Re-annotation of the Liriodendron chinense genome identifies novel genes and improves genome annotation quality

Liriodendron chinense is a very popular tree used in landscaping because of its beautiful flowers and unique leaf shape. Although the L. chinense genome was released in 2018 based on PacBio long reads and genetic linkage map and provides a valuable resource for gene function discovery and transcriptome analyses of L. chinense. Yet, that version of the L. chinense genome relied on ab initio annotation and a small amount of transcriptome data, and lacks 5′ UTRs and 3′ UTRs and alternative splicing (AS) annotation; hence, it is imperative that an improved annotation be sought. Herein, we re-annotated the structure and function of genes across the entire L. chinense nuclear genome based on PacBio long reads and Illumina short reads retrieved from near-round organization types. This updated annotation of the L. chinense genome, Lchi2.1, includes a total of 42,831 gene models with a high proportion (92.8%) of complete BUSCOs. Among the Lchi2.1 annotation, 21,324 genes were modified, 15,770 novel genes were added, 14,851 genes were augmented with information on the 5′ UTRs and 3′ UTRs, and 6751 genes were found as alternatively spliced isoforms at the whole-genome scale. Additionally, we re-analyzed the transcriptome data across various stages of leaf shape development for L. chinense, founding many genes enriched to post-embryonic plant morphogenesis, plant organ formation, and anatomical structure formation involved in morphogenesis, which suggests these genes could be related to leaf morphological processes. Overall, the updated annotation of the L. chinense genome presented in this study will contribute to gene functional studies in L. chinense and its comparative genomic analysis with related plant species.