Draft Genome Sequence of the Endophytic Bacterium Enterobacter spp. MR1, Isolated from Drought Tolerant Plant (Butea monosperma)

Parakhia, Manoj V.; Tomar, R. S.; Malaviya, Bipin J.; Dhingani, R. M.; Rathod, Visha M.; Thakkar, Jalpa; Golakiya, B. A.

doi:10.1007/s12088-013-0429-5

Cited by 10 publications

(5 citation statements)

References 6 publications

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“…The reference based approach was conducted on MIRA v. 4 82 , a software that maps read data against a consensus sequence of a reference assembly (simple mapping). MIRA has been useful for assembling complicated genomes with many repetitive sequences [83][84][85] . MIRA produces BAM files as output, which were subsequently used to generate consensus sequences in SAMTOOLS 86 .…”

Section: Methodsmentioning

confidence: 99%

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Serna-Sánchez

Pérez‐Escobar

Bogarín

et al. 2021

Sci Rep

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Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

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Section: Methodsmentioning

confidence: 99%

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Serna-Sánchez

Pérez‐Escobar

Bogarín

et al. 2021

Sci Rep

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“…To produce contiguous, linear plastid genome sequences we relied on a refence-based and de-novo approaches. The reference based approach was conducted on MIRA v. 4 84 , a software that maps read data against a consensus sequence of a reference assembly (simple mapping). MIRA has been useful for assembling complicated genomes with many repetitive sequences 85–87 .…”

Section: Methodsmentioning

confidence: 99%

“…The reference based approach was conducted on MIRA v. 4 84 , a software that maps read data against a consensus sequence of a reference assembly (simple mapping). MIRA has been useful for assembling complicated genomes with many repetitive sequences [85][86][87] . MIRA produces BAM files as output, which were subsequently used to generate consensus sequences in SAMTOOLS 88 .…”

Section: Plastid Genome Assembly and Annotationmentioning

confidence: 99%

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Serna-Sánchez

Pérez‐Escobar

Bogarín

et al. 2019

Preprint

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24 Recent phylogenomic analyses have solved evolutionary relationships between most of the 25 Orchidaceae subfamilies and tribes, yet phylogenetic relationships remain unclear within the 26 42 43 45 46 47 100, PP = 0.77-1.0), and only a few positions remained unresolved. Here, the relationship between 128 Codonorchidae+Orchideae was moderately supported (LBS = 86) together with that of 129 Cymbidiinae and the remaining Cymbidieae (LBS = 62). The monophyly of Nervilieae and 130 Triphoreae was moderately supported (LBS = 79), as well as the phylogenetic relationships of 131 Nervilieae+Triphoreae and the remainder of Epidendroideae (LBS = 75), and Epidendreae and 132 Coelia + Eria (LBS = 52) (Fig. 2). 133 134 2.3 Molecular characterisation of plastid genomes 135 Whole plastome sequences belonging to 97 species (11 sequenced here and 86 reported in 136 NCBI) were annotated for 75 protein-coding genes. Five additional genes were recovered when 137 concatenating this data matrix with the protein coding regions matrix used by Givnish 2 , giving a 138 6

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“…Some endophytic bacteria whose genomes have been sequenced include: eleven endophytic bacteria isolated from Poison Ivy (Toxicodendron radicans) (Tran et al, 2015), an endophytic bacterium Enterobacter sp. MR1, isolated from drought tolerant plant (Buteamonosperma) (Parakhia et al, 2014) and an endophytic bacterium isolated from poplar trees (Taghavi et al, 2009).…”

Section: Whole Genome Sequencing In Endophyte Researchmentioning

confidence: 99%

Endophytic Bacteria: Hidden Protective Associates of Plants against Biotic and Abiotic Stresses

2019

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An endophyte is a microorganism, usually bacterium or fungus, which lives within the internal tissue of a host plant, causing no apparent harm. Some characteristics of an endophyte include ability to promote plant growth and to confer plant tolerance to biotic and abiotic stresses. Endophytic bacteria spread across many phyla including the Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. Endophytic bacteria are recruited by hosts and they get attached to the surface and eventually find their way into the internal tissues where they spread to the intercellular spaces of host plants. These bacteria have been isolated and characterized from different plants. Currently, culture-independent methods such as sequencing of the 16S rRNA gene or metalogenomics are used for identification and characterization of endophytes. The mechanisms by which the endophyte-induced plant protection is brought about can be through direct and/or indirect methods. The direct strategy antagonizes phytopathogens by the production of chemical substances while the indirect mechanisms improve resistance of hosts to pathogens. Global gene expression studies on some common endophytic bacteria implicated these direct and indirect strategies of bacterial-induced protection. More research should be geared towards how the economic importance of endophytic bacteria could be utilized to enhance global food security.

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Draft Genome Sequence of the Endophytic Bacterium Enterobacter spp. MR1, Isolated from Drought Tolerant Plant (Butea monosperma)

Cited by 10 publications

References 6 publications

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Endophytic Bacteria: Hidden Protective Associates of Plants against Biotic and Abiotic Stresses

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