NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Lemoine, Frédéric; Correia, Damien; Lefort, Vincent; Doppelt-Azeroual, Olivia; Mareuil, Fabien; Cohen-Boulakia, Sarah; Gascuel, Olivier

doi:10.1093/nar/gkz303

Cited by 605 publications

(436 citation statements)

References 33 publications

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“…The best fitting model (GY+F+I+G4) was determined by ModelFinder (Kalyaanamoorthy et al, 2017) as implemented in IQ-TREE according to the Akaike information criterion (AIC), and Bayesian information criterion (BIC). Maximum likelihood (ML) analyses were performed with IQ-TREE (Nguyen et al, 2015) using the ultrafast bootstrap approximation (UFBoot; Hoang et al, 2018) with 1,000 replicates and the SH-like approximate likelihood ratio test (SH-aLRT), also with 1,000 bootstrap replicates, and TreeDyn was used for further enhancement of phylogenetic tree analysis (Dereeper et al, 2008; Lemoine et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

Mehmood

Abdullah

Ubaid

et al. 2020

Preprint

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The genus Nicotiana of the family Solanaceae, commonly referred to as tobacco plants, are a group cultivated as garden ornamentals. Besides their use in the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history, which is tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species, namely N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes showed typical quadripartite structure, consisting of a pair of inverted repeats (IR) regions (25,323–25,369 bp each) separated by a large single copy (LSC) region (86,510 –86,716 bp) and a small single copy (SSC) region (18,441–18,555 bp). Comparative analyses of Nicotiana plastid genomes showed similar GC content, gene content, codon usage, simple sequence repeats, oligonucleotide repeats, RNA editing sites and substitutions with currently available Solanaceae genomes sequences. We identified twenty highly polymorphic regions mostly belonging to intergenic spacer regions (IGS), which could be appropriate for the development of robust and cost-effective markers to infer the phylogeny of genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. The relaxed molecular clock analyses estimated that the speciation event between N. rustica and knightiana appeared 0.56 Ma (HPD 0.65–0.46). The biogeographical analysis showed a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicated that four genes involved in different plastid functions, such as DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations of the following genes might have contributed to the survival and better adaptation during the evolutionary history of tobacco species.

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Section: Methodsmentioning

confidence: 99%

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

Mehmood

Abdullah

Ubaid

et al. 2020

Preprint

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“…Arabidopsis protein sequences were extracted from TAIR database (https://www.arabidopsis.org) and protein sequences from Lupinus angustifolius, Medicago truncatula, Cicer arietinum, Glycine max were downloaded from NCBI database (https://www.ncbi.nlm.nih.gov/guide/proteins/). Phylogenetic trees were constructed using the phylogeny tool NGPhylogeny.fr (https://ngphylogeny.fr/) (Lemoine et al ., 2019). The bootstrap consensus tree was inferred from 500 replicates.…”

Section: Methodsmentioning

confidence: 99%

Developmental atlas of white lupin cluster roots

Gallardo

Hufnagel

Soriano

et al. 2020

Preprint

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During the course of evolution, plants have developed various strategies to improve micronutrient acquisition, such as cluster roots. These spectacular structures are dedicated to efficient phosphate remobilization and acquisition. When exposed to Pi-limitation, white lupin forms cluster roots made of dense clusters of short specialized roots, called rootlets. Although the physiological activity of rootlets has been well studied, their development remains poorly described. Here, we provide a developmental atlas of white lupin early rootlet development, using molecular markers derived from the model plant Arabidopsis. We first focused on cell division patterns to determine which cells contribute to the rootlet primordium. Then, we identified homologs of previously described tissue specific genes based on protein sequence analysis and also using detailed transcriptomic data covering rootlet development. This study provides a comprehensive description of the developmental phases of rootlet formation, highlighting that rootlet primordium arises from divisions in pericycle, endodermis and cortex. We describe that rootlet primordium patterning follows eight stages during which tissue differentiation is established progressively.HighlightWhite lupin cluster roots consist in the formation of numerous rootlets whose development can be divided in 8 stages and involves divisions in the pericycle, endodermis and cortex.

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“…A multiple sequence alignment was also carried out using the NPhylogeny.fr tool. The latter being a MAFFT program [9].…”

Section: Methodsmentioning

confidence: 99%

Genome Analysis of SARS-CoV-2 Isolate from Bangladesh

Hasan

Khan

Ahsan

et al. 2020

Preprint

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Recently the first genome sequence for a Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 isolate from Bangladesh became available. The sequencing was carried out by the Child Health Research Foundation and provided the first insight into the genetic details of the viral strain responsible for the SARS-CoV-2 infections in Bangladesh. Here we carried out a comparative study were we explored the phylogenetic relationship between the Bangladeshi isolate with other isolates from different parts of the world. Afterwards we identified single nucleotide variants in the Bangladeshi isolate, using the Wuhan virus reference sequence. We found a total of 9 variants in the Bangladeshi isolate using 2 separate tools. Barring 2, the rest of these variants were also observed in other isolates from different countries. Most of the variants occurred in the ORF1ab gen. Another noteworthy finding was a sequence of three consecutive variants in the N protein gene that were observed in other isolates as well. Lastly the phylogenetic analysis revealed a close relationship between the Bangladeshi isolate and those from Taiwan,

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NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Cited by 605 publications

References 33 publications

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

Developmental atlas of white lupin cluster roots

Genome Analysis of SARS-CoV-2 Isolate from Bangladesh

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