Protocols

Standard Illumina library preparation using Nextera XT kit followed by paired-end sequencing on HiSeq 2500 platform to generate comprehensive metagenomic datasets from phylloplane microbial communitie...

Manual identification and curation of large genome fragments using GC content, coverage patterns, and taxonomic profiles to assemble complete extrachromosomal genomes.

Comprehensive Hidden Markov Model analysis of metagenomic sequences to identify and quantify metabolic functions across biogeochemical pathways. Uses both standardized TIGR-FAM and custom HMM database...

Construction of phylogenetic trees using concatenated ribosomal protein genes to determine evolutionary relationships. Uses IQ-TREE with maximum likelihood approach and bootstrap support.

Taxonomic classification of microbial communities using ribosomal protein S3 (rpS3) marker genes identified through Hidden Markov Models and phylogenetic analysis.