Li
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, Qinghai, China
| | - Ying Liu
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, Qinghai, China
| | - Yushou Ma
- Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Xining, Qinghai, China
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Su X, Liu T, Liu YP, Harris AJ, Chen JY. Adaptive radiation in Orinus, an endemic alpine grass of the Qinghai-Tibet Plateau, based on comparative transcriptomic analysis. JOURNAL OF PLANT PHYSIOLOGY 2022; 277:153786. [PMID: 35963042 DOI: 10.1016/j.jplph.2022.153786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The species of Orinus (Poaceae) are important alpine plants with a variety of phenotypic traits and potential usages in molecular breeding toward drought-tolerant forage crops. However, the genetic basis of evolutionary adaption and diversification in the genus is still unclear. In the present study, we obtained transcriptomes for the two most divergent species, O. thoroldii and O. kokonoricus, using the Illumina platform and de novo assembly. In total, we generated 23,029 and 24,086 unigenes with N50 values of 1188 and 1203 for O. thoroldii and O. kokonoricus respectively, and identified 19,005 pairs of putative orthologs between the two species of Orinus. For these orthologs, estimations of non-synonymous/synonymous substitution rate ratios indicated that 568 pairs may be under strongly positive selection (Ka/Ks > 1), and Gene Ontogeny (GO) enrichment analysis revealed that significantly enriched pathways were in DNA repair and resistance to abiotic stress. Meanwhile, the divergence times of species between O. thoroldii and O. kokonoricus occurred 3.2 million years ago (Mya), and the recent evolutionary branch is an allotetraploid species, Cleistogenes songorica. We also detected a Ks peak of ∼0.60 for Orinus. Additionally, we identified 188 pairs of differentially expressed genes (DEGs) between the two species of Orinus, which were significantly enrich in stress resistance and lateral root development. Thus, we considered that the species diversification and evolutionary adaption of this genus was initiated by environmental selection, followed by phenotypic differentiation, finally leading to niche separation in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Tao Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Yu Ping Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jin Yuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
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