未来技术学院（海峡联合学院、海峡联合研究院）

For easier access to data resources from our previously published articles, we have uploaded key datasets to figshare. Readers with any data-related inquiries are welcome to contact the corresponding author directly at lfgu@fafu.edu.cn.

1. Yubang Gao; Huiyuan Wang; Hangxiao Zhang; Yongsheng Wang; Jinfeng Chen; Lianfeng Gu*. (2018). PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq, Bioinformatics, 34(9): 1580-1582

We have uploaded all compressed files associated with this article's website to figshare:

https://doi.org/10.6084/m9.figshare.27215193.v1

For more detailed instructions on PRAPI installation and usage, please refer to our Bio-101 documentation: Liufu, Y., Liu, X., Wu, L., Zhang, H., Gao, Y*. and Gu, L*. (2022). An Analysis Pipeline for Identification of RNA Modification, Alternative Splicing and Polyadenylation Using Third Generation Sequencing. Bio-101: e4433. DOI: 10.21769/BioProtoc.4433.

2. Yong Zhang; Yongcheng Wei; Jingxiang Meng; Yujiao Wang; Sen Nie; Zeyu Zhang; Huiyuan Wang; Yongkang Yang; Yubang Gao; Ji Wu; Tuhe Li; Xuqing Liu; Hangxiao Zhang; Lianfeng Gu*. (2023) Chromosome-scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. Plant Journal. 114(6), 1490-1505.

We have deposited the complete genome assemblies and corresponding annotation files for C. equisetifolia, C. glauca, and C. cunninghamiana on figshare:

https://figshare.com/articles/dataset/Chromosome-scale_de_novo_genome_assembly_andannotation_of_three_representative_Casuarina_species_C_equisetifolia_C_glauca_and_C_cunninghamiana/24411997

3. Yushan Zheng*; Deming Yang; Jundong Rong1; Liguang Chen; Qiang Zhu; Tianyou He; Lingyan Chen; Jing Ye; Lili Fan; Yubang Gao; Hangxiao Zhang; Lianfeng Gu*. (2022). Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma Bamboo (Dendrocalamus latiflorus Munro), Journal of Integrative Plant Biology, 64(3): 649-670

The resourcesare available at the following link:

https://figshare.com/articles/dataset/Allele_aware_chromosome_scale_assembly_of_theallopolyploid_genome_of_hexaploid_Ma_bamboo_Dendrocalamus_latiflorus_Munro_/24411913

4. Jundong Rong, Yushan Zheng*, Zeyu Zhang, Jun Zhang, Yuying Gu, Tian Hua, Mengna Zhao, Lili Fan, Zhiwen Deng, Yanmei Pan, Bingjun Li, Liguang Chen, Tianyou He, Lingyan Chen, Jing Ye, Hangxiao Zhang, Lianfeng Gu*. (2024). De novo Whole-Genome Assembly of the 10-Gigabase Fokienia Hodginsii Genome to Reveal Differential Epigenetic Events Between Callus and Xylem. Advanced Science, 2402644.

The genome assembly and annotation were uploaded to figshare:

(https://doi.org/10.6084/m9.figshare.26064412.v1).

5. Jutang Jiang, Zeyu Zhang, Yucong Bai, Xiaojing Wang, Yuping Dou, Ruiman Geng, Chongyang Wu, Hangxiao Zhang, Cunfu Lu, Lianfeng Gu*, Jian Gao* (2024). Chromosomal‐level genome and metabolome analyses of highly heterozygous allohexaploid Dendrocalamus brandisii elucidate shoot quality and developmental characteristics. Journal of Integrative Plant Biology. 66(6), 1087-1105.

The assembled genome andthe annotation files were uploaded to figshare with

DOI:10.6084/m9.figshare.24455197.

Professor Gu Lianfeng currently serves as a full-time professor at the Fujian Agriculture and Forestry University, and is the Deputy Director of the Proteomics Research Center and a doctoral supervisor. In 2012, Professor Gu obtained a Ph.D. in Bioinformatics from the Chinese Academy of Sciences. In 2015, he returned to China from the University of California, Riverside, USA. He was selected as a Class C high-level talent in Fujian Province in 2016 and received the 14th Forestry Youth Science and Technology Award in 2017. He is currently a high-level talent introduced to Fujian Province and a Golden Mountain Scholar at Fujian Agriculture and Forestry University. Professor Gu has led three national natural science foundation projects and three National Key Research and Development Program of China, accumulating a total of over five million yuan. As the corresponding author, he has published multiple papers on forest tree epigenetics in journals such as Genome Biology, Plant Physiology, Tree Physiology, Plant Journal, and Journal of Integrative Plant Biology over the past five years, with an H-index of 36. For more information about our published work, please visit our Publications page.

Education Experiences

2012 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

Work Experiences

2015- Fujian Agriculture and Forestry University

Honors and Awards

The 14th Forestry Youth Science and Technology Award

Fujian Province High-level Talent

Teaching Activities

I am responsible for teaching courses in Forest Tree Genetics and Breeding, Fundamentals and Applications of Biology, Forest Tree Bioinformatics, and Advances in Molecular Biology. Additionally, I serve as the class advisor for undergraduate students. Over the past five years, I have taught a total of three undergraduate courses, accumulating 114 class hours with 190 students in attendance. During the same period, I have taught three graduate courses, totaling 144 class hours with 156 students.

In the past five years, I have successfully guided five doctoral students to graduation and supervised the graduation of 13 master's students. I have demonstrated a clear commitment to fostering students' moral and intellectual development, and as a result, I was honored with the title of Outstanding Teacher for the year 2020.

Research Fields

Research summary:

The research group has consistently focused on forest tree epigenetics, with a primary emphasis on the herbaceous bamboo of the Poaceae family, widely planted in Fujian, and the model tree species, poplar. The group has dissected the rapid growth and flowering regulation mechanisms of bamboo and the epigenetic responses of forest trees to different stress.

(1) Established an efficient and convenient bamboo functional gene research system

The group successfully developed an efficient expression vector system based on bamboo mosaic virus carrying exogenous genes. The modified virus vector can drive the expression of up to 4.5kb length fragment reporter system (RUBY) in both bamboo and moso bamboo, showing a distinct betaine red color indicator (Journal of Integrative Plant Biology, 2023; Cover Figure). This technology provides a high-efficiency, effective, and short experimental period for studying functional genes in bamboo, becoming a powerful tool for the functional genomics research of bamboo in the Poaceae family. Additionally, the group established transient transformation processes for moso bamboo and bamboo, as well as a virus-induced gene silencing system for forest trees. To further understand the gene functions of bamboo, the group deciphered the hexaploid bamboo genotyping genome, revealing macroscopic collinearity relationships between scattered and clumped bamboos and some differences in microscopic collinearity (Journal of Integrative Plant Biology, 2022). These achievements were reported in media such as the Chinese Science Bulletin and featured as cover stories in the JIPB journal.

(2) Advanced epigenetic regulation research on bamboo growth and development

The long flowering period and rapid shoot growth of bamboo are two representative biological characteristics. Therefore, the group has focused on the regulation of methylation and circular RNA on flowering and shoot growth. The study found that as moso bamboo ages, the CHH methylation level gradually accumulates from vegetative to reproductive growth, a change induced by 24nt-siRNA and DRM2, laying an important foundation for revealing the mechanism of DNA methylation regulation of moso bamboo flowering (Plant Journal, 2021). The related work has been reported in journals such as Annual Review of Entomology, Plant Physiology, and Plant Communications. The rapid shoot growth of moso bamboo is another important biological characteristic. Cellular morphology of underground rhizomes of moso bamboo revealed noticeable differences in cell morphology from the base of the mother bamboo to the bamboo whip, showing a decrease in angle near the whip region. It was observed that the farther the lateral bud is from the mother bamboo, the higher the methylation level, with methylation inhibition causing delayed root development in moso bamboo. The decrease in N⁶-methyladenosine modification (m⁶A) and 5mC was observed, both leading to poly(A) tail shortening (Tree Physiology, 2023). This study provides preliminary insights into the early stages of understanding the development of plant root systems and the regulatory mechanisms of epigenetic modifications. Systematic analysis of methylation modifications and post-transcriptional regulation mechanisms at different positions and stages of moso bamboo shoots revealed that late-stage shoots have higher 5-methylcytosine levels, lower DNA methylation levels of the CG type, and higher N6-methyladenosine modification levels in RNA, compared to early-stage shoots (Plant Physiology, 2022).

The group also found that circular RNA has obvious stage specificity at different heights of bamboo shoots, regulating key development genes and being regulated by miRNA (Plant and Cell Physiology, 2019). Furthermore, moso bamboo circular RNA was found to be regulated by m6A (JIPB, 2020) and post-transcriptional regulation (Bioinformatics, 2019). Genetic transformation of candidate circular RNA produced distinct phenotypic characteristics, advancing the study of the generation, degradation, and functional mechanisms of moso bamboo circular RNA (Genomics, Proteomics & Bioinformatics, 2023).

(3) Promoted research on m6A regulation response to secondary growth methylation stress in forest trees

The regulation of m6A in the secondary wood of forest trees under adversity stress has not been reported. The group first established a system for direct quantitative detection of m⁶A modification at the single-base and single-transcript levels. Through this system, it was discovered that m⁶A is a widely present RNA modification in the secondary wood of poplar, playing an important role in regulating RNA splicing and translation (Genome Biology, 2021; Journal of Integrative Plant Biology, 2021). Since its publication in 2021, the results have been cited 72 times by journals such as Nature Biotechnology and Nature Communication. It was found that under drought stress, the m⁶A modification rate of transcripts related to cellulose, hemicellulose, and lignin synthesis in secondary wood significantly increased, leading to a significant downregulation of the expression of these genes, providing a new perspective for the epigenetic response regulation of poplar secondary wood under drought stress (Plant Physiology, 2022). Considering the widespread planting of Casuarina equisetifoliaalong the coast, with characteristics such as drought resistance, salt and alkali resistance, and strong adaptability, the group explored the genetic resources of different Casuarina varieties at the molecular level, constructed three chromosome-level genomes, and deciphered the regulation mechanism of DNA methylation on its growth and development (Plant Journal, 2023) and stem-differentiating xylem (Plant Journal, 2018). Key candidate genes of Casuarina were obtained, laying the foundation for the study of epigenetics in the resistance of forest trees.

Teachings

I undertake the teaching of courses in Forest Tree Genetics and Breeding, Fundamentals and Applications of Biology, Forest Tree Bioinformatics, and Advances in Molecular Biology, as well as the responsibilities of being a class advisor for undergraduate students.