Bt Research 2024, Vol.15, No.1, 20-29 http://microbescipublisher.com/index.php/bt 22 insecticidal proteins they produce. This diversity is often attributed to horizontal gene transfer, which allows Bt strains to acquire new genetic elements, including plasmids and transposons. For instance, the genome of Bt strain HS18-1 contains nine plasmids, encoding multiple virulence factors and insertion sequences (Sun et al., 2021). The genetic diversity of Bt strains can be assessed using techniques such as Multi-Locus Sequence Typing (MLST) and Random Amplified Polymorphic DNA (RAPD) analysis. A study on Bt strains from Kuwait revealed significant genetic variation among local isolates, highlighting the unique DNA patterns of different strains (Qasem et al., 2015). Furthermore, evolutionary genomics studies have shown that Bt strains possess a high degree of genomic plasticity, enabling them to adapt to various ecological niches and host organisms. 3 Methods for Comparative Genomic Analysis 3.1 Genomic sequencing techniques Genomic sequencing is a fundamental step in comparative genomic analysis, providing the raw data necessary for subsequent bioinformatics and comparative studies. Various sequencing technologies have been employed to sequence the genomes of Bacillus thuringiensis (Bt) strains. For instance, next-generation sequencing (NGS) technologies, such as those used in the sequencing of Bt X022, offer high-throughput capabilities and have been instrumental in oBtaining comprehensive genomic data (Quan et al., 2016). Additionally, PacBio RS II sequencers have been utilized for complete genome sequencing, as demonstrated in the studies of Bt strain BM-Bt15426 and Bt ATCC 10792, providing long-read sequences that are crucial for assembling complex genomes and identifying plasmids (Chelliah et al., 2019). 3.2 Bioinformatics tools and software Bioinformatics tools and software are essential for analyzing and interpreting genomic data. The RAST server is commonly used for functional annotation of sequenced genomes, as seen in the analysis of Bt X022 (Quan et al., 2016). Other tools, such as antiSMASH, are employed for in silico investigation of biosynthetic gene clusters, which can predict the production of biopesticidal metabolites (Adeniji et al., 2021). Comparative genomic studies also utilize phylogenomic analyses to clarify taxonomic relationships and evolutionary mechanisms. For example, phylogenomic trees based on core gene sequences have been used to distinguish between Bacillus cereus and Bt strains, proposing the recognition of two Bt genomovars (Baek et al., 2019). Additionally, tools for plasmid content analysis and the identification of virulence factors and antibiotic resistance genes are crucial for understanding the pathogenic potential and evolutionary adaptations of Bt strains (Bolotin et al., 2017; Liu et al., 2017). 3.3 Data integration and comparative approaches Integrating genomic data with other omics data, such as proteomics, enhances the understanding of the functional implications of genomic variations. Comparative analyses of genomic and proteomic data have revealed discrepancies between genome annotations and protein expression profiles, highlighting the importance of multi-omics approaches. For instance, in Bt 4.0718, certain genes related to insect pathogenicity were not detected in the proteomic data, suggesting gene silencing or low expression levels (Rang et al., 2015). Comparative genomic analyses also focus on identifying evolutionary mechanisms, such as the role of mobile genetic elements, prophages, and plasmids in genome plasticity and adaptation. Studies have shown that prophages can mobilize chromosomally encoded Cry-toxins, contributing to the rapid evolution and adaptation of Bt strains. Furthermore, comparative genomic studies of Bt strains in bacterial consortia have provided insights into their cooperative mechanisms and responses to environmental factors, which are essential for optimizing their use in biotechnological applications (Jia et al., 2016). 4 Genomic Features of Bt Strains 4.1 Core and pan-genome analysis The core and pan-genome analysis of Bacillus thuringiensis (Bt) strains reveals significant insights into their genetic diversity and evolutionary mechanisms. Comparative genomic studies have shown that Bt strains possess
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