Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis
Chromosome rearrangements during plant evolution can lead to alterations in genome structure and gene function, thereby influencing species adaptation and evolutionary processes. Gymnosperms, as an ancient group of plants, offer valuable insights into the morphological, physiological, and ecological...
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MDPI AG
2025-08-01
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| Series: | Plants |
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| author | Haoran Liao Lianghui Zhong Yujie He Jie He Yuhan Wu Ying Guo Lina Mei Guibing Wang Fuliang Cao Fangfang Fu Liangjiao Xue |
| author_facet | Haoran Liao Lianghui Zhong Yujie He Jie He Yuhan Wu Ying Guo Lina Mei Guibing Wang Fuliang Cao Fangfang Fu Liangjiao Xue |
| author_sort | Haoran Liao |
| collection | DOAJ |
| description | Chromosome rearrangements during plant evolution can lead to alterations in genome structure and gene function, thereby influencing species adaptation and evolutionary processes. Gymnosperms, as an ancient group of plants, offer valuable insights into the morphological, physiological, and ecological characteristics of early terrestrial flora. The reconstruction of ancestral karyotypes in gymnosperms may provide critical clues for understanding their evolutionary history. In this study, we inferred the ancestral gymnosperm karyotype (AGK), which comprises 12 chromosomes, and conducted a collinearity analysis with existing gymnosperm genomes. Our findings indicate that chromosome numbers have remained remarkably stable throughout the evolution of gymnosperms. For species with multiplied chromosome numbers, such as gnetophytes, weak collinearities with the AGK were observed. Comparisons between the AGK and gnetophyte genomes revealed a biased pattern regarding retained duplication blocks. Furthermore, our analysis of transposable elements in <i>Welwitschia mirabilis</i> identified enriched regions containing LINE-1 retrotransposons within the syntenic blocks. Syntenic analysis between the AGK and angiosperms also demonstrated a biased distribution across chromosomes. These results provide a fundamental resource for further characterization of chromosomal evolution in gymnosperms. |
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| institution | Kabale University |
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| language | English |
| publishDate | 2025-08-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj-art-b7d6cce49b6f46fcae8f764b38aa1a802025-08-20T03:36:22ZengMDPI AGPlants2223-77472025-08-011415236110.3390/plants14152361Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic AnalysisHaoran Liao0Lianghui Zhong1Yujie He2Jie He3Yuhan Wu4Ying Guo5Lina Mei6Guibing Wang7Fuliang Cao8Fangfang Fu9Liangjiao Xue10State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, ChinaChromosome rearrangements during plant evolution can lead to alterations in genome structure and gene function, thereby influencing species adaptation and evolutionary processes. Gymnosperms, as an ancient group of plants, offer valuable insights into the morphological, physiological, and ecological characteristics of early terrestrial flora. The reconstruction of ancestral karyotypes in gymnosperms may provide critical clues for understanding their evolutionary history. In this study, we inferred the ancestral gymnosperm karyotype (AGK), which comprises 12 chromosomes, and conducted a collinearity analysis with existing gymnosperm genomes. Our findings indicate that chromosome numbers have remained remarkably stable throughout the evolution of gymnosperms. For species with multiplied chromosome numbers, such as gnetophytes, weak collinearities with the AGK were observed. Comparisons between the AGK and gnetophyte genomes revealed a biased pattern regarding retained duplication blocks. Furthermore, our analysis of transposable elements in <i>Welwitschia mirabilis</i> identified enriched regions containing LINE-1 retrotransposons within the syntenic blocks. Syntenic analysis between the AGK and angiosperms also demonstrated a biased distribution across chromosomes. These results provide a fundamental resource for further characterization of chromosomal evolution in gymnosperms.https://www.mdpi.com/2223-7747/14/15/2361gymnospermancestral karyotypecollinearitychromosome stabilityLINE-1 |
| spellingShingle | Haoran Liao Lianghui Zhong Yujie He Jie He Yuhan Wu Ying Guo Lina Mei Guibing Wang Fuliang Cao Fangfang Fu Liangjiao Xue Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis Plants gymnosperm ancestral karyotype collinearity chromosome stability LINE-1 |
| title | Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis |
| title_full | Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis |
| title_fullStr | Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis |
| title_full_unstemmed | Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis |
| title_short | Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis |
| title_sort | construction of ancestral chromosomes in gymnosperms and the application in comparative genomic analysis |
| topic | gymnosperm ancestral karyotype collinearity chromosome stability LINE-1 |
| url | https://www.mdpi.com/2223-7747/14/15/2361 |
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