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Photographs showing the species of Orinus in their habitats: (a) O. kokonoricus, (b) O. intermedius, and (c) O. thoroldii
Source publication
We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, as well as to investigate putative hybrid origins of O. intermedius and to provide additional insights into relationships among species. The genus Orinus comprises three cl...
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When two species meet in secondary contact, the production of low fitness hybrids may be prevented by the adaptive evolution of increased prezygotic isolation, a process known as reinforcement. Theoretical challenges to the evolution of reinforcement are generally cast as a coordination problem, i.e., “how can statistical associations between trait...
Citations
... This valuable forage resource exhibits high stress resistance that is used to generate high-quality agricultural varieties and improve forage utilisation by livestock [5,6]. On the QTP, Orinus contributes to soil stabilisation and sand fixation, which are pivotal in ecological and conservation contexts, due to its prolific root system and high drought, cold, and alkali resistance [4,7,8]. There have been numerous recent reports on the adaptation of high-altitude species to extreme habitats, including cold and drought conditions [9][10][11]. ...
... Phylogenetic trees generated using the Orinus and wheat AP2/ERF, bHLH, C2H2, GRAS, HD-ZIP, MADSbox, R2R3-MYB, NAC, TALE, and WRKY TF family members were divided into 13,24,5,10,4,12,9,8,6, and 7 subfamilies, respectively, with most family members assigned to known subfamilies. During evolution, however, the AP2/ERF and C2H2 TF families in Orinus developed new subfamily branches, while the GRAS and MADS-box TF families were found to exhibit subfamily loss, and the bHLH gene family exhibits both above phenomena. ...
Background
Transcription factors (TFs) are crucial regulators of plant growth, development, and resistance to environmental stresses. However, comprehensive understanding of the roles of TFs in speciation of Orinus, an extreme-habitat plant on the Qinghai-Xizang (Tibet) Plateau, is limited.
Results
Here, we identified 52 TF families, including 2125 members in Orinus, by methodically analysing domain findings, gene structures, chromosome locations, conserved motifs, and phylogenetic relationships. Phylogenetic trees were produced for each Orinus TF family using protein sequences together with wheat (Triticum aestivum L.) TFs to indicate the subgroups. The differences between Orinus and wheat species in terms of TF family size implies that both Orinus- and wheat-specific subfamily contractions (and expansions) contributed to the high adaptability of Orinus. Based on deep mining of RNA-Seq data between two species of Orinus, O. thoroldii and O. kokonoricus, we obtained differentially expressed TFs (DETFs) in 20 families, most of which were expressed higher in O. thoroldii than in O. kokonoricus. In addition, Cis-element analysis shows that MYC and G-box elements are enriched in the promoter region of DETFs, suggesting that jasmonic acid (JA) and abscisic acid (ABA) act synergistically in Orinus to enhance the signalling of related abiotic stress responses, ultimately leading to an improvement in the stress tolerance and speciation adaptation of Orinus.
Conclusions
Our data serve as a genetic resource for Orinus, not only filling the gap in studies of TF families within this genus but also providing preliminary insights into the molecular mechanisms underlying speciation in Orinus.
... In addition, they have been used to resolve genetic structures and population demography in many diverse grass species such as Oryza sativa, Leymus racemosus, Orinus thoroldii, and O. kokonoricus (Cai et al., 2017;Liu et al., 2019;Zhang & Jia, 2002 We believe that, taken together, our results can provide a scientific basis for improved protection and sustainable utilization (e.g., as forage) of P. villosa within the fragile desert grassland ecosystems where the species occurs. ...
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 (GST) 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.
... We used AFLPs because they remain extremely efficient for investigating genetic diversity, genetic structure, and population demography due to their high levels of polymorphism (Wang, Wang, Liu, Yang, & Chen, 2008), their reproducible, reliable re-sults that are unaffected by the developmental stage of plant materials, and their universality among plant species. In addition, they have been used to resolve genetic structures and population demography in many diverse grass species such as Oryza sativa , Leymus racemosus , Orinus thoroldii and O. kokonoricus (Zhang & Jia, 2002;Sim, 2005;Li, 2015;Cai, 2017;Liu, Harris, Gao, Su, & Ren, 2019). Our main objectives were to (1) analyze the genetic structure from 43 populations of P. villosa from Inner Mongolian Plateau using an AFLP dataset, (2) test whether historical genetic divergence occurred among populations in response to Quaternary climate oscillations, and (3) evaluate the abiotic factors that are most influential in driving the distributions of P. villosa . ...
... The selective amplification was conducted in 25 μl volume of reaction mixture containing of 1.0 μl EcoR I/Mse I primer combinations (AAC/CAA, AAG/CAC, ACA/CAG, ACT/CAT, ACC/CTA, ACG/CTC, AGC/CTG, AGG/CTT; Table 1). Subsequently, we separated the fluorescently-labeled fragments on an ABI PRISM 377 DNA Calibrator (Applied Biosystems) using GeneScan ROX-500 with an internal size standard, allowing visual inspection of all individual sites (Liu, Harris, Gao, Su, & Ren, 2019). We recorded the presence or absence of AFLP amplification bands ( Figure S2) in a binary matrix as 1 or 0, respectively, based on interpretations from GeneScan 3.1 (Applied Biosystems). ...
We sought to generate a preliminary demographic framework for Psammochloa villosa to support of future studies of this ecologically important desert grass species, its conservation, and sustainable utilization. Psammochloa villosa occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. Here, 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 1728 well-defined amplified bands from eight pairs of primers, of which 1654 bands (95.72%) were polymorphic.All these values indicate that there is abundant genetic diversity, but limited gene flow in P. villosa. However, an analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within 43 populations of the species (64.16%), 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 the 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 inter-glacial 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, which can be used to design in-situ conservation actions and to prioritize sustainable utilization of germplasm resources.
... Therefore, we tested 25 alternative hypotheses for parental contribution, ranging from none, to the existence of F1 hybrids, to very small contributions from potential donors involving only 5% of loci (Supplementary File 1). Within an analysis, hybridization can be evaluated between only two lineages or species (see also Liu et al., 2019). Thus, we performed the tests of the 25 hypotheses on three datasets: a dataset of all sampled accessions of the three species of Lilium, a dataset comprising only LG and LS (in total 49 individuals with population codes ...
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.
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.
