Tree Genetics and Molecular Breeding 2024, Vol.14, No.2, 69-80 http://genbreedpublisher.com/index.php/tgmb 71 microarray analyses and protein interaction data (Kemmeren et al., 2002; Troyanskaya et al., 2003). The complexity of the poplar genome, with its large number of paralogous genes and transposable elements, further complicates the annotation process (Lescot et al., 2004). 3.3 Advances in computational tools for genome annotation Recent advances in computational tools have significantly improved the accuracy and efficiency of genome annotation. Tools like GenoCanyon use unsupervised statistical learning to integrate multiple computational and experimental annotations, predicting functional regions in the genome with high accuracy (Lu et al., 2015). The development of semi-automated methods, such as SamPler, allows for the optimization of annotation algorithms by selecting the best parameters based on manual curation of a sample set of genes (Cruz et al., 2019). Additionally, bioinformatics enrichment tools categorize and analyze large gene lists to identify biological processes relevant to the study, enhancing the functional annotation of genes (Huang et al., 2008). These advancements provide powerful resources for annotating the poplar genome and understanding its functional genomics. 4 Case Studies 4.1 Detailed analysis of key functional genes in poplar The analysis of key functional genes in poplar has been significantly advanced through various genomic studies. For instance, a comprehensive genome-wide analysis of structural variation in three intercrossable poplar species (Populus nigra, Populus deltoides, and Populus trichocarpa) identified numerous insertions and deletions (INDELs) and copy number variations (CNVs) affecting thousands of genes. These structural variations were found to be associated with transposable elements and stress response genes, providing insights into the functional dynamics of the poplar genome (Figure 1) (Pinosio et al., 2016). Figure 1 Genomic distribution of INDELs and genic CNVs (Adopted from Pinosio et al., 2016) Image caption: The number of deletions (dark blue track, y axes range = 0-20), insertions (blue track, y axes range = 0-40), genic CNVs (yellow track, y axes range = 0-15), annotated genes (red track, y axes range = 0-80), and the repetitiveness of the genome (green track, y axes range = 0-10) are represented in windows of 250 kb along the 19 Populus trichocarpa chromosomes (outer gray bars). Predicted centromeric regions are highlighted in red (Adopted from Pinosio et al., 2016) Pinosio et al. (2016) demonstrated structural variations in the poplar genome, which are predominantly concentrated in regions of low gene density and closely associated with transposon activity. Genes affected by structural variations exhibit lower expression levels than average, and these genes have higher dN/dS ratios,
RkJQdWJsaXNoZXIy MjQ4ODYzMg==