Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard
Abstract We analyzed the genome sequence of an endophytic bacterial strain Pseudomonas putida TJI51 isolated from mango bark tissues. Next generation DNA sequencing and short read de novo assembly generated the 5,805,096 bp draft genome of P. putida TJI51. Out of 6,036 protein coding genes in P. put...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Sociedade Brasileira de Genética
|
| Series: | Genetics and Molecular Biology |
| Subjects: | |
| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000300465&lng=en&tlng=en |
| _version_ | 1819103919412871168 |
|---|---|
| author | Huma Asif David J. Studholme Asifullah Khan M. Aurongzeb Ishtiaq A. Khan M. Kamran Azim |
| author_facet | Huma Asif David J. Studholme Asifullah Khan M. Aurongzeb Ishtiaq A. Khan M. Kamran Azim |
| author_sort | Huma Asif |
| collection | DOAJ |
| description | Abstract We analyzed the genome sequence of an endophytic bacterial strain Pseudomonas putida TJI51 isolated from mango bark tissues. Next generation DNA sequencing and short read de novo assembly generated the 5,805,096 bp draft genome of P. putida TJI51. Out of 6,036 protein coding genes in P. putida TJI51 sequences, 4,367 (72%) were annotated with functional specifications, while the remaining encoded hypothetical proteins. Comparative genome sequence analysis revealed that the P. putida TJI51genome contains several regions, not identified in so far sequenced P. putida genomes. Some of these regions were predicted to encode enzymes, including acetylornithine deacetylase, betaine aldehyde dehydrogenase, aldehyde dehydrogenase, benzoylformate decarboxylase, hydroxyacylglutathione hydrolase, and uroporphyrinogen decarboxylase. The genome of P. putida TJI51 contained three nonribosomal peptide synthetase gene clusters. Genome sequence analysis of P. putidaTJI51 identified this bacterium as an endophytic resident. The endophytic fitness might be linked with alginate, which facilitates bacterial colonization in plant tissues. Genome sequence analysis shed light on the presence of a diverse spectrum of metabolic activities and adaptation of this isolate to various niches. |
| first_indexed | 2024-12-22T01:58:06Z |
| format | Article |
| id | doaj.art-5bd098809f8e4b5eb3023f0575d854ee |
| institution | Directory Open Access Journal |
| issn | 1678-4685 |
| language | English |
| last_indexed | 2024-12-22T01:58:06Z |
| publisher | Sociedade Brasileira de Genética |
| record_format | Article |
| series | Genetics and Molecular Biology |
| spelling | doaj.art-5bd098809f8e4b5eb3023f0575d854ee2022-12-21T18:42:43ZengSociedade Brasileira de GenéticaGenetics and Molecular Biology1678-468539346547310.1590/1678-4685-GMB-2015-0186S1415-47572016000300465Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchardHuma AsifDavid J. StudholmeAsifullah KhanM. AurongzebIshtiaq A. KhanM. Kamran AzimAbstract We analyzed the genome sequence of an endophytic bacterial strain Pseudomonas putida TJI51 isolated from mango bark tissues. Next generation DNA sequencing and short read de novo assembly generated the 5,805,096 bp draft genome of P. putida TJI51. Out of 6,036 protein coding genes in P. putida TJI51 sequences, 4,367 (72%) were annotated with functional specifications, while the remaining encoded hypothetical proteins. Comparative genome sequence analysis revealed that the P. putida TJI51genome contains several regions, not identified in so far sequenced P. putida genomes. Some of these regions were predicted to encode enzymes, including acetylornithine deacetylase, betaine aldehyde dehydrogenase, aldehyde dehydrogenase, benzoylformate decarboxylase, hydroxyacylglutathione hydrolase, and uroporphyrinogen decarboxylase. The genome of P. putida TJI51 contained three nonribosomal peptide synthetase gene clusters. Genome sequence analysis of P. putidaTJI51 identified this bacterium as an endophytic resident. The endophytic fitness might be linked with alginate, which facilitates bacterial colonization in plant tissues. Genome sequence analysis shed light on the presence of a diverse spectrum of metabolic activities and adaptation of this isolate to various niches.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000300465&lng=en&tlng=enMangifera indicabacterial genomicsplant-associated bacteriaendophyte |
| spellingShingle | Huma Asif David J. Studholme Asifullah Khan M. Aurongzeb Ishtiaq A. Khan M. Kamran Azim Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard Genetics and Molecular Biology Mangifera indica bacterial genomics plant-associated bacteria endophyte |
| title | Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard |
| title_full | Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard |
| title_fullStr | Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard |
| title_full_unstemmed | Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard |
| title_short | Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard |
| title_sort | comparative genomics of an endophytic pseudomonas putida isolated from mango orchard |
| topic | Mangifera indica bacterial genomics plant-associated bacteria endophyte |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000300465&lng=en&tlng=en |
| work_keys_str_mv | AT humaasif comparativegenomicsofanendophyticpseudomonasputidaisolatedfrommangoorchard AT davidjstudholme comparativegenomicsofanendophyticpseudomonasputidaisolatedfrommangoorchard AT asifullahkhan comparativegenomicsofanendophyticpseudomonasputidaisolatedfrommangoorchard AT maurongzeb comparativegenomicsofanendophyticpseudomonasputidaisolatedfrommangoorchard AT ishtiaqakhan comparativegenomicsofanendophyticpseudomonasputidaisolatedfrommangoorchard AT mkamranazim comparativegenomicsofanendophyticpseudomonasputidaisolatedfrommangoorchard |