Draft genome assembly of Lacticaseibacillus paracasei MSR2 isolated from Bangladesh

TL;DR

This paper presents the draft genome of Lacticaseibacillus paracasei MSR2, a yogurt-isolated strain from Bangladesh.

Contribution

The novel contribution is the draft genome assembly of a newly isolated Lacticaseibacillus paracasei strain from Bangladesh.

Findings

The genome is 3,085,195 base pairs long and assembled into 132 contigs.

It encodes 2,903 predicted proteins.

Abstract

This study reports the draft genome sequence of Lacticaseibacillus paracasei MSR2, a strain isolated from yogurt in Bangladesh in 2024. The genome consists of a 3,085,195 base pair chromosome assembled into 132 contigs, encoding 2,903 predicted proteins.

Tables

TABLE 1. Genomic features of Lacticaseibacillus paracasei MSR2

Description of source
Location	Kishoreganj, Bangladesh
Time	2024
Type	Yogurt
Sequencing summary
Coverage	111.8×
Total bases	3,074,103
GC content	46.27%
Reads	865,257
Assembly report
Contigs	132
GC content	46.5%
Contig L50	10
Genome length	3.1 Mb
Contig N50	98.4 kb
Annotation report
Genes	3,079
CDs	2,903
CDs (without protein)	105
ncRNAs	3
tRNA	58

Full text

ANNOUNCEMENTS

Lacticaseibacillus paracasei, a probiotic commonly present in dairy products, supports host health by offering numerous benefits (1, 2). L. paracasei has also been reported to exhibit antifungal and antibacterial activities (3). This study presents the draft genome assembly of L. paracasei MSR2.

A yogurt sample was collected from Kishoreganj, Bangladesh, in February 2024. The sample was spread onto De Man–Rogosa–Sharpe (MRS) agar (HiMedia, India) and incubated overnight at 37°C. A single colony from the pure culture was inoculated into MRS broth and incubated overnight at 37°C with shaking at 120 rpm. One milliliter of broth was used for genomic DNA extraction. DNA extraction was carried out using the Qiagen DNeasy Blood & Tissue Mini Kit (250) following the manufacturer’s protocol. After cell lysis, the sample was centrifuged at 14,000 rpm for 5 minutes to remove cellular debris. The DNA was further purified using the CDC PULSENET Total DNA Extraction protocol using the same kit. DNA quality was assessed using a Nanodrop spectrophotometer and a Qubit 4.0 Fluorometer. For Qubit measurements, a working solution was prepared by mixing Qubit Reagent and Qubit Buffer in a 1:200 ratio. Whole-genome sequencing was performed at the Genomic Centre, icddr’b, Mohakhali, Dhaka, Bangladesh. The DNA fragments were size selected using AMPure XP beads to isolate those within the desired range, typically 200–300 base pairs (bp) for standard Illumina sequencing libraries. The library for sequencing was prepared using the Illumina DNA Prep Reagent Kit and an automated liquid handler (epMotion 5075) for tagging the adapters with DNA fragments. After library preparation, sequencing was carried out using the Illumina MiSeq platform with paired-end 2 × 150 bp reads following the standard protocol provided by the manufacturer. Illumina’s bcl2fastq software version 2.20.0 (https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html) was utilized with default parameters to demultiplex the raw reads and convert them into FASTQ format. For further downstream analysis, raw paired-end reads from the MiSeq platform were used.

FASTQC version 0.9.1 (www.bioinformatics.bbsrc.ac.uk/projects/fastqc) was employed to assess the quality of the raw data (4). Sickle version 1.3 tool was used to trim the paired-end sequence, where the trimming length was set to 20 (5). For assembly, Spades version 4.0.0 was applied with default parameters (6). The assembly was polished using Pilon version 1.24 (7). The species was identified using a whole genome-based taxonomic analysis in the Type (Strain) Genome Server (https://tygs.dsmz.de). Default parameters were used for all software unless otherwise specified.

The genome of L. paracasei MSR2 is 3,085,195 bp long with a GC content of 46.5%. The assembly contains 132 contigs with a coverage of 111.8×. A total of 3,019 genes were predicted, of which 2,852 are protein-coding genes. The details of genomic features are presented in Table 1.