Harnessing transposable elements for plant functional genomics and genome engineering

Xiao Yuan Tao; Shou Li Feng; Lu Yuan; Yan Jun Li; Xin Jia Li; Xue Ying Guan; Zhong Hua Chen; Sheng Chun Xu

doi:10.1016/j.tplants.2025.03.007

Harnessing transposable elements for plant functional genomics and genome engineering

Xiao Yuan Tao
, Shou Li Feng
, Lu Yuan
, Yan Jun Li
, Xin Jia Li
, Xue Ying Guan
, Zhong Hua Chen
, Sheng Chun Xu

School of Science

Xianghu Laboratory
Zhejiang University
University of Adelaide
Zhejiang Academy of Agricultural Sciences

Research output: Contribution to journal › Article › peer-review

25 Citations (Scopus)

166 Downloads (Pure)

Abstract

Transposable elements (TEs) constitute a large portion of many plant genomes and play important roles in regulating gene expression and in driving genome evolution and crop domestication. Despite advances in understanding the functions and mechanisms of TEs, a comprehensive review of their integrated knowledge and cutting-edge biotechnological applications of TEs is still needed. We provide a thorough overview that connects discoveries, mechanisms, and technologies associated with plant TEs. We discuss the identification and function of TEs driven by functional genomics, epigenetic regulation of TEs, and utilization of active TEs in plant functional genomics and genome engineering. In summary, expanding the knowledge and application of TEs will be beneficial to crop breeding and plant synthetic biology in the future.

Original language	English
Pages (from-to)	1130-1146
Number of pages	17
Journal	Trends in Plant Science
Volume	30
Issue number	10
DOIs	https://doi.org/10.1016/j.tplants.2025.03.007
Publication status	Published - Oct 2025

Notes

WIP FH TBA

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 2 Zero Hunger

Keywords

cis-regulatory modules (CRMs)
crop breeding
crop improvement
genome evolution
neofunctionalization
non-coding RNAs
transposon

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10.1016/j.tplants.2025.03.007Licence: CC BY-NC-ND

Full textFinal published version, 2.17 MBLicence: CC BY-NC-ND

Cite this

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title = "Harnessing transposable elements for plant functional genomics and genome engineering",

abstract = "Transposable elements (TEs) constitute a large portion of many plant genomes and play important roles in regulating gene expression and in driving genome evolution and crop domestication. Despite advances in understanding the functions and mechanisms of TEs, a comprehensive review of their integrated knowledge and cutting-edge biotechnological applications of TEs is still needed. We provide a thorough overview that connects discoveries, mechanisms, and technologies associated with plant TEs. We discuss the identification and function of TEs driven by functional genomics, epigenetic regulation of TEs, and utilization of active TEs in plant functional genomics and genome engineering. In summary, expanding the knowledge and application of TEs will be beneficial to crop breeding and plant synthetic biology in the future.",

keywords = "cis-regulatory modules (CRMs), crop breeding, crop improvement, genome evolution, neofunctionalization, non-coding RNAs, transposon",

author = "Tao, \{Xiao Yuan\} and Feng, \{Shou Li\} and Lu Yuan and Li, \{Yan Jun\} and Li, \{Xin Jia\} and Guan, \{Xue Ying\} and Chen, \{Zhong Hua\} and Xu, \{Sheng Chun\}",

year = "2025",

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doi = "10.1016/j.tplants.2025.03.007",

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T1 - Harnessing transposable elements for plant functional genomics and genome engineering

AU - Tao, Xiao Yuan

AU - Feng, Shou Li

AU - Yuan, Lu

AU - Li, Yan Jun

AU - Li, Xin Jia

AU - Guan, Xue Ying

AU - Chen, Zhong Hua

AU - Xu, Sheng Chun

PY - 2025/10

Y1 - 2025/10

N2 - Transposable elements (TEs) constitute a large portion of many plant genomes and play important roles in regulating gene expression and in driving genome evolution and crop domestication. Despite advances in understanding the functions and mechanisms of TEs, a comprehensive review of their integrated knowledge and cutting-edge biotechnological applications of TEs is still needed. We provide a thorough overview that connects discoveries, mechanisms, and technologies associated with plant TEs. We discuss the identification and function of TEs driven by functional genomics, epigenetic regulation of TEs, and utilization of active TEs in plant functional genomics and genome engineering. In summary, expanding the knowledge and application of TEs will be beneficial to crop breeding and plant synthetic biology in the future.

AB - Transposable elements (TEs) constitute a large portion of many plant genomes and play important roles in regulating gene expression and in driving genome evolution and crop domestication. Despite advances in understanding the functions and mechanisms of TEs, a comprehensive review of their integrated knowledge and cutting-edge biotechnological applications of TEs is still needed. We provide a thorough overview that connects discoveries, mechanisms, and technologies associated with plant TEs. We discuss the identification and function of TEs driven by functional genomics, epigenetic regulation of TEs, and utilization of active TEs in plant functional genomics and genome engineering. In summary, expanding the knowledge and application of TEs will be beneficial to crop breeding and plant synthetic biology in the future.

KW - cis-regulatory modules (CRMs)

KW - crop breeding

KW - crop improvement

KW - genome evolution

KW - neofunctionalization

KW - non-coding RNAs

KW - transposon

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JO - Trends in Plant Science

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ER -

Harnessing transposable elements for plant functional genomics and genome engineering

Abstract

Notes

UN SDGs

Keywords

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