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Ma S, Shen Y, Li M, Jiang R, Cai L, Wu T, Gao L, Wu M, He P. Establishment of Novel Simple Sequence Repeat Markers in Phragmites australis and Application in Wetlands of Nanhui Dongtan, Shanghai. BIOLOGY 2025; 14:356. [PMID: 40282221 PMCID: PMC12025300 DOI: 10.3390/biology14040356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 04/29/2025]
Abstract
Common reed (Phragmites australis) is a widely distributed perennial herb of high ecological significance in wetlands worldwide. This research developed 15 SSR markers through whole-genome sequencing and assessed the genetic diversity across four representative reed populations (DB, JPDP, YJRHK, DD) in the coastal wetlands of Nanhui Dongtan, Shanghai. A total of 113.5 alleles (Na) were detected, averaging 7.567 alleles per locus, with an expected heterozygosity (He) of 0.690 and a Shannon diversity index (I) of 1.485. Polymorphism information content (PIC) values (ranging from 0.577 to 0.872, average 0.770) indicated strong resolution power for discriminating subtle genetic differences across populations. Among the four populations, JPDP displayed the highest genetic diversity parameters (Na = 12.667; I = 2.020), whereas DD exhibited the lowest, consistent with intensive demographic screening under saline stress and competition from Spartina alterniflora. Bayesian clustering analysis (STRUCTURE) and UPGMA dendrograms further revealed that the four populations split into two major subgroups, which underlines both the influence of geographic and ecological factors on genetic structuring and the persistence of gene flow. In sum, the newly developed SSR markers demonstrated robustness and sensitivity in elucidating the overall high genetic diversity but moderate genetic differentiation of reed populations in Nanhui Dongtan. These findings not only offer insights into local adaptation mechanisms in coastal wetlands but also provide a technical basis for the conservation and utilization of P. australis.
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Affiliation(s)
- Shaozu Ma
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (S.M.); (Y.S.); (R.J.); (L.C.); (T.W.); (L.G.)
| | - Yifei Shen
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (S.M.); (Y.S.); (R.J.); (L.C.); (T.W.); (L.G.)
| | - Min Li
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA;
| | - Ruitong Jiang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (S.M.); (Y.S.); (R.J.); (L.C.); (T.W.); (L.G.)
| | - Luyi Cai
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (S.M.); (Y.S.); (R.J.); (L.C.); (T.W.); (L.G.)
| | - Tingting Wu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (S.M.); (Y.S.); (R.J.); (L.C.); (T.W.); (L.G.)
| | - Linxi Gao
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (S.M.); (Y.S.); (R.J.); (L.C.); (T.W.); (L.G.)
| | - Meiqin Wu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (S.M.); (Y.S.); (R.J.); (L.C.); (T.W.); (L.G.)
| | - Peimin He
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (S.M.); (Y.S.); (R.J.); (L.C.); (T.W.); (L.G.)
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Cui J, Yang Q, Zhang J, Ju C, Cui S. Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis. Int J Mol Sci 2025; 26:546. [PMID: 39859262 PMCID: PMC11764873 DOI: 10.3390/ijms26020546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 12/28/2024] [Accepted: 12/28/2024] [Indexed: 01/27/2025] Open
Abstract
As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae.
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Affiliation(s)
- Jipeng Cui
- College of Life Sciences, Capital Normal University, Haidian District, Beijing 100048, China; (J.C.); (Q.Y.); (J.Z.); (C.J.)
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing 100048, China
| | - Qianhui Yang
- College of Life Sciences, Capital Normal University, Haidian District, Beijing 100048, China; (J.C.); (Q.Y.); (J.Z.); (C.J.)
| | - Jiyue Zhang
- College of Life Sciences, Capital Normal University, Haidian District, Beijing 100048, China; (J.C.); (Q.Y.); (J.Z.); (C.J.)
| | - Chuanli Ju
- College of Life Sciences, Capital Normal University, Haidian District, Beijing 100048, China; (J.C.); (Q.Y.); (J.Z.); (C.J.)
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing 100048, China
| | - Suxia Cui
- College of Life Sciences, Capital Normal University, Haidian District, Beijing 100048, China; (J.C.); (Q.Y.); (J.Z.); (C.J.)
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing 100048, China
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Wang Q, Chen X, Meng Y, Niu M, Jia Y, Huang L, Ma W, Liang C, Li Z, Zhao L, Dang Z. The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants. Int J Mol Sci 2024; 25:2084. [PMID: 38396759 PMCID: PMC10888960 DOI: 10.3390/ijms25042084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Caragana, a xerophytic shrub genus widely distributed in northern China, exhibits distinctive geographical substitution patterns and ecological adaptation diversity. This study employed transcriptome sequencing technology to investigate 12 Caragana species, aiming to explore genic-SSR variations in the Caragana transcriptome and identify their role as a driving force for environmental adaptation within the genus. A total of 3666 polymorphic genic-SSRs were identified across different species. The impact of these variations on the expression of related genes was analyzed, revealing a significant linear correlation (p < 0.05) between the length variation of 264 polymorphic genic-SSRs and the expression of associated genes. Additionally, 2424 polymorphic genic-SSRs were located in differentially expressed genes among Caragana species. Through weighted gene co-expression network analysis, the expressions of these genes were correlated with 19 climatic factors and 16 plant functional traits in various habitats. This approach facilitated the identification of biological processes associated with habitat adaptations in the studied Caragana species. Fifty-five core genes related to functional traits and climatic factors were identified, including various transcription factors such as MYB, TCP, ARF, and structural proteins like HSP90, elongation factor TS, and HECT. The roles of these genes in the ecological adaptation diversity of Caragana were discussed. Our study identified specific genomic components and genes in Caragana plants responsive to heterogeneous habitats. The results contribute to advancements in the molecular understanding of their ecological adaptation, lay a foundation for the conservation and development of Caragana germplasm resources, and provide a scientific basis for plant adaptation to global climate change.
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Affiliation(s)
- 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Xing’er Chen
- 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yue Meng
- 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yuanyuan Jia
- 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Lei Huang
- 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Wenhong Ma
- 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Cunzhu Liang
- 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhiyong 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Liqing Zhao
- 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - 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 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
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