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Charles C. Davis - One of the best experts on this subject based on the ideXlab platform.
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the perfect storm gene tree estimation error incomplete lineage sorting and ancient gene flow explain the most recalcitrant ancient angiosperm clade Malpighiales
bioRxiv, 2020Co-Authors: Zhenxiang Xi, Emily Moriarty Lemmon, Alan R Lemmon, Austin R Mast, Christopher E Buddenhagen, Charles C. DavisAbstract:The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order alone includes nine of the top ten most unstable nodes in angiosperms, and the recalcitrant relationships along the backbone of the order have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 15%, 52%, and 32% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.
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widespread ancient whole genome duplications in Malpighiales coincide with eocene global climatic upheaval
New Phytologist, 2019Co-Authors: Liming Cai, Andre M Amorim, Manickam Sugumaran, Joshua S Rest, Liang Liu, Charles C. DavisAbstract:Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (Ks ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.
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widespread ancient whole genome duplications in Malpighiales coincide with eocene global climatic upheaval
bioRxiv, 2017Co-Authors: Liming Cai, Andre M Amorim, Manickam Sugumaran, Joshua S Rest, Liang Liu, Charles C. DavisAbstract:Ancient whole genome duplications (WGDs) are important in eukaryotic genome evolution, and are especially prominent in plants. Recent genomic studies from large vascular plant clades, including ferns, gymnosperms, and angiosperms suggest that WGDs may represent a crucial mode of speciation. Moreover, numerous WGDs have been dated to events coinciding with major episodes of global and climatic upheaval, including the mass extinction at the KT boundary (~65 Ma) and during more recent intervals of global aridification in the Miocene (~10-5 Ma). These findings have led to the hypothesis that polyploidization may buffer lineages against the negative consequences of such disruptions. Here, we explore WGDs in the large, and diverse flowering plant clade Malpighiales using a combination of transcriptomes and complete genomes from 42 species. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Our results provide strong support for the hypothesis that WGD is an important mode of speciation in plants. Importantly, we also identify that these events are clustered around the Eocene-Paleocene Transition (~54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climate Optimum represents another, previously unrecognized, period of prolific WGDs in plants, and lends support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during major episodes of global change. Malpighiales, in particular, may have been particularly influenced by these events given their predominance in the tropics where Eocene warming likely had profound impacts owing to the relatively tight thermal tolerances of tropical organisms.
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Combined Morphological and Molecular Phylogeny of the Clusioid Clade (Malpighiales) and the Placement of the Ancient Rosid Macrofossil Paleoclusia
International Journal of Plant Sciences, 2013Co-Authors: Brad R. Ruhfel, Peter F. Stevens, Charles C. DavisAbstract:Premise of research. The clusioid clade is a member of the large rosid order Malpighiales and contains ∼1900 species in five families: Bonnetiaceae, Calophyllaceae, Clusiaceae sensu stricto (s.s.), Hypericaceae, and Podostemaceae. Despite recent efforts to clarify their phylogenetic relationships using molecular data, no such data are available for several critical taxa, including especially Hypericum ellipticifolium (previously recognized in Lianthus), Lebrunia, Neotatea, Thysanostemon, and the second-oldest rosid fossil (∼90 Ma), Paleoclusia chevalieri. Here, we (i) assess congruence between phylogenies inferred from morphological and molecular data, (ii) analyze morphological and molecular data simultaneously to place taxa lacking molecular data, and (iii) use ancestral state reconstructions (ASRs) to examine the evolution of traits that have been important for circumscribing clusioid taxa and to explore the placement of Paleoclusia.Methodology. We constructed a morphological data set including 69 char...
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Phylogenetic relationships and divergence times of the three Rafflesiaceae species and two Tetrastigma species included in this study.
2013Co-Authors: Yuguo Wang, Joshua S Rest, M Sugumaran, Robert K. Bradley, Christopher J. Marx, Charles C. DavisAbstract:Phylogenetic relationships (A) and divergence times (B). Holoparasitic Rafflesiaceae (red) is a member of the order Malpighiales, and its obligate host Tetrastigma (blue) is a member of the Vitaceae family. The approximate divergence time between the parasite and host clade is 115 Ma [24]–[27]. Mitochondrial genome sequences generated in this study are marked with asterisks, and the node age error bars (95% highest posterior density intervals) are shown in green. The accepted phylogenetic relationships are based on APG III [38] and Qiu et al. [40], and the divergence times of Rafflesiaceae and Tetrastigma are based on Bendiksby et al. [48] and Chen et al. [49], respectively.
Kenneth J Wurdack - One of the best experts on this subject based on the ideXlab platform.
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phylogenomics and a posteriori data partitioning resolve the cretaceous angiosperm radiation Malpighiales
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Merran L Matthews, Kenneth J Wurdack, Brad R. Ruhfel, Peter K Endress, Andre M Amorim, Hanno Schaefer, M Sugumaran, Peter F. StevensAbstract:The angiosperm order Malpighiales includes ∼16,000 species and constitutes up to 40% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics during the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 additional clades in Malpighiales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas (Erythroxylaceae), and passion flowers (Passifloraceae). We found that commonly used a priori approaches for partitioning concatenated data in maximum likelihood analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a posteriori using a Bayesian mixture model. We also found better branch support in trees inferred from a taxon-rich, data-sparse matrix, which deeply sampled only the phylogenetically critical placeholders, than in trees inferred from a taxon-sparse matrix with little missing data. Although this matrix has more missing data, our a posteriori partitioning strategy reduced the possibility of producing multiple distinct but equally optimal topologies and increased phylogenetic decisiveness, compared with the strategy of partitioning by gene. These approaches are likely to help improve phylogenetic resolution in other poorly resolved major clades of angiosperms and to be more broadly useful in studies across the Tree of Life.
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Malpighiales phylogenetics gaining ground on one of the most recalcitrant clades in the angiosperm tree of life
American Journal of Botany, 2009Co-Authors: Kenneth J Wurdack, Charles C. DavisAbstract:: The eudicot order Malpighiales contains ∼16000 species and is the most poorly resolved large rosid clade. To clarify phylogenetic relationships in the order, we used maximum likelihood, Bayesian, and parsimony analyses of DNA sequence data from 13 gene regions, totaling 15604 bp, and representing all three genomic compartments (i.e., plastid: atpB, matK, ndhF, and rbcL; mitochondrial: ccmB, cob, matR, nad1B-C, nad6, and rps3; and nuclear: 18S rDNA, PHYC, and newly developed low-copy EMB2765). Our sampling of 190 taxa includes representatives from all families of Malpighiales. These data provide greatly increased support for the recent additions of Aneulophus, Bhesa, Centroplacus, Ploiarium, and Rafflesiaceae to Malpighiales; sister relations of Phyllanthaceae + Picrodendraceae, monophyly of Hypericaceae, and polyphyly of Clusiaceae. Oxalidales + Huaceae, followed by Celastrales are successive sisters to Malpighiales. Parasitic Rafflesiaceae, which produce the world's largest flowers, are confirmed as embedded within a paraphyletic Euphorbiaceae. Novel findings show a well-supported placement of Ctenolophonaceae with Erythroxylaceae + Rhizophoraceae, sister-group relationships of Bhesa + Centroplacus, and the exclusion of Medusandra from Malpighiales. New taxonomic circumscriptions include the addition of Bhesa to Centroplacaceae, Medusandra to Peridiscaceae (Saxifragales), Calophyllaceae applied to Clusiaceae subfamily Kielmeyeroideae, Peraceae applied to Euphorbiaceae subfamily Peroideae, and Huaceae included in Oxalidales.
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the complete nucleotide sequence of the cassava manihot esculenta chloroplast genome and the evolution of atpf in Malpighiales rna editing and multiple losses of a group ii intron
Theoretical and Applied Genetics, 2008Co-Authors: Henry Daniell, Kenneth J Wurdack, Anderson Kanagaraj, Seung Bum Lee, Christopher A Saski, Robert K JansenAbstract:The complete sequence of the chloroplast genome of cassava (Manihot esculenta, Euphorbiaceae) has been determined. The genome is 161,453 bp in length and includes a pair of inverted repeats (IR) of 26,954 bp. The genome includes 128 genes; 96 are single copy and 16 are duplicated in the IR. There are four rRNA genes and 30 distinct tRNAs, seven of which are duplicated in the IR. The infA gene is absent; expansion of IRb has duplicated 62 amino acids at the 3' end of rps19 and a number of coding regions have large insertions or deletions, including insertions within the 23S rRNA gene. There are 17 intron-containing genes in cassava, 15 of which have a single intron while two (clpP, ycf3) have two introns. The usually conserved atpF group II intron is absent and this is the first report of its loss from land plant chloroplast genomes. The phylogenetic distribution of the atpF intron loss was determined by a PCR survey of 251 taxa representing 34 families of Malpighiales and 16 taxa from closely related rosids. The atpF intron is not only missing in cassava but also from closely related Euphorbiaceae and other Malpighiales, suggesting that there have been at least seven independent losses. In cassava and all other sequenced Malphigiales, atpF gene sequences showed a strong association between C-to-T substitutions at nucleotide position 92 and the loss of the intron, suggesting that recombination between an edited mRNA and the atpF gene may be a possible mechanism for the intron loss.
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explosive radiation of Malpighiales supports a mid cretaceous origin of modern tropical rain forests
The American Naturalist, 2005Co-Authors: Charles C. Davis, Kenneth J Wurdack, Campbell O. Webb, Carlos Jaramillo, Michael J. DonoghueAbstract:Fossil data have been interpreted as indicating that Late Cretaceous tropical forests were open and dry adapted and that mod- ern closed-canopy rain forest did not originate until after the Cretaceous-Tertiary (K/T) boundary. However, some mid-Cretaceous leaf floras have been interpreted as rain forest. Molecular divergence- time estimates within the clade Malpighiales, which constitute a large percentage of species in the shaded, shrub, and small tree layer in tropical rain forests worldwide, provide new tests of these hypotheses. We estimate that all 28 major lineages (i.e., traditionally recognized families) within this clade originated in tropical rain forest well before the Tertiary, mostly during the Albian and Cenomanian (112-94 Ma). Their rapid rise in the mid-Cretaceous may have resulted from the origin of adaptations to survive and reproduce under a closed forest canopy. This pattern may also be paralleled by other similarly diverse lineages and supports fossil indications that closed-canopy tropical rain forests existed well before the K/T boundary. This case illustrates that dated phylogenies can provide an important new source of ev- idence bearing on the timing of major environmental changes, which may be especially useful when fossil evidence is limited or controversial.
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molecular phylogenetic analysis of phyllanthaceae phyllanthoideae pro parte euphorbiaceae sensu lato using plastid rbcl dna sequences
American Journal of Botany, 2004Co-Authors: Kenneth J Wurdack, Petra Hoffmann, Rosabelle Samuel, Anette Y De Bruijn, Michelle Van Der Bank, Mark W ChaseAbstract:: Analysis of plastid rbcL DNA sequence data of the pantropical family Phyllanthaceae (Malpighiales) and related biovulate lineages of Euphorbiaceae sensu lato is presented. Sampling for this study includes representatives of all 10 tribes and 51 of the 60 genera attributed to Euphorbiaceae-Phyllanthoideae. Centroplacus and Putranjivaceae (Phyllanthoideae-Drypeteae) containing a paraphyletic Drypetes are excluded from Phyllanthaceae. Croizatia, previously thought to be a "basal" member of Euphorbiaceae-Oldfieldioideae (Picrodendraceae), falls within Phyllanthaceae. Phyllanthaceae with the mentioned adjustments form a monophyletic group consisting of two sister clades that mostly correspond to the distribution of tanniniferous leaf epidermal cells and inflorescence structure. With the exception of bigeneric Hymenocardieae and monotypic Bischofieae, none of the current Phyllanthoideae (Phyllanthaceae) tribal circumscriptions are supported by rbcL. Antidesma, Bischofia, Hymenocardia, Martretia, and Uapaca, all of which have previously been placed in monogeneric families, are confirmed as members of Phyllanthaceae. Savia is polyphyletic, and Cleistanthus appears paraphyletic. Paraphyly of Phyllanthus is also indicated, but this pattern lacks bootstrap support. Morphological characters are discussed and mapped for inflorescence structure, tanniniferous epidermal cells, breeding system, and fruit and embryo type. A table summarizes the main characters of six euphorbiaceous lineages.
Hélène Bergès - One of the best experts on this subject based on the ideXlab platform.
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Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis
Molecular Biology Reports, 2019Co-Authors: Zirlane Portugal Costa, Luiz Augusto Cauz-santos, Marcelo Carnier Dornelas, Hélène Bergès, Geovani Tolfo Ragagnin, Marie-anne Van Sluys, Alessandro De Mello Varani, Maria Lucia Carneiro VieiraAbstract:A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome evolution. However, not much information is available on the structure and evolutionary role of TEs in the Passifloraceae family (Malpighiales order). Against this backdrop, we identified, characterized, and inferred the potential genomic impact of the TE repertoire found in the available genomic resources for Passiflora edulis, a tropical fruit species. A total of 250 different TE sequences were identified (96% Class I, and 4% Class II), corresponding to similar to 19% of the P. edulis draft genome. TEs were found preferentially in intergenic spaces (70.4%), but also overlapping genes (30.6%). LTR-RTs accounted for 181 single elements corresponding to similar to 13% of the draft genome. A phylogenetic inference of the reverse transcriptase domain of the LTR-RT revealed association of 37 elements with the Copia superfamily (Angela, Ale, Tork, and Sire) and 128 with the Gypsy (Del, Athila, Reina, CRM, and Galadriel) superfamily, and Del elements were the most frequent. Interestingly, according to insertion time analysis, the majority (95.9%) of the LTR-RTs were recently inserted into the P. edulis genome (
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A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species
Scientific Reports, 2018Co-Authors: Carla Freitas Munhoz, Luiz Augusto Cauz-santos, Nathalie Rodde, Stéphane Cauet, Marcelo Carnier Dornelas, Zirlane Portugal Costa, Alina Carmen Egoávil Reátegui, Philippe Leroy, Alessandro De Mello Varani, Hélène BergèsAbstract:Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes.
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The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales
Frontiers in Plant Science, 2017Co-Authors: Luiz Augusto Cauz-santos, Carla De Freitas Munhoz, Nathalie Rodde, Stéphane Cauet, A. A. Santos, Helen Alves Penha, Marcelo Carnier Dornelas, Alessandro M. Varani, Giancarlo Conde Xavier Oliveira, Hélène BergèsAbstract:The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the Passiflora edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single-copy (SSC) region of 13,378 bp and a large single-copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome of P. edulis differs from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151 bp, 3,765 bp and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.
Luiz Augusto Cauz-santos - One of the best experts on this subject based on the ideXlab platform.
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Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis
Molecular Biology Reports, 2019Co-Authors: Zirlane Portugal Costa, Luiz Augusto Cauz-santos, Marcelo Carnier Dornelas, Hélène Bergès, Geovani Tolfo Ragagnin, Marie-anne Van Sluys, Alessandro De Mello Varani, Maria Lucia Carneiro VieiraAbstract:A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome evolution. However, not much information is available on the structure and evolutionary role of TEs in the Passifloraceae family (Malpighiales order). Against this backdrop, we identified, characterized, and inferred the potential genomic impact of the TE repertoire found in the available genomic resources for Passiflora edulis, a tropical fruit species. A total of 250 different TE sequences were identified (96% Class I, and 4% Class II), corresponding to similar to 19% of the P. edulis draft genome. TEs were found preferentially in intergenic spaces (70.4%), but also overlapping genes (30.6%). LTR-RTs accounted for 181 single elements corresponding to similar to 13% of the draft genome. A phylogenetic inference of the reverse transcriptase domain of the LTR-RT revealed association of 37 elements with the Copia superfamily (Angela, Ale, Tork, and Sire) and 128 with the Gypsy (Del, Athila, Reina, CRM, and Galadriel) superfamily, and Del elements were the most frequent. Interestingly, according to insertion time analysis, the majority (95.9%) of the LTR-RTs were recently inserted into the P. edulis genome (
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A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species
Scientific Reports, 2018Co-Authors: Carla Freitas Munhoz, Luiz Augusto Cauz-santos, Nathalie Rodde, Stéphane Cauet, Marcelo Carnier Dornelas, Zirlane Portugal Costa, Alina Carmen Egoávil Reátegui, Philippe Leroy, Alessandro De Mello Varani, Hélène BergèsAbstract:Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes.
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The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales
Frontiers in Plant Science, 2017Co-Authors: Luiz Augusto Cauz-santos, Carla De Freitas Munhoz, Nathalie Rodde, Stéphane Cauet, A. A. Santos, Helen Alves Penha, Marcelo Carnier Dornelas, Alessandro M. Varani, Giancarlo Conde Xavier Oliveira, Hélène BergèsAbstract:The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the Passiflora edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single-copy (SSC) region of 13,378 bp and a large single-copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome of P. edulis differs from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151 bp, 3,765 bp and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.
Djieto-lordon C. - One of the best experts on this subject based on the ideXlab platform.
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Fruit preference, parasitism, and offspring fitness of Fopius arisanus (Hymenoptera: Braconidae) exposed to Bactrocera dorsalis' (Diptera: Tephritidae) infested fruit species
2019Co-Authors: Nanga S.n., Hanna R., Gnanvossou D., Fotso Kuate A., Fiaboe K.k.m., Djieto-lordon C.Abstract:Fopius arisanus (Sonan) (Hymenoptera: Braconidae) is a koinobiont solitary parasitoid of various fruit flies, particularly those in the genus Bactrocera. Researchers introduced F. arisanus into Africa for the biological control of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), a pest of a wide range of fruit trees and vegetables. However, the suitability of host fruit species as egg-laying substrates for parasitoid development remains poorly investigated in tropical Africa. The present study examines the preference and performance of F. arisanus on B. dorsalis reared on eleven fruit species through laboratory choice-test trials. We assessed the oviposition activity, parasitism rate, developmental time, and offspring fitness of F. arisanus on nine cultivated and two wild host fruits species. Oviposition attempts were higher on Psidium guajava (L.) (Myrtales: Myrtaceae) and Mangifera indica (L.) (Sapindales: Anacardiaceae) than on the other host fruits tested. The wasp parasitized host eggs in P. guajava in no-choice experiments. Psidium guajava, Irvingia wombulu (Vermoesen) (Malpighiales: Irvingiaceae), and Irvingia gabonensis (Aubry_Lecomte) Baill (Malpighiales: Irvingiaceae) were suitable for parasitism in choice tests. Of all host fruits tested, the body and hind tibia lengths of both parasitoid sexes emerging from M. indica were longer than on the others. The female ovipositor was long on Annona squamosa (L.) (Magnoliales: annonaceae) and short on Eribotrya japonica ([Thunb.] Lindl.; Rosales: Rosaceae). We obtained the longest preimaginal developmental time for both sexes on E. japonica and the shortest for females and males on Carica papaya (L.) (Brassicales: Caricaceae). These results demonstrate the ability of some tested fruit species to serve for the permanent establishment of F. arisanus in the field.Federal Ministry for Economic Cooperation and Development, GermanyPeer Revie
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Fruit preference, parasitism, and offspring fitness of Fopius arisanus (Hymenoptera: Braconidae) exposed to Bactrocera dorsalis' (Diptera: Tephritidae) infested fruit species
'Oxford University Press (OUP)', 2019Co-Authors: Nanga S.n., Hanna R., Gnanvossou D., Fotso Kuate A., Fiaboe K.k.m., Djieto-lordon C.Abstract:Fopius arisanus (Sonan) (Hymenoptera: Braconidae) is a koinobiont solitary parasitoid of various fruit flies, particularly those in the genus Bactrocera. Researchers introduced F. arisanus into Africa for the biological control of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), a pest of a wide range of fruit trees and vegetables. However, the suitability of host fruit species as egg-laying substrates for parasitoid development remains poorly investigated in tropical Africa. The present study examines the preference and performance of F. arisanus on B. dorsalis reared on eleven fruit species through laboratory choice-test trials. We assessed the oviposition activity, parasitism rate, developmental time, and offspring fitness of F. arisanus on nine cultivated and two wild host fruits species. Oviposition attempts were higher on Psidium guajava (L.) (Myrtales: Myrtaceae) and Mangifera indica (L.) (Sapindales: Anacardiaceae) than on the other host fruits tested. The wasp parasitized host eggs in P. guajava in no-choice experiments. Psidium guajava, Irvingia wombulu (Vermoesen) (Malpighiales: Irvingiaceae), and Irvingia gabonensis (Aubry_Lecomte) Baill (Malpighiales: Irvingiaceae) were suitable for parasitism in choice tests. Of all host fruits tested, the body and hind tibia lengths of both parasitoid sexes emerging from M. indica were longer than on the others. The female ovipositor was long on Annona squamosa (L.) (Magnoliales: annonaceae) and short on Eribotrya japonica ([Thunb.] Lindl.; Rosales: Rosaceae). We obtained the longest preimaginal developmental time for both sexes on E. japonica and the shortest for females and males on Carica papaya (L.) (Brassicales: Caricaceae). These results demonstrate the ability of some tested fruit species to serve for the permanent establishment of F. arisanus in the field
