Genomics and Applied Biology 2024, Vol.15, No.2, 75-88 http://bioscipublisher.com/index.php/gab 78 studies (Li et al., 2020). The choice of species for comparison should be guided by the research question, phylogenetic relationships, and the availability of genomic data. For example, comparative genomics can be used to study evolutionarily conserved protein functions in marine microbes, providing insights into their adaptation and evolutionary history (Cordone et al., 2021). The inclusion of a diverse range of species, including non-model organisms, enhances the power of comparative analyses to uncover functional genomic elements and evolutionary patterns (Stone et al., 2005). By leveraging advanced sequencing technologies, bioinformatics tools, carefully selected data sources, and comparative genomics continues to expand our understanding of genome structure, function, and evolution across the tree of life. 4 Genome Structure and Organization of E. ulmoides 4.1 Overview of E. ulmoides genome E. ulmoides, a tree species known for its medicinal and industrial applications, has recently been the subject of extensive genomic research. A high-quality haploid chromosome-scale genome assembly was achieved using PacBio and Hi-C technologies, resulting in a significantly improved assembly quality compared to previous versions. The scaffold N50 increased 28-fold to 53.15 MB, and the repetitive sequence content increased by 158.24 MB, while the number of gaps decreased dramatically (Li et. al., 2020). The genome assembly anchored 92.87% of the 26,001 predicted protein-coding genes to 17 chromosomes, providing a robust foundation for further genomic studies (Table 1) (Li et. al., 2020). Additionally, a high-quality chromosome-level female genome was assembled, revealing 31,665 protein-coding genes and confirming two whole-genome duplication events (Du et al., 2023). Table 1 Statistics for the Eucommia genome and gene annotation (Adopted From Li et. al., 2020) Assembly Estimated genome size 1.02Gb Total assembly size 947.84Mb Number of contigs 564 N50 of contigs 13.16Mb Longest contigs 34.99Mb Sequence anchored to the Hi–C map 947.86Mb Number of scaffolds after Hi–C assembly 501 N50 of scaffolds after Hi–C assembly 53.15Mb Longest scaffold after Hi–C assembly 79.92Mb Estimated genome size 1.02Gb Total assembly size 947.84Mb Annotation GCcontent 0.3517 Number of genes 26001 Percentage of gene length in genome 16.84% Mean gene length 6138.21 Mean coding sequence length 1108.8 Mean exon number per gene 4.85 Mean exon length 228.56 Mean intron length 1305.93 rRNAs 2099 tRNAs 825 miRNAs 1032 snRNAs 875 Repeat content 62.50% 4.2 Comparative analysis with related species Comparative genomic analyses have provided insights into the evolutionary history of E. ulmoides. The chloroplast genome of E. ulmoides was compared with that of Aucuba japonica, confirming their sister
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