On July 16, 2024, *Molecular Horticulture* published online a research paper from Professor Xia Rui's group at the College of Horticulture, South China Agricultural University, titled "Diversification of FT-like genes in the PEBP family contributes to the variation of flowering traits in Sapindaceae species." The study utilized genomic data of Sapindaceae plants (Li et al. 2024) and extensive transcriptome analysis combined with experimental validation, revealing that variations in the coding and promoter regions of FT genes may be the underlying mechanism for the diverse flowering traits observed in Sapindaceae species.
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Professor Xia Rui's team from South China Agricultural University published a research paper titled "SynGAP: a synteny-based toolkit for gene structure annotation polishing" in the internationally renowned journal *Genome Biology* (IF: 10.1). The study developed a tool named SynGAP (Synteny-based Gene structure Annotation Polisher), which corrects gene structure annotations in genomic studies based on synteny. By leveraging the synteny between closely related species, SynGAP identifies and corrects potential errors and omissions in the original gene structure annotations, thereby optimizing the accuracy of gene annotations.
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On May 28, 2024, the Journal of Integrative Plant Biology (JIPB) published online a research paper titled “SapBase: A central portal for functional and comparative genomics of Sapindaceae species” by Professor Xia Rui's team from South China Agricultural University [[1](https://doi.org/10.1111/jipb.13680)]. This study constructed the Sapindaceae genome database, SapBase (www.sapindaceae.com), which integrates data access, data analysis, and structural visualization. The database aims to provide:The most comprehensive genomic resource database for Sapindaceae plants; The most convenient gene expression database for Sapindaceae plants;The most aesthetically pleasing visualization tools for gene expression in Sapindaceae.
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On May 17, 2024, Huang Xing, Yang Yinghua, Chen Peike, and Lv Zixin from Professor Xia Rui's research group faced the most important exam of their graduate student life—the thesis defense. The thesis defense committee included Professor Zhang Jisen, the chair of the committee, and committee members Professor Wu Hong, Professor Hu Guibing, Professor Wu Shuang, and Professor He Shengbo. The defense secretary was Teacher Zeng ZaoHai, and the graduate students' supervisors were Professor Xia Rui and Associate Researcher Hao Yanwei.
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As the sun returns and the seasons turn, XIALAB has completed its seventh year. This year, we continued to forge ahead, delving deeper into the fields of lychee biology and bioinformatics analysis. This year, we actively engaged in academic exchanges, hosting an international academic conference and two bioinformatics training sessions. This year, we achieved remarkable results, earning recognition and numerous honors from various quarters. This year was also the year with the most graduates and the most new students joining XIALAB.
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On December 30, 2023, Professor Xia Rui's team from South China Agricultural University published online in *Science Bulletin* (IF: 18.9) a research paper titled "sRNAminer: a Multifunctional Toolkit for Next-Generation Sequencing Small RNA Data Mining in Plants." The study developed a multifunctional plant small RNA analysis tool called sRNAminer. With this tool, researchers can conduct one-stop small RNA analysis and visualization.
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From November 11 to 15, the International Horticulture Research Conference marked its 10th year. Many leading academics and young scholars in the field of horticulture from both domestic and international communities gathered in Guangzhou, the City of Flowers, to share the latest achievements and research progress in horticulture and to jointly promote international exchange and cooperation.The conference was co-hosted by South China Agricultural University, Nanjing Agricultural University, and *Horticulture Research*. It was organized by the College of Horticulture at South China Agricultural University and the State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Bioresources, with support from Professor Xia Rui's group at the College of Horticulture. Professor Xia Rui and Editor-in-Chief Cheng Zongming of *Horticulture Research* jointly served as the chairs of the conference.
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On November 15, 2023, Professor Xia Rui's team from South China Agricultural University published online in *Plant Biotechnology Journal* a research paper titled “MicroRNA482/2118 is lineage-specifically involved in gibberellin signaling via the regulation of GID1 expression by targeting noncoding PHAS genes and subsequently instigated phasiRNAs.” This study, through the analysis of PHAS genes triggered by microRNA482/2118 (miR482/2118) in lychee, discovered a lineage-specific regulatory pathway—lychee miR482/2118 regulates the expression of GID1 by targeting noncoding PHAS genes, thereby producing phasiRNAs that participate in gibberellin signaling.
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On September 22, 2023, Professor Xia Rui's team from the College of Horticulture at South China Agricultural University (State Key Laboratory of Conservation and Utilization of Subtropical Agricultural Bioresources) published online in Molecular Plant a research paper titled "TBtools-II: A One for All, All for One Bioinformatics Platform for Biological Big-data Mining." The paper systematically introduces and describes the new version of TBtools, namely TBtools-II. Building on TBtools-I, TBtools-II has optimized and added over 100 new functions, developed a plugin mode, and established a Plugin Store. These innovations address the primary conflict between the comprehensiveness and flexibility of software functions.
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Graduation is the arrival of parting, but also the prelude to a new beginning.We replace the sadness of parting with joy and sweat, and dispel the fatigue of study and work through a sport.Here it comes! The XIALAB "Graduation Cup" Badminton Recreational Tournament has arrived, as everyone has been eagerly anticipating.
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From April 24 to 28, 2023, the Chinese Society of Plant Physiology and Plant Molecular Biology held its 2023 National Academic Annual Conference and the 60th-anniversary Celebration in Wuhan. The conference, themed "Plant Sciences Empowering Agricultural Innovation," organized a series of academic, celebratory, and commemorative activities. During the event, the 2023 Wei Zhiming Young Innovator Award was presented, with Professor Xia Rui from the College of Horticulture at South China Agricultural University receiving this prestigious honor.
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On March 28, 2023, Elsevier released the 2022 "Highly Cited Chinese Researchers" list with great fanfare. A total of 5,216 scholars made it to the list, representing 504 universities, enterprises, and research institutions across China. The list covers 10 major academic fields and 84 first-level disciplines under the Ministry of Education.In our university, 20 scholars were included in the list, ranking 57th among all universities in China. Among them, Professor Xia Rui and Professor Chen Chengjie from our research group were selected in the fields of Biology and Horticulture, respectively.
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How long has it been since we last went out to have fun? The first thing to do after the semester began was, of course, to see if we still had the energy to go out and enjoy ourselves. So in February, we decided to go hiking together, taking advantage of the spring breeze, the warm sunshine, and our youthful spirits.On the morning of February 18th, a group of 28 of us from XIALAB gathered at the foot of Baiyun Mountain at nine o'clock. The weather was perfect, with the sun being neither too hot nor too cold. So we set off towards the summit! The spring air was refreshing, and the morning truly was the best time for hiking. We decided to push ourselves to reach the top before regrouping.
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On February 10, 2023, the journal *Science* published online a cover article titled "Taxon-specific, phased siRNAs underlie a speciation locus in monkey-flowers" from Dr. Wu Yuan's research group at the University of Connecticut. Dr. Mei Liang is the first author of the paper. Professor Xia Rui and Associate Professor Liu Yuanlong from the College of Horticulture at South China Agricultural University completed the small RNA sequencing work for this study.
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The importance of genome sequences and annotations is self-evident for every research group involved in molecular biology. The extensive sequencing of genomes has provided a significant boost to molecular research, but it has also given rise to some issues. For example, every time we perform gene cloning, students are required to first verify the mRNA transcript sequence used for primer design with RNA-seq data. In fact, aside from model organisms (whose annotations are not 100% accurate either), the gene structure annotations in most organisms' genomes contain numerous problems, meaning that most gene structure annotations are inaccurate. Therefore, it is necessary to manually confirm the sequences before designing primers for gene function studies.Naturally, the annotation of lychee genes is also not perfect. Our lab spent a month completing the correction of the lychee genome annotation！
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As another year draws to a close, our XIALAB research group holds an annual year-end summary meeting at the end of each year. This is a time for reflection and a prelude to what’s next. We review the ups and downs, the challenges and setbacks, the joys and achievements, the happiness and sorrows of the past year. We distill all the experiences and lessons, accomplishments and rewards, regrets and uncertainties, excitement and happiness into a single phrase: “All that is past is prologue, and all that is to come can be anticipated.”。
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Recently, the journal *Horticultural Plant Journal* published online a research paper titled “Species-specific regulatory pathways of small RNAs play sophisticated roles in flower development in *Dimocarpus longan* Lour.” by Professor Xia Rui’s team from South China Agricultural University.
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Recently, Professor Xia Rui’s team from the College of Horticulture at South China Agricultural University published a research paper titled “Biogenesis of Reproductive PhasiRNAs: Exceptions to the Rules” in *Plant Biotechnology Journal*. The study conducted large-scale PHAS analysis across hundreds of plant species and discovered that reproductive phasiRNAs exhibit unconventional biogenesis patterns beyond the known norms.
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On June 5, 2022, Zhang Keyu, a graduate from the 2018 Dingying Innovation Class in Horticulture and mentored by Professor Xia Rui's team, participated in the final of the Fourth "Graduation Thesis Competition for Plant Production Majors in Guangdong Provincial Undergraduate Universities." The competition was organized by the Teaching Guidance Committee for Plant Production Majors in Guangdong Provincial Undergraduate Universities and hosted by South China Agricultural University. Zhang Keyu won the Special Prize in the competition.
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On July 4, 2022, Professor Xia Rui's team from South China Agricultural University published online in *iMeta* an article titled "A painless way to customize Circos plot: From data preparation to visualization using TBtools."In this article, the authors developed the "Advanced Circos" feature in TBtools, providing a simple method for constructing Circos plots. The "Advanced Circos" feature offers a user-friendly interface for customizing parameter settings and can be used to visualize various genome-level data, such as genome association information, alignment data, gene density, and QTL locations.
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As another graduation season arrives, the 2nd "Graduation Cup" Recreational Badminton Tournament of XIALAB is here as scheduled.When everyone knows each other well, the competition begins the moment the draw is made, with each person hoping to get a good draw and perform to the best of their ability. Amidst everyone's gasps of astonishment, the match-up list finally emerges, bringing joy to some and disappointment to others.
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In May, at the transition from spring to summer, three members of the XIALAB research group—Liu Bo, Feng Xiuwen, and Liu Yilun—also reached a significant milestone in their academic careers: their thesis defenses.The defense venue was arranged in Room 317 of the Science and Technology Building at South China Agricultural University. On the morning of May 13th, the group members arrived at the venue early to prepare intensively and energetically for the defense. Everyone worked together to decorate the venue and adjust the equipment, striving for perfection in every detail. The three senior students who were about to defend their theses were also making their final preparations with a sense of nervousness.
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Recently, the research team from the College of Horticulture at South China Agricultural University completed the decoding of the lychee genome. The results were published in *Nature Genetics* under the title "Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars". XIALAB was one of the main contributors to this work. Ph.D. student Feng Yunting (co-first author) completed the majority of the analysis tasks. Dr. Chen Chengjie (who has joined the university as a faculty member), Ph.D. students Zhang Yanqing and Zheng Jiakun, and master's students Li Jiawei and Mai Yingxiao also participated in the data analysis of the lychee genome, becoming co-authors of the paper.
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On December 27th, the Institute of Scientific and Technical Information of China (referred to as "ISTIC") released the "2021 Statistical Report on China's Scientific and Technological Papers" and selected the "100 Most Influential International Academic Papers in China."The paper titled "TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data," published by our research group in the internationally renowned journal *Molecular Plant* in 2020, has been successfully selected as one of the 100 Most Influential International Academic Papers in China in 2020.
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The XIALAB consists of a molecular biology laboratory and a bioinformatics analysis workshop.
The molecular laboratory, spanning 100 square meters, is equipped with a comprehensive range of fundamental instruments for molecular and cell biology experiments, including nucleic acid extraction and purification, gene cloning, gene expression analysis, protein purification and characterization, plants tissue culture, plants transgenic technology as well as high-through library construction.
The bioinformatics workshop is built for addressing the high-through data analysis problem. With the help of two high-performance servers and multiple workstations, requirements from data generation and analysis to experimental validation can be satisfied.
Ph.D. Horticulture, Virginia Polytechnic Institute and State University, USA, 2013
M.S. Pomology, South China Agricultural University, China, 2007
B.S. Horticulture, South China Agricultural University, China, 2004
Since 2000, we step into the “big data” era, with the advanced development of high-throughput technologies, huge amount of biological data are generated. The flower sexual determination and flower development are hot topics and valuable agronomic traits in fruit crops . Our research areas mainly focus on the mechanism underlying of flower sex determination and flower development in tropical and subtropical fruit trees involving lychee, longan and papaya by combining the genetics, comparative genomics, cell biology, bioinformatics and multiple high-throughput deep sequencing techniques.
