Evidence map›Paper›PMID 41808406›Full record

ArticlePlant communications2026

A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.

Yu-Tao Bao, Ren-Gang Zhang, Hui Liu, Zhi-Chao Li, Si-Qian Jiao, Kai-Hua Jia, Shan-Shan Zhou, Shuai Nie, Xue-Mei Yan, Tian-Le Shi and 12 more

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Article in Plant communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed
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1 citing paper in PubMed.

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5 · Who and what money

Authors and funding

22 authors.

Yu-Tao BaoState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
Ren-Gang ZhangYunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
Hui LiuDepartment of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå 90187, Sweden.
Zhi-Chao LiState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
Si-Qian JiaoState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Pingdingshan University, Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan 467000, China.
Kai-Hua JiaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, China.
Shan-Shan ZhouState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
Shuai NieState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China.
Xue-Mei YanState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Tian-Le ShiState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China.
Xue-Chan TianState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255000, China.
Shi-Wei ZhaoState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
Lei KongState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
Zhao-Yang ChenState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
Hai-Yao MaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
Xiao-Lei YangNational Tree Breeding Station for Platycladus orientalis in Jiaxian, Forest Farm of Jiaxian County, Jiaxian 467100, China.
Charles ChenDepartment of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
Yousry Aly El-KassabyDepartment of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
Ilga PorthDépartement des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC G1V 0A6, Canada.
Xiao-Ru WangState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå 90187, Sweden. Electronic address: xiao-ru.wang@umu.se.
Jian-Feng MaoState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå, Sweden. Electronic address: jianfeng.mao@umu.se.
Wei ZhaoDepartment of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå 90187, Sweden; Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China. Electronic address: zhao.wei@umu.se.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Gymnosperms, particularly conifers, exhibit a high abundance of transposable elements (TEs) in their giga-scale genomes. TEs interact both antagonistically and cooperatively with the host genome, promoting structural and genetic innovations across evolutionary lineages. However, how TEs shape the coding space of gymnosperm genomes remains a key unresolved question. Here, we present a high-quality genome assembly for the keystone conifer Platycladus orientalis, with a contig N50 of 57.54 Mb-the highest continuity reported to date-to investigate the role of TEs. Comparative genomics confirms the absence of recent whole-genome duplication and the presence of genome expansion in gymnosperms, revealing complex interactions among recurrent TE proliferation, low DNA removal rates, and DNA methylation-mediated silencing. Computational evidence indicates that TE-mediated gene duplication and pseudogenization provide a genetic basis for adaptive evolution and functional innovation, significantly shaping gene family dynamics and the emergence of species-specific genes. Additionally, TEs capture and duplicate an average of ∼400,000 coding gene fragments per gymnosperm genome, facilitating exon shuffling and triggering epigenetic conflicts between source genes and captured exon fragments. Genes from which fragments are captured (donor genes) show significantly higher levels of exon methylation than genes not captured by TEs (free genes), whereas syntenic donor genes exhibit lower levels of silencing responses than non-syntenic donor genes. This study provides valuable genomic resources and offers insights into the evolutionary patterns and principles underlying the large genome size and complexity of gymnosperms.

Indexed as

Chromosomes, PlantCycadopsidaDNA Transposable ElementsGene DuplicationGenome, PlantPseudogenesEvolution, MolecularGenomicsDNA Transposable Elementsgene duplicationgene fragment capturegenome expansiongymnospermspseudogenizationtransposable elements

Identifiers

PMID41808406
PMCPMC13477047

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