Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences

López-Fernández, Hugo; Duque, Pedro; Henriques, Sílvia F.; Vázquez, Noé; Fdez-Riverola, Florentino; Vieira, Cristina; Reboiro-Jato, Miguel; Vieira, Jorge

doi:10.1007/s12539-018-0312-5

Cited by 14 publications

(6 citation statements)

References 17 publications

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“…To find and extract protein encoding segments larger than 100 bp, we have used getorf, using the emboss Docker image available at pegi3s Bioinformatics Docker images project (htttps:pegi3s.github.io/dockerfiles). Then, we selected the protein encoding segments that show similarity with reference S-RNase sequences, using tblastx (Expect value (e) < 0.05), as implemented in SEDA 58 , 59 , using as query Prunus S3-RNase (AJ298312), Malus Sh-RNase (AB032247), and Fragaria putative S-RNase (gi561957436, gi561674690 and gi561985884) 24 . Based on this information, we manually annotated the corresponding genome region to identify the exons of each gene.…”

Section: Methodsmentioning

confidence: 99%

The identification of the Rosa S-locus and implications on the evolution of the Rosaceae gametophytic self-incompatibility systems

Vieira

Pimenta

Gomes

et al. 2021

Sci Rep

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In Rosaceae species, two gametophytic self-incompatibility (GSI) mechanisms are described, the Prunus self-recognition system and the Maleae (Malus/Pyrus/Sorbus) non-self- recognition system. In both systems the pistil component is a S-RNase gene, but from two distinct phylogenetic lineages. The pollen component, always a F-box gene(s), in the case of Prunus is a single gene, and in Maleae there are multiple genes. Previously, the Rosa S-locus was mapped on chromosome 3, and three putative S-RNase genes were identified in the R. chinensis ‘Old Blush’ genome. Here, we show that these genes do not belong to the S-locus region. Using R. chinensis and R. multiflora genomes and a phylogenetic approach, we identified the S-RNase gene, that belongs to the Prunus S-lineage. Expression patterns support this gene as being the S-pistil. This gene is here also identified in R. moschata, R. arvensis, and R. minutifolia low coverage genomes, allowing the identification of positively selected amino acid sites, and thus, further supporting this gene as the S-RNase. Furthermore, genotype–phenotype association experiments also support this gene as the S-RNase. For the S-pollen GSI component we find evidence for multiple F-box genes, that show the expected expression pattern, and evidence for diversifying selection at the F-box genes within an S-haplotype. Thus, Rosa has a non-self-recognition system, like in Maleae species, despite the S-pistil gene belonging to the Prunus S-RNase lineage. These findings are discussed in the context of the Rosaceae GSI evolution. Knowledge on the Rosa S-locus has practical implications since genes controlling floral and other ornamental traits are in linkage disequilibrium with the S-locus.

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Section: Methodsmentioning

confidence: 99%

The identification of the Rosa S-locus and implications on the evolution of the Rosaceae gametophytic self-incompatibility systems

Vieira

Pimenta

Gomes

et al. 2021

Sci Rep

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“…This approach will retrieve nucleotide sequences showing similarity at the amino acid level with the SLF reference sequences beyond the F-box motif. To the obtained dataset we added the predicted CDSs from the annotated genomes, and removed identical sequences, after merging the headers, using SEDA 4 (López-Fernández et al, 2019). As before, sequences were aligned using Muscle and a Bayesian phylogenetic tree was obtained using ADOPS (Reboiro-Jato et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

Predicting Specificities Under the Non-self Gametophytic Self-Incompatibility Recognition Model

et al. 2019

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Non-self gametophytic self-incompatibility (GSI) recognition system is characterized by the presence of multiple F-box genes tandemly located in the S -locus, that regulate pollen specificity. This reproductive barrier is present in Solanaceae, Plantaginacea and Maleae (Rosaceae), but only in Petunia functional assays have been performed to get insight on how this recognition mechanism works. In this system, each of the encoded S -pollen proteins (called SLFs in Solanaceae and Plantaginaceae /SFBBs in Maleae) recognizes and interacts with a sub-set of non-self S -pistil proteins, called S-RNases, mediating their ubiquitination and degradation. In Petunia there are 17 SLF genes per S -haplotype, making impossible to determine experimentally each SLF specificity. Moreover, domain –swapping experiments are unlikely to be performed in large scale to determine S -pollen and S -pistil specificities. Phylogenetic analyses of the Petunia SLFs and those from two Solanum genomes, suggest that diversification of SLF s predate the two genera separation. Here we first identify putative SLF genes from nine Solanum and 10 Nicotiana genomes to determine how many gene lineages are present in the three genera, and the rate of origin of new SLF gene lineages. The use of multiple genomes per genera precludes the effect of incompleteness of the genome at the S -locus. The similar number of gene lineages in the three genera implies a comparable effective population size for these species, and number of specificities. The rate of origin of new specificities is one per 10 million years. Moreover, here we determine the amino acids positions under positive selection, those involved in SLF specificity recognition, using 10 Petunia S -haplotypes with more than 11 SLF genes. These 16 amino acid positions account for the differences of self-incompatible (SI) behavior described in the literature. When SLF and S-RNase proteins are divided according to the SI behavior, and the positively selected amino acids classified according to hydrophobicity, charge, polarity and size, we identified fixed differences between SI groups. According to the in silico 3D structure of the two proteins these amino acid positions interact. Therefore, this methodology can be used to infer SLF/S-RNase specificity recognition.

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“…To obtain phylogenies representative of the virilis phylad, we started by downloading all the D. virilis coding sequences (CDS) available at FlyBase ( ftp://ftp.flybase.net/genomes/Drosophila_virilis/current/fasta/ ). We further used SEDA 71 to retrieve only those CDS of genes located on scaffolds anchored to chromosomes (Muller E: scaffolds 12,822; 13,047; 12,855 and 12,954; Muller B: scaffolds 13,246; 12,963 and 12,723 and Muller C: scaffolds 12,823; 10,324; 12,875 and 13,324). When more than one isoform was available for the same gene only the longest one was retrieved.…”

Section: Methodsmentioning

confidence: 99%

Multiple loci linked to inversions are associated with eye size variation in species of the Drosophila virilis phylad

Reis

Wiegleb

Julien

et al. 2020

Sci Rep

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The size and shape of organs is tightly controlled to achieve optimal function. Natural morphological variations often represent functional adaptations to an ever-changing environment. For instance, variation in head morphology is pervasive in insects and the underlying molecular basis is starting to be revealed in the Drosophila genus for species of the melanogaster group. However, it remains unclear whether similar diversifications are governed by similar or different molecular mechanisms over longer timescales. To address this issue, we used species of the virilis phylad because they have been diverging from D. melanogaster for at least 40 million years. Our comprehensive morphological survey revealed remarkable differences in eye size and head shape among these species with D. novamexicana having the smallest eyes and southern D. americana populations having the largest eyes. We show that the genetic architecture underlying eye size variation is complex with multiple associated genetic variants located on most chromosomes. Our genome wide association study (GWAS) strongly suggests that some of the putative causative variants are associated with the presence of inversions. Indeed, northern populations of D. americana share derived inversions with D. novamexicana and they show smaller eyes compared to southern ones . Intriguingly, we observed a significant enrichment of genes involved in eye development on the 4th chromosome after intersecting chromosomal regions associated with phenotypic differences with those showing high differentiation among D. americana populations. We propose that variants associated with chromosomal inversions contribute to both intra- and interspecific variation in eye size among species of the virilis phylad.

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Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences

Cited by 14 publications

References 17 publications

The identification of the Rosa S-locus and implications on the evolution of the Rosaceae gametophytic self-incompatibility systems

The identification of the Rosa S-locus and implications on the evolution of the Rosaceae gametophytic self-incompatibility systems

Predicting Specificities Under the Non-self Gametophytic Self-Incompatibility Recognition Model

Multiple loci linked to inversions are associated with eye size variation in species of the Drosophila virilis phylad

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