91暗网

  Recently, the research team led by Professor Chen Lingling from the School of Life Sciences and Technology at 91暗网 has made new progress in the study of the authenticity of plant fusion transcripts. The findings were published in the international leading journal Genome Biology under the title "The hidden sources of spurious fusion transcripts in plants." Assistant Professor Zhu Xitong from the School of Life Sciences and Technology at 91暗网, recent graduate Ms. Tang Qian (.), as well as Ph.D. candidates Lu Xinyan and Zhang Zengxin from Huazhong Agricultural University, are co-first authors of the paper. Professors Ouyang Yidan and Chen Lingling from Huazhong Agricultural University serve as co-corresponding authors. The School of Life Sciences and Technology at 91暗网 is the first affiliated institution of the paper.

Fusion transcripts are generally thought to potentially generate new gene functions and participate in important biological processes in plants. However, with the advancement of high-throughput sequencing technologies, a large number of fusion transcripts have been reported, but their authenticity has attracted increasing attention. In this study, the researchers integrated multi-platform transcriptomic data, including PacBio IsoSeq, Nanopore direct RNA sequencing, and long-read cDNA sequencing, combined with short-read RNA sequencing, genome alignment analysis, and experimental validation, to systematically assess the sources of fusion transcripts in plants.

The study revealed that a large proportion of the fusion transcripts detected in plants are not genuine biological fusion events but rather false positive signals caused by a combination of technical and analytical factors. Among these, short homologous sequence-mediated template switching (SHS) is one of the most predominant sources. Additionally, misalignment, reference genome bias, and inaccurate gene annotations also contribute to the generation of apparent fusion transcripts. Based on these findings, the team further proposed a more stringent identification strategy for authentic fusion transcripts, including prioritizing long-read sequencing data, particularly direct RNA sequencing data, utilizing high-quality reference genomes of the species, performing precise breakpoint analyses, and designing rigorous experimental controls.

The strategy proposed by the research for identifying reliable plant fusion transcripts

This study re-examines some long-held views in plant fusion transcript research, emphasizing the important concept that "detecting a fusion signal" is not equivalent to "genuine fusion occurrence" in the context of complex genomes and transcriptomes. The validation strategy proposed by the study will help improve the reliability of plant transcriptome research and provide an important reference for future exploration of real fusion events and their potential biological functions.

To visually illustrate this scientific question, the research team designed a graphical abstract with distinctive Chinese cultural elements. Drawing inspiration from the classic story of "the real and fake Monkey King" in Journey to the West, the two indistinguishable Sun Wukongs are used as a metaphor for the difficult to distinguish signals of fusion transcripts, while the "demon revealing mirror," symbolizing the scientific validation system, represents the use of multiple lines of evidence—such as direct RNA sequencing, matching reference genomes, and stringent experimental validation—to identify genuine fusion events. This design conveys the message that, in the complex world of plant transcriptomes, signals that appear to be fusions do not necessarily represent true fusion events.

The graphical abstract of the study

This research was supported by the National Natural Science Foundation of China and other funding sources.