BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S-Locus

Vázquez, Noé; López-Fernández, Hugo; Vieira, Cristina; Fdez-Riverola, Florentino; Vieira, Jorge; Reboiro-Jato, Miguel

doi:10.1007/s12539-019-00320-3

Cited by 9 publications

(16 citation statements)

References 49 publications

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“…Using the Blast DataBase Manager software (BDBM; Vázquez et al, 2019) Reformat FASTA option, sequence headers were reformatted in order to show the species name and accession numbers only. Since SLF genes are always intronless (Wang et al, 2004), then we obtained all open reading frames (ORFs) from these genomes using the Get ORF operation of BDBM (that uses the getorf command of EMBOSS; Vázquez et al, 2019), with a minimum and maximum size of 300 and 10000 bp, respectively. We then prepared a Blast database for each of the resulting FASTA files, using the Make Blast Database option of BDBM (Vázquez et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

“…Thus, in this work we used nine genome assemblies from eight Solanum species and 10 genomes from seven Nicotiana species publicly available. Only four of these are self-incompatible species, and thus we searched for both genes and pseudogenes, using Blast DataBase Manager (BDBM 1 ; Vázquez et al, 2019). The high number of genomes analyzed also implies that it is unlikely that a given SLF will be missing in all genomes simply by chance.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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“…C. canephora is a self-sterile, diploid and allogamous plant [5,6]. In this view, vegetative propagation is the most common practice, ensuring uniform crop development, high yields, better coffee quality and better maturation patterns [7][8][9], although it reduces the species genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

Root Trait Variability in Coffea canephora Genotypes and Its Relation to Plant Height and Crop Yield

et al. 2020

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Coffee breeding based on root traits is important to identify productive genotypes under adverse environmental conditions. This study assessed the diversity of root traits in Coffea canephora and its correlation with plant height and crop yield. Undisturbed soil samples were collected down to 60 cm from 43 coffee genotypes, in which one of them was propagated by seed and all others by stem cutting. The roots were washed, scanned, and processed to quantify root length density, root volume, root superficial area, and root diameter. Additionally, plant height and crop yield were also assessed. Root length density ranged from 40 to 1411 mm cm−3, root volume from 6 to 443 mm3 cm−3, root superficial area from 61 to 1880 mm2 cm−3, and root diameter from 0.6 to 1.1 mm. Roots were concentrated in the topsoil (0–20 cm) for most genotypes. In deeper depths (30–60 cm), root length density, root volume, and root superficial area were higher in genotypes 14, 25, 31, and 32. Positive correlations were found between root traits and both plant height and crop yield. The results of this work may contribute to the overall cultivation of C. canephora, specially for crop breeding in adverse environmental conditions.

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“…When more than one isoform was available for the same gene only the longest one was retrieved. Next, we used Splign-Compart (as implemented in BDBM 72 , and the D. virilis CDS obtained above as references to annotate CDS in D. americana (H5 and W11 35 ; SF12, Northern, Central and Southern populations 41 ), as well as in D. novamexicana (15010-1031.00) contigs 41 . To obtain the CDS for the D. americana populations, we used Coral 1.4 73 with default parameters to reconstruct the gene sequences showing the major frequent variant at polymorphic sites in the pool-seq reads of each population 41 , prior to contig assembly using Abyss 2.0 74 with K = 25 and default parameters.…”

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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BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S-Locus

Cited by 9 publications

References 49 publications

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

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

Root Trait Variability in Coffea canephora Genotypes and Its Relation to Plant Height and Crop Yield

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

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