ALTER: program-oriented conversion of DNA and protein alignments

Glez-Peña, Daniel; Gómez-Blanco, Daniel; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino; Posada, David

doi:10.1093/nar/gkq321

Cited by 398 publications

(196 citation statements)

References 25 publications

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“…A multiple sequence alignment of the retrieved JmjC domain-containing proteins was performed using ClustalO with default parameters (Sievers et al, 2011). The resulting alignment was converted to Phylip format using Alter (Glez-Peña et al, 2010). RAxML 8.2.10 was used to generate a maximum likelihood tree with fixed base frequencies, the GAMMA model, and "autoMRE" as parameter to calculate the optimal number bootstrap repeats (Stamatakis et al, 2008).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

et al. 2017

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The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA sequencing of allelic six-rowed spike3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone Lys demethylase with a conserved zinc finger and Jumonji C and N domain. Sanger sequencing of this candidate gene in independent allelic vrs3 mutants revealed a series of mutations in conserved domains, thus confirming our candidate as the VRS3 gene and suggesting that the row type in barley is determined epigenetically. Global transcriptional profiling in developing shoot apical meristems of vrs3 suggested that VRS3 acts as a transcriptional activator of the row-type genes VRS1 (Hv.HOMEOBOX1) and INTERMEDIUM-C (INT-C; Hv.TEOSINTE BRANCHED1). Comparative transcriptome analysis of the row-type mutants vrs3, vrs4 (Hv.RAMOSA2), and int-c confirmed that all three genes act as transcriptional activators of VRS1 and quantitative variation in the expression levels of VRS1 in these mutants correlated with differences in the number of developed lateral spikelets. The identification of genes and pathways affecting seed number in small grain cereals will enable to further unravel the transcriptional networks controlling this important yield component.

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Section: Phylogenetic Analysismentioning

confidence: 99%

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

et al. 2017

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“…For the ML analysis we used IQ-Tree (Nguyen et al 2015) through its webserver (Trifinopoulos et al 2016) using 10,000 non parametric bootstrap replicates plus 10,000 replicates of Shimodaira-Hasegawa approximate likelihood ratio (SH-aLRT) (Anisimova et al 2011) and 10,000 ultrafast bootstrap (UFBoot) approximation replicates (Minh et al 2013). We converted the alignment to nexus format in the online server Alter (Glez-Peña et al 2010) available at http://sing.ei.uvigo.es/ALTER/, to be used in MrBayes v3.2 Ronquist 2001, Ronquist andHuelsenbeck 2003) for a BI. For this, we ran the analysis in independent duplicates, each with 1,000,000 generations for MCMC with a sampling frequency of 500 generations.…”

Section: Methodsmentioning

confidence: 99%

Description of a new species of Homonota (Reptilia, Squamata, Phyllodactylidae) from the central region of northern Paraguay

Cacciali¹,

Morando²,

Ávila³

et al. 2018

ZSE

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Homonota is a gecko distributed in central and southern South America with 12 species allocated in three groups. In this work, we performed molecular and morphological analyses of samples of Homonota from the central region of northern Paraguay, comparing the data with those of related species of the group: H. horrida and H. septentrionalis. We found strong molecular evidence (based on 16S, Cyt-b, and PRLR gene sequences) to distinguish this lineage as a new species. Morphological statistical analysis showed that females of the three species are different in metric characters (SVL and TL as the most contributing variables), whereas males are less differentiated. No robust differences were found in meristic characters. The most remarkable trait for the diagnosis of the new species is the presence of well-developed keeled tubercles on the sides of the neck, and lack of a white band (crescent-shaped) in the occipital area, which is present in H. horrida and H. septentrionalis. Nevertheless, in our sample, we found three specimens (one juvenile and two young adults) that exhibit the white occipital band. Thus, this character seems only reliable in adults of the new species. The new species is parapatric to H. septentrionalis, both inhabiting the Dry Chaco of Paraguay.

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“…Results of alignment were visualized and exported with MSA Viewer [34]. According to the respective requirements of the different software applications, the formats of the sequences were converted using the online server Alter [35]. The best substitution model for each gene (analyzed separately) of our dataset was identified using PartitionFinder2 [36], with linked branch lengths (supported by most of the phylogenetic programs) via PhyML 3.0 analysis [37].…”

Section: Methodsmentioning

confidence: 99%

Cryptic Diversity in the Neotropical Gecko Genus Phyllopezus Peters, 1878 (Reptilia: Squamata: Phyllodactylidae): A New Species from Paraguay

Cacciali

Lotzkat

Gamble

et al. 2018

International Journal of Zoology

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The gecko genus Phyllopezus is distributed mainly along South America's "Dry Diagonal" (Caatinga, Cerrado, and Chaco). The genus has been the subject of recent taxonomic analyses and includes four described species and seven candidate species referred to here as Phyllopezus pollicaris sensu lato. In Paraguay, Phyllopezus is known from the Chaco and Cerrado where it is abundant, and also from a small isolated population from a rocky hill formation named "Cordillera de Los Altos" (Los Altos mountain range). Here we analyzed genetic samples from across its range, including new samples from Paraguay, using DNA barcoding analysis of the mitochondrial 16S gene and phylogenetic analyses using both Bayesian and Maximum Likelihood methods. We found genetic and morphological differences among geckos from the Los Altos mountain range and the remaining Phyllopezus populations. Using both molecular and morphological evidence we describe a new Phyllopezus species, sister to P. przewalskii. Genetic differentiation among described and putative Phyllopezus species is greater than their morphological differences, which likely accounts for these cryptic taxa remaining undescribed for so long.

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ALTER: program-oriented conversion of DNA and protein alignments

Cited by 398 publications

References 25 publications

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

Description of a new species of Homonota (Reptilia, Squamata, Phyllodactylidae) from the central region of northern Paraguay

Cryptic Diversity in the Neotropical Gecko Genus Phyllopezus Peters, 1878 (Reptilia: Squamata: Phyllodactylidae): A New Species from Paraguay

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