1
|
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.
Collapse
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
| |
Collapse
|
2
|
Lv T, Harris AJ, Liu Y, Liu T, Liang R, Ma Z, Su X. Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker. Ecol Evol 2021; 11:10258-10276. [PMID: 34367573 PMCID: PMC8328423 DOI: 10.1002/ece3.7831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 01/26/2023] Open
Abstract
Psammochloa villosa is an ecologically important desert grass that occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. We sought to generate a preliminary demographic framework for P. villosa to support the future studies of this species, its conservation, and sustainable utilization. To accomplish this, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1,728 well-defined amplified bands from eight pairs of primers, of which 1,654 bands (95.7%) were polymorphic. Results obtained from the AFLPs suggested effective alleles among populations of 1.32, a Nei's standard genetic distance value of 0.206, a Shannon index of 0.332, a coefficient of gene differentiation (G ST) of 0.469, and a gene flow parameter (Nm) of 0.576. All these values indicate that there is abundant genetic diversity in P. villosa, but limited gene flow. An analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within populations (64.2%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in this species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last interglacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau and provides a resource that can be used to design in situ conservation actions and prioritize sustainable utilization.
Collapse
Affiliation(s)
- Ting Lv
- School of GeosciencesQinghai Normal UniversityXiningChina
- Academy of Plateau Science and SustainabilityXiningChina
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Yuping Liu
- Academy of Plateau Science and SustainabilityXiningChina
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Tao Liu
- School of GeosciencesQinghai Normal UniversityXiningChina
| | - Ruifang Liang
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Zilan Ma
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Xu Su
- School of GeosciencesQinghai Normal UniversityXiningChina
- Academy of Plateau Science and SustainabilityXiningChina
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Earth Surface Processes and Ecological Conservation of the Qinghai‐Tibet PlateauQinghai Normal UniversityXiningChina
| |
Collapse
|
3
|
Gao Y, Harris AJ, Li H, Gao X. Hybrid Speciation and Introgression Both Underlie the Genetic Structures and Evolutionary Relationships of Three Morphologically Distinct Species of Lilium (Liliaceae) Forming a Hybrid Zone Along an Elevational Gradient. FRONTIERS IN PLANT SCIENCE 2020; 11:576407. [PMID: 33365039 PMCID: PMC7750405 DOI: 10.3389/fpls.2020.576407] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/02/2020] [Indexed: 05/28/2023]
Abstract
We studied hybrid interactions of Lilium meleagrinum, Lilium gongshanense, and Lilium saluenense using an integrative approach combining population genetics, fieldwork, and phenological research. These three species occur along an elevational gradient, with L. meleagrinum occurring at lower elevations, L. saluenense at higher elevations, and L. gongshanense between them. The species show strong morphological differentiation despite there being no clear environmental barriers to gene flow among them. Lilium gongshanense is likely to have a hybrid origin based on our prior work, but its progenitors remain uncertain. We sought to determine whether gene flow occurs among these three parapatric species, and, if so, whether L. gongshanense is a hybrid of L. meleagrinum and/or L. saluenense. We analyzed data from multiple chloroplast genes and spacers, nuclear internal transcribed spacer (ITS), and 18 nuclear Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) microsatellites for accessions of the three species representing dense population-level sampling. We also inferred phenology by examining species in the field and using herbarium specimens. We found that there are only two types of chloroplast genomes shared among the three species and that L. gongshanense forms two distinct groups with closest links to other species of Lilium based on ITS. Taken together, L. gongshanense is unlikely to be a hybrid species resulting from a cross between L. meleagrinum and L. saluenense, but gene flow is occurring among the three species. The gene flow is likely to be rare according to evidence from all molecular datasets, and this is corroborated by detection of only one putative hybrid individual in the field and asynchronous phenology. We suspect that the rarity of hybridization events among the species facilitates their continued genetic separation.
Collapse
Affiliation(s)
- Yundong Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Huaicheng Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Xinfen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| |
Collapse
|