De novo genome assembly of Bacillus altitudinis 19RS3 and Bacillus altitudinis T5S-T4, two plant growth-promoting bacteria isolated from Ilex paraguariensis St. Hil. (yerba mate) Article Swipe
Iliana Julieta Cortese
,
María Lorena Castrillo
,
Andrea Liliana Onetto
,
Gustavo Ángel Bich
,
Pedro Darío Zapata
,
Margarita Ester Laczeski
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pone.0248274
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pone.0248274
Plant growth-promoting bacteria (PGPB) are a heterogeneous group of bacteria that can exert beneficial effects on plant growth directly or indirectly by different mechanisms. PGPB-based inoculant formulation has been used to replace chemical fertilizers and pesticides. In our previous studies, two endophytic endospore-forming bacteria identified as Bacillus altitudinis were isolated from roots of Ilex paraguariensis St. Hil. seedlings and selected for their plant growth-promoting (PGP) properties shown in vitro and in vivo . The purposes of this work were to assemble the genomes of B . altitudinis 19RS3 and T5S-T4, using different assemblers available for Windows and Linux and to select the best assembly for each strain. Both genomes were also automatically annotated to detect PGP genes and compare sequences with other genomes reported. Library construction and draft genome sequencing were performed by Macrogen services. Raw reads were filtered using the Trimmomatic tool. Genomes were assembled using SPAdes, ABySS, Velvet, and SOAPdenovo2 assemblers for Linux, and Geneious and CLC Genomics Workbench assemblers for Windows. Assembly evaluation was done by the QUAST tool. The parameters evaluated were the number of contigs ≥ 500 bp and ≥ 1000 bp, the length of the longest contig, and the N50 value. For genome annotation PROKKA, RAST, and KAAS tools were used. The best assembly for both genomes was obtained using Velvet. The B . altitudinis 19RS3 genome was assembled into 15 contigs with an N50 value of 1,943,801 bp. The B . altitudinis T5S-T4 genome was assembled into 24 contigs with an N50 of 344,151 bp. Both genomes comprise several genes related to PGP mechanisms, such as those for nitrogen fixation, iron metabolism, phosphate metabolism, and auxin biosynthesis. The results obtained offer the basis for a better understanding of B . altitudinis 19RS3 and T5S-T4 and make them promissory for bioinoculant development.
Related Topics
Concepts
Genome
Biology
Contig
Sequence assembly
Bacterial genome size
Genomics
Computational biology
Genetics
Gene
Transcriptome
Gene expression
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1371/journal.pone.0248274
- OA Status
- gold
- Cited By
- 16
- References
- 68
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W3135188462Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1371/journal.pone.0248274Digital Object Identifier
- Title
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De novo genome assembly of Bacillus altitudinis 19RS3 and Bacillus altitudinis T5S-T4, two plant growth-promoting bacteria isolated from Ilex paraguariensis St. Hil. (yerba mate)Work title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2021Year of publication
- Publication date
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2021-03-11Full publication date if available
- Authors
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Iliana Julieta Cortese, María Lorena Castrillo, Andrea Liliana Onetto, Gustavo Ángel Bich, Pedro Darío Zapata, Margarita Ester LaczeskiList of authors in order
- Landing page
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https://doi.org/10.1371/journal.pone.0248274Publisher landing page
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.1371/journal.pone.0248274Direct OA link when available
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Genome, Biology, Contig, Sequence assembly, Bacterial genome size, Genomics, Computational biology, Genetics, Gene, Transcriptome, Gene expressionTop concepts (fields/topics) attached by OpenAlex
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16Total citation count in OpenAlex
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2025: 3, 2024: 4, 2023: 6, 2022: 2, 2021: 1Per-year citation counts (last 5 years)
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68Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.seedlings | 57 |
| abstract_inverted_index.sequences | 119 |
| abstract_inverted_index.services. | 134 |
| abstract_inverted_index.PGPB-based | 24 |
| abstract_inverted_index.annotation | 199 |
| abstract_inverted_index.assemblers | 92, 152, 161 |
| abstract_inverted_index.beneficial | 13 |
| abstract_inverted_index.endophytic | 41 |
| abstract_inverted_index.evaluation | 165 |
| abstract_inverted_index.identified | 44 |
| abstract_inverted_index.indirectly | 20 |
| abstract_inverted_index.parameters | 173 |
| abstract_inverted_index.promissory | 294 |
| abstract_inverted_index.properties | 65 |
| abstract_inverted_index.sequencing | 129 |
| abstract_inverted_index.SOAPdenovo2 | 151 |
| abstract_inverted_index.Trimmomatic | 141 |
| abstract_inverted_index.altitudinis | 47, 86, 220, 238, 287 |
| abstract_inverted_index.fertilizers | 33 |
| abstract_inverted_index.formulation | 26 |
| abstract_inverted_index.mechanisms, | 260 |
| abstract_inverted_index.mechanisms. | 23 |
| abstract_inverted_index.metabolism, | 268, 270 |
| abstract_inverted_index.pesticides. | 35 |
| abstract_inverted_index.bioinoculant | 296 |
| abstract_inverted_index.construction | 125 |
| abstract_inverted_index.development. | 297 |
| abstract_inverted_index.automatically | 111 |
| abstract_inverted_index.biosynthesis. | 273 |
| abstract_inverted_index.heterogeneous | 6 |
| abstract_inverted_index.understanding | 283 |
| abstract_inverted_index.paraguariensis | 54 |
| abstract_inverted_index.growth-promoting | 1, 63 |
| abstract_inverted_index.endospore-forming | 42 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 89 |
| corresponding_author_ids | https://openalex.org/A5062186276, https://openalex.org/A5073623153, https://openalex.org/A5039727445, https://openalex.org/A5026200431, https://openalex.org/A5026693778, https://openalex.org/A5002506913 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 6 |
| corresponding_institution_ids | https://openalex.org/I151201029, https://openalex.org/I17994240 |
| citation_normalized_percentile.value | 0.76770834 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |