Whole genome sequence data of Paenibacillus tyrfis YSS-72.2.G2, a chitinolytic bacterium newly isolated from a National Park of Vietnam

Paenibacillus tyrfis YSS-72.2.G2 is a soil chitinolytic bacterium newly isolated from Yok Don National Park of Vietnam. Our previous results demonstrated that this bacterium was a strong chitinase producer, possessed plant growth promotion, and had high activity against phytopathogenic fungi. However, the genome sequence of this strain is unknown. This work aimed to establish data on the genome sequence of P. tyrfis YSS-72.2.G2 and its chitinase system for further assessments regarding biocontrol mechanisms and plant growth promotion. The P. tyrfis YSS-72.2.G2 genome is 7,756,121 bp in size and 53.4 % G+C. It harbors 6,948 protein-coding genes, 5 rRNA genes, 82 tRNA genes, 4 ncRNA genes, 99 pseudo genes, and 5 CRISPR arrays. Genes involved in heavy metal resistance (5 genes), iron acquisition (5 genes), and IAA biosynthesis (5 genes) were predicted in the genome. There were 234 carbohydrate-active enzymes found in this genome; among them, 13 enzymes possibly possess activity against phytopathogens. Chitin-degrading system of YSS-72.2.G2 contains 15 chitinolytic enzymes. In addition, 28 gene clusters coding for antimicrobial metabolites were identified, of these, 14 show no sequence similarities to the known clusters. The raw sequences were submitted to the Sequence Read Archive on the National Center for Biotechnology Information with accession number PRJNA946889. The genome sequence of P. tyrfis YSS-72.2.G2 has been deposited in the DDBJ/GenBank/EMBL database under accession number NZ_BSDJ00000000. Data provide insight into the genomic information of strain YSS-72.2.G2. This is the first work reporting data on the genome sequence of P. tyrfis isolated from Vietnam.


a b s t r a c t
Paenibacillus tyrfis YSS-72.2.G2 is a soil chitinolytic bacterium newly isolated from Yok Don National Park of Vietnam.Our previous results demonstrated that this bacterium was a strong chitinase producer, possessed plant growth promotion, and had high activity against phytopathogenic fungi.However, the genome sequence of this strain is unknown.This work aimed to establish data on the genome sequence of P. tyrfis YSS-72.2.G2 and its chitinase system for further assessments regarding biocontrol mechanisms and plant growth promotion.The P. tyrfis YSS-72.2.G2 genome is 7,756,121 bp in size and 53.4 % G + C. It harbors 6,948 protein-coding genes, 5 rRNA genes, 82 tRNA genes, 4 ncRNA genes, 99 pseudo genes, and 5 CRISPR arrays.Genes involved in heavy metal resistance (5 genes), iron acquisition (5 genes), and IAA biosynthesis (5 genes) were predicted in the genome.There were 234 carbohydrate-active enzymes found in this genome; among them, 13 enzymes possibly possess activity against phytopathogens.Chitin-degrading system of YSS-72.2.G2 contains 15 chitinolytic enzymes.In addition, 28 gene clusters coding for antimicrobial metabolites were identified, of these, 14 show no sequence similarities to the known clusters.The raw sequences were submitted to the Sequence Read Archive on the National Center for Biotechnology Information with accession number PRJNA946889.

Value of the Data
• Data elucidates the biocontrol ability and plant-growth promotion of P. tyrfis YSS-72.2.G2 isolated from the Central Highlands of Vietnam.• Data provides an insight into the genomic information of chitinolytic bacterium P. tyrfis YSS-72.2.G2.• Data can be useful for comparing the genome sequence of P. tyrfis YSS-72.2.G2 isolated from the Central Highlands and others.• Data can be valuable for further examinations concerning crop production using gene expression approaches.

Background
The chitinolytic bacterium, P. tyrfis YSS-72.2.G2, was newly isolated from the soil sample collected from Yok Don National Park in the Central Highlands region of Vietnam.Experimental data showed that this bacterium exhibited high activities of chitinase, protease, cellulase, and amylase; produced indole acetic acid (IAA) and siderophore; and displayed high antagonistic activity (65.67 % inhibition) against phytopathogenic fungi [1] .To the best of our knowledge, no genome sequences of P. tyrfis have been reported from Vietnam to date.In addition, experimental studies about the chitinase system, extracellular enzymes, and secondary metabolites of P. tyrfis have been undocumented.This work aims to establish data on the genome sequence of P. tyrfis YSS-72.2.G2 and its chitinase system to provide genomic information for further evaluations regarding biofertilizer and biocontrol mechanisms.

Data Description
The genome of strain YSS-72.2.G2 is 7,756,121 bp in length and has a 53.4 % G + C content generated from 130 contigs ( Fig. 1 ).Of these contigs, the maximum size was 505,185 bp, and the minimum was 207 bp.DFAST analysis showed that 6,948 protein-coding genes, 5 rRNA genes, 82 tRNA genes, 4 ncRNA genes, 99 pseudo genes, and 5 CRISPR arrays were predicted from the genome.Among the predicted proteins, there are 2,922 deduced hypothetical proteins and 4,018 functional proteins ( Table 1 ).The raw sequences were submitted to the Sequence Read Archive on the National Center for Biotechnology Information with accession number PRJNA946889 and can be accessed at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA946889 .The genome sequence of P. tyrfis YSS-72.2.G2 has been deposited in the DDBJ/GenBank/EMBL database under accession number NZ_BSDJ0 0 0 0 0 0 0 0 and can be accessed at https://www.ncbi.nlm.nih.gov/nuccore/NZ_BSDJ0 0 0 0 0 0 0 0.1 .
Bacterial GH18 chitinases are grouped into three subfamilies (A, B, and C).These subfamilies play different properties in the hydrolysis of chitin.Subfamily A chitinases usually show high chitinase activity against crystalline chitin compared to subfamilies B and C [2] .As shown in Fig. 3 , seven chitinases of strain YSS-72.2.G2 were grouped into subfamily A, and two chitinases (PtChiC and PtChiD) were clarified into subfamily B.
It was demonstrated that plant family 19 chitinases are subdivided into three classes (I, II, and IV) based on the arrangement of the loop structure and organization of the domain.Differences in the loop structure of chitinases can affect the substrate binding activity of each chitinase, and therefore, chitinases may show a difference in enzymatic properties and biological function.Bacterial GH19 chitinases have no loops I, II, V, and the C-terminal loop [3][4] .As shown in Fig. 4 , the loop structure of PtChiB of strain YSS-72.2.G2 was different from that of reported plant and bacterial GH19 chitinases.The catalytic domain of PtChiB has loops II, III, IV, and V compared to characterized bacterial GH19 chitinases, which contain loops III and IV.Compared to GH19 chitinases of plant classes I and II, which have loops I, II, III, IV, V, and the C-terminal, the catalytic domain of PtChiB lacks only loop I.
The ability to produce antimicrobial metabolites is important for the biocontrol of plant pathogens.Antimicrobial metabolites are clarified into three classes: polyketides, nonribosomal peptides, and ribosomally synthesized post-translationally modified peptides [5] .This work found 28 gene clusters responsible for antimicrobial metabolite biosynthesis from the P. tyr- fis YSS-72.2.G2 genome ( Table 2 ).Among them, 14 show no identities to the known clusters ( Table 3 and Fig. 5 ).

Genomic DNA extraction, library preparation, and genomic sequencing
Bacterial cells of P. tyrfis YSS-72.2.G2 were cultured on Luria-Bertani agar plate at 30 °C for 24 h.The extraction of the genomic DNA was performed using the QIAamp DNA mini kit (Qiagen, Germany), according to the instructions of the manufacturer.High-quality DNA (OD 260/280 = 1.8 to 2.0) was used for the next steps.Genomic libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, USA) per the manufacturer's instructions.Finally, prepared libraries were used for sequencing (2 ×150 Paired-End) using V3 chemistry (Illumina, USA) with the Illumina MiSeq platform [1] .

Genomic assembly, functional annotation, and data analysis
Guppy 3.0.3was used for base calling in order to get quick sequencing reads.Trimmomatic 0.36 [6] was used to trim the reads.Unicycler 0.4.8 [7] was used to assemble the edited sequences, and Pilon 1.23 [8] was used to polish them.Ultimately, the web-based annotation pipeline known as DFAST [9] was used to automatically annotate the draft genome sequence.The draft genome was submitted to the DNA Data Bank of Japan (DDBJ) database.CAZymes were analyzed using the dbCAN2 metaserver [10] .Phylogeny of deduced chitinases was analyzed using MEGA 6.0 software [11] .Putative gene clusters responsible for antimicrobial metabolite biosynthesis were predicted using antiSMASH 6.0 [12] .

Limitations
Not applicable.

Ethics Statement
The current work does not involve human subjects, animal experiments, or any data collected from social media platforms.
2.G2.This is the first work reporting data on the genome sequence of P. tyrfis isolated from Vietnam.© 2024 The Author(s).Published by Elsevier Inc.