Publication: Comprehensive genome assembly and functional annotation of escherichia coli using next generation sequencing data
Date
2026-01
Authors
Nor, Aiman Rusyaidi Mohd
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Abstract
Escherichia coli is widely used as an indicator of fecal contamination in aquatic
environments and serves as an important reservoir of antimicrobial resistance genes,
particularly extended-spectrum β-lactamase (ESBL). This study aimed to perform
comprehensive genome assembly and functional annotation of environmental ESBLproducing
E.coli isolates obtained from Sungai Klang and Sungai Terengganu using
next-generation sequencing data. Raw Illumina paired-end sequencing reads for 68 E.
coli strains, generated by the National Hydraulic Research Institute of Malaysia
(NAHRIM), were subjected to quality assessment and preprocessing to remove lowquality
and short reads. De novo genome assembly was conducted using SPAdes and
Unicycler, followed by comparative assembly quality evaluation using QUAST. Gene
prediction and functional annotation were performed using Prokka, and functional
interpretation was further supported by Gene Ontology (GO) analysis.The results
showed variation in raw read quality among the datasets. Following trimming and
filtering, the total number of reads decreased, with total clean reads being lower than
the initial raw reads due to the removal of low-quality bases, short sequences, and
contaminant reads, thereby improving overall data quality. Comparative analysis
revealed that SPAdes assemblies were more fragmented and exhibited larger total
assembly lengths, resulting in higher predicted coding sequences, rRNA, and tRNA
counts compared to Unicycler assemblies. GO analysis indicated enrichment of
functional categories related to membrane components, transport activity,
transcriptional regulation, stress response, and antibiotic resistance, highlighting
mechanisms that support environmental survival, pathogenicity, and antimicrobial
resistance. Overall, this study provides valuable genomic insights into environmental
ESBL-producing E.coli and underscores the importance of assembly strategy selection
for accurate genome annotation and public health surveillance.