Triticeae Genomics and Genetics, 2024, Vol.15, No.2, 66-76 http://cropscipublisher.com/index.php/tgg 69 gene validation (Pang et al., 2020). Additionally, the development of ORFeome libraries, such as the one for Zymoseptoria tritici, enables the functional characterization of genes and their encoded proteins, facilitating the study of gene function and interactions (Chaudhari et al., 2019). Advances in genome engineering technologies, such as CRISPR/Cas, further enhance the potential for functional genomics studies and the development of improved Triticeae varieties (Hensel, 2019). Figure 1 Challenges and strategies for homolog inference in theTriticeaetribe in the pangenomic era (Adopted from Chen et al., 2020) Image caption: (A) Frequent polyploidization events shaped the complex relationships between Triticeae species; (B) Multiple-level scenarios for pairwise comparison of assemblies as centered by IWGSC RefSeqv1.1; Triticum-Aegilops is considered a combined genus; (C) Hierarchical organization of currently published high-quality genome assemblies that are available in the TGT database; (D) Polypoid genomes are decomposed into multiple diploid subgenomes for pairwise comparison; (E) A model showing that each assembly of variety 1 and variety 2 has one well-annotated gene (filled box); these genes would be computationally considered orthologs derived from one gene in an ancient species; The unfilled box indicates a duplicated pseudogene that is not annotated or has lost its function; (F) A modified model in which the assembly of the middle species is available and an ancient gene duplication event followed by reciprocal loss of function was uncovered. Gene A1 and gene a2 originated from the paralogous genes Am and gene am in the middle species, respectively; (G) A model showing that gene loss events or incomplete gene annotations hinder accurate orthology inference between closely related genomes (Adopted from Chen et al., 2020) By leveraging these genomic resources and tools, researchers can enhance the productivity and resilience of Triticeae crops, addressing the challenges posed by a growing global population and changing environmental conditions.
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