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Dang Z, Li J, Liu Y, Song M, Lockhart PJ, Tian Y, Niu M, Wang Q. RADseq-based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna. THE PLANT GENOME 2024; 17:e20303. [PMID: 36740755 DOI: 10.1002/tpg2.20303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/30/2022] [Indexed: 06/18/2023]
Abstract
Genetic diversity reflects the survival potential, history, and population dynamics of an organism. It underlies the adaptive potential of populations and their response to environmental change. Reaumuria trigyna is an endemic species in the Eastern Alxa and West Ordos desert regions in China. The species has been considered a good candidate to explore the unique survival strategies of plants that inhabit this area. In this study, we performed population genomic analyses based on restriction-site associated DNA sequencing to understand the genetic diversity, population genetic structure, and differentiation of the species. Analyses of 92,719 high-quality single-nucleotide polymorphisms (SNPs) indicated that overall genetic diversity of R. trigyna was low (HO = 0.249 and HE = 0.208). No significant genetic differentiation was observed among the investigated populations. However, a subtle population genetic structure was detected. We suggest that this might be explained by adaptive diversification reinforced by the geographical isolation of populations. Overall, 3513 outlier SNPs were located in 243 gene-coding sequences in the R. trigyna transcriptome. Potential sites under diversifying selection occurred in genes (e.g., AP2/EREBP, E3 ubiquitin-protein ligase, FLS, and 4CL) related to phytohormone regulation and synthesis of secondary metabolites which have roles in adaptation of species. Our genetic analyses provide scientific criteria for evaluating the evolutionary capacity of R. trigyna and the discovery of unique adaptions. Our findings extend knowledge of refugia, environmental adaption, and evolution of germplasm resources that survive in the Ordos area.
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Affiliation(s)
- Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiabin Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Yanan Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Miaomiao Song
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Peter J Lockhart
- School of Natural Sciences, College of Sciences, Massey University, Palmerston North, New Zealand
| | - Yunyun Tian
- Ministry of Education Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Miaomiao Niu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qinglang Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Vieu JC, Koubínová D, Grant JR. Population Genetic Structure and Diversity of Cryptic Species of the Plant Genus Macrocarpaea (Gentianaceae) from the Tropical Andes. PLANTS (BASEL, SWITZERLAND) 2023; 12:1710. [PMID: 37111932 PMCID: PMC10145315 DOI: 10.3390/plants12081710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/29/2023] [Accepted: 04/14/2023] [Indexed: 06/19/2023]
Abstract
The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial-interglacial periods are thought to have profoundly affected species distribution, richness and diversity around the world. While the effect of the PCO on population dynamics at temperate latitudes is well known, considerable questions remain about its impact on the biodiversity of neotropical mountains. Here, we use amplified fragment length polymorphism molecular markers (AFLPs) to investigate the phylogeography and genetic structure of 13 plant species belonging to the gentian genus Macrocarpaea (Gentianaceae) in the tropical Andes. These woody herbs, shrubs or small trees show complex and potentially reticulated relationships, including cryptic species. We show that populations of M. xerantifulva in the dry system of the Rio Marañón in northern Peru have lower levels of genetic diversity compared to other sampled species. We suggest that this is due to a recent demographic bottleneck resulting from the contraction of the montane wet forests into refugia because of the expansion of the dry system into the valley during the glacial cycles of the PCO. This may imply that the ecosystems of different valleys of the Andes might have responded differently to the PCO.
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Ha YH, Gil HY, Kim SC, Choi K, Kim JH. Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing. Sci Rep 2022; 12:16262. [PMID: 36171257 PMCID: PMC9519971 DOI: 10.1038/s41598-022-20513-z] [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] [Received: 05/17/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea.,Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Kyung Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
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Zuo YW, He P, Zhang JH, Li WQ, Ning DH, Zeng YL, Yang Y, Xia CY, Zhang H, Deng HP. Contrasting Responses of Multispatial Soil Fungal Communities of Thuja sutchuenensis Franch., an Extremely Endangered Conifer in Southwestern China. Microbiol Spectr 2022; 10:e0026022. [PMID: 35735985 PMCID: PMC9431436 DOI: 10.1128/spectrum.00260-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022] Open
Abstract
Thuja sutchuenensis Franch. is an endangered species in southwest China, distributed sporadically in mountainous areas. Soil property and soil fungal community play a crucial role in plant growth and survival. Nevertheless, understanding soil properties and the soil fungal community in the areas where T. sutchuenensis is distributed is extremely limited. Hence, this study collected a total of 180 soil samples from five altitudinal distribution areas (altitudinal gradients) and three vertical depths throughout four horizontal distances from the base of each tree. The results found that altitudinal gradients and vertical depths altered soil properties, including pH, organic matter content, water content, total nitrogen, phosphorus, and potassium, and available nitrogen, phosphorus, and potassium. The fungal alpha diversity indexes (Chao1 and Shannon) and beta diversity were dramatically decreased with elevation. In addition, high altitudes (2,119 m) harbored the highest relative abundance of ectomycorrhizal fungi (27.57%) and the lowest relative abundance of plant-pathogenic fungi (1.81%). Meanwhile, we identified a series of fungal communities, such as Tomentella, Piloderma, Cortinarius, Sebacina, and Boletaceae, that play an essential role in the survival of T. sutchuenensis. The correlation analysis and random forest model identified that water content and total phosphorus showed strong relationships with fungal characteristics and were the primary variables for Zygomycota and Rozellomycota. Collectively, the findings of this integrated analysis provide profound insights into understanding the contrasting responses of T. sutchuenensis soil fungal communities and provide a theoretical basis for T. sutchuenensis habitat restoration and species conservation from multispatial perspectives. IMPORTANCE The present study highlights the importance of fungal communities in an endangered plant, T. sutchuenensis. Comparative analysis of soil samples in nearly all extant T. sutchuenensis populations identified that soil properties, especially soil nutrients, might play critical roles in the survival of T. sutchuenensis. Our findings prove that a series of fungal communities (e.g., Tomentella, Piloderma, and Cortinarius) could be key indicators for T. sutchuenensis survival. In addition, this is the first time that large-scale soil property and fungal community investigations have been carried out in southwest China, offering important values for exploring the distribution pattern of regional soil microorganisms. Collectively, our findings display a holistic picture of soil microbiome and environmental factors associated with T. sutchuenensis.
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Affiliation(s)
- You-wei Zuo
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Ping He
- Chongqing Academy of Science and Technology, Low Carbon and Ecological Environment Protection Research Center, Liangjiang New Area, Chongqing, China
| | - Jia-hui Zhang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Wen-qiao Li
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Deng-hao Ning
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Yu-lian Zeng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Ying Yang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Chang-ying Xia
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Huan Zhang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Hong-ping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Beibei, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Institute of Resources Botany, School of Life Sciences, Southwest University, Beibei, Chongqing, China
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Zuo YW, Zhang JH, Ning DH, Zeng YL, Li WQ, Xia CY, Zhang H, Deng HP. Comparative Analyses of Rhizosphere Bacteria Along an Elevational Gradient of Thuja sutchuenensis. Front Microbiol 2022; 13:881921. [PMID: 35591985 PMCID: PMC9111514 DOI: 10.3389/fmicb.2022.881921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Thuja sutchuenensis Franch. is an endangered species in southwestern China, primarily distributed in 800-2,100 m of inaccessible mountainous areas. Rhizosphere soil physicochemical properties and bacterial communities play an essential role in managing plant growth and survival. Nonetheless, the study investigating rhizosphere soil properties and bacterial communities of T. sutchuenensis is limited. The present study investigated soil properties, including soil pH, organic matter, water content, nitrogen, phosphorus, and potassium contents, and bacterial communities in nearly all extant T. sutchuenensis populations at five elevational gradients. Our results demonstrated that the increase in elevation decreased rhizosphere and bulk soil phosphorus content but increased potassium content. In addition, the elevational gradient was the dominant driver for the community composition differentiation of soil bacterial community. Proteobacteria and Acidobacteria were the dominant bacterial phyla distributed in the rhizosphere and bulk soils. Co-occurrence network analysis identified key genera, including Bradyrhizobium, Acidicapsa, Catenulispora, and Singulisphaera, that displayed densely connected interactions with many genera in the rhizosphere soil. The dominant KEGG functional pathways of the rhizosphere bacteria included ABC transporters, butanoate metabolism, and methane metabolism. Further correlation analysis found that soil phosphorus and potassium were the dominant drivers for the diversity of soil bacteria, which were distinctively contributed to the phylum of Planctomycetes and the genera of Blastopirellula, Planctomycetes, and Singulisphaera. Collectively, this comprehensive study generated multi-dimensional perspectives for understanding the soil bacterial community structures of T. sutchuenensis, and provided valuable findings for species conservation at large-scale views.
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Affiliation(s)
- You-wei Zuo
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Jia-hui Zhang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Deng-hao Ning
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Yu-lian Zeng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Wen-qiao Li
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Chang-ying Xia
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Huan Zhang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Hong-ping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
- Chongqing Academy of Science and Technology, Low Carbon and Ecological Environment Protection Research Center, Chongqing, China
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Yao Z, Wang X, Wang K, Yu W, Deng P, Dong J, Li Y, Cui K, Liu Y. Chloroplast and Nuclear Genetic Diversity Explain the Limited Distribution of Endangered and Endemic Thuja sutchuenensis in China. Front Genet 2021; 12:801229. [PMID: 35003229 PMCID: PMC8733598 DOI: 10.3389/fgene.2021.801229] [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: 10/25/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Narrow-ranged species face challenges from natural disasters and human activities, and to address why species distributes only in a limited region is of great significance. Here we investigated the genetic diversity, gene flow, and genetic differentiation in six wild and three cultivated populations of Thuja sutchuenensis, a species that survive only in the Daba mountain chain, using chloroplast simple sequence repeats (cpSSR) and nuclear restriction site-associated DNA sequencing (nRAD-seq). Wild T. sutchuenensis populations were from a common ancestral population at 203 ka, indicating they reached the Daba mountain chain before the start of population contraction at the Last Interglacial (LIG, ∼120-140 ka). T. sutchuenensis populations showed relatively high chloroplast but low nuclear genetic diversity. The genetic differentiation of nRAD-seq in any pairwise comparisons were low, while the cpSSR genetic differentiation values varied with pairwise comparisons of populations. High gene flow and low genetic differentiation resulted in a weak isolation-by-distance effect. The genetic diversity and differentiation of T. sutchuenensis explained its survival in the Daba mountain chain, while its narrow ecological niche from the relatively isolated and unique environment in the "refugia" limited its distribution.
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Affiliation(s)
- Zhi Yao
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Xinyu Wang
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Kailai Wang
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Wenhao Yu
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Purong Deng
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jinyi Dong
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Yonghua Li
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Kaifeng Cui
- Changbai Mountain Academy of Sciences, Joint Key Laboratory of Community and Biodiversity for Jilin Province and Changbai Mountain, Jilin, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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