scholarly journals Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha

2019 ◽  
Vol 37 (3) ◽  
pp. 730-756 ◽  
Author(s):  
Irene Julca ◽  
Marina Marcet-Houben ◽  
Fernando Cruz ◽  
Carlos Vargas-Chavez ◽  
John Spencer Johnston ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Duplication Event ◽  
Aphid Species ◽  
Common Finding ◽  
Segmental Duplications ◽  
Genome Duplication Event ◽  
Phloem Sap ◽  
Recent Species ◽  
Species Specific

Abstract Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.

scholarly journals Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

2017 ◽  
Author(s):  
Alex B. Brohammer ◽  
Thomas JY. Kono ◽  
Nathan M. Springer ◽  
Suzanne E. McGaugh ◽  
Candice N. Hirsch
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Duplicate Gene ◽  
Duplication Event ◽  
Inbred Lines ◽  
Whole Genome ◽  
Ancestral State ◽  
Genome Duplication Event ◽  
Number Variation ◽  
And Function

SUMMARYMaize is a diverse paleotetraploid species with widespread presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization and differential fractionation refers to non-shared gene loss events between individuals. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variable syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable compared to syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.SIGNIFICANCE STATEMENTThere is a large amount of presence/absence variation for gene content in maize. One mechanism that has been hypothesized to contribute to this variation is differential fractionation between individuals following the maize whole genome duplication event. Using comparative genomics, with sorghum and rice representing the ancestral state, we observed little evidence of differential fractionation among elite inbred lines and the few differentially fractionated genes identified did not appear to confer functional significance.

scholarly journals A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

GigaScience ◽  
2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Zheng Fan ◽  
Tao Yuan ◽  
Piao Liu ◽  
Lu-Yu Wang ◽  
Jian-Feng Jin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Hox Genes ◽  
Genome Duplication ◽  
Duplication Event ◽  
Whole Genome ◽  
High Quality ◽  
Genome Duplication Event ◽  
Whole Genome Duplication Event ◽  
Chromosome Level

Abstract Background The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event. Results We present a chromosome-level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi-C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes. Conclusions The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species’ adaptation to the environment.

scholarly journals Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution

2015 ◽  
Vol 7 (7) ◽  
pp. 1856-1870 ◽  
Author(s):  
Thomas H. Clarke ◽  
Jessica E. Garb ◽  
Cheryl Y. Hayashi ◽  
Peter Arensburger ◽  
Nadia A. Ayoub
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Duplication Event ◽  
Silk Gland ◽  
Gene Duplication Event

scholarly journals Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis

2020 ◽  
Author(s):  
Zhichao Xu ◽  
Ranran Gao ◽  
Xiangdong Pu ◽  
Rong Xu ◽  
Jiyong Wang ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Functional Divergence ◽  
Duplication Event ◽  
Scutellaria Baicalensis ◽  
Comparative Genome Analysis ◽  
Biosynthetic Genes ◽  
Genome Duplication Event ◽  
Comparative Genome ◽  
Scutellaria Barbata ◽  
Species Specific

AbstractScutellaria baicalensis and Scutellaria barbata, common medicinal plants of the Lamiaceae family, produce specific flavonoid compounds with antioxidant and antitumor activities, including baicalein, scutellarein, norwogonin, wogonin, and their glycosides. Here, we reported two chromosome-level genome assemblies of S. baicalensis and S. barbata with significant quantitative chromosomal variation (2n = 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred far earlier than previously reported, and a whole-genome duplication event was identified. The insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and rearrangement. The comparative genome analysis of congeneric species elucidated the species-specific evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific tandem duplication of the phenylalanine ammonia lyase (PAL) and chalcone synthase (CHS) genes, and the S. barbata-specific duplication of 4-CoA ligase (4CL) genes. In addition, the paralogous duplication, collinearity, and expression diversity of CYP82D subfamily members revealed the functional divergence of flavone hydroxylase genes between S. baicalensis and S. barbata. These Scutellaria genomes highlight the common and species-specific evolution of flavone biosynthetic genes, promoting the development of molecular breeding and the study of the biosynthesis and regulation of bioactive compounds.

scholarly journals Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses

2019 ◽  
Author(s):  
Bei Gao ◽  
Moxian Chen ◽  
Xiaoshuang Li ◽  
Yuqing Liang ◽  
Daoyuan Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Physcomitrella Patens ◽  
Duplication Event ◽  
Land Plant ◽  
Phylogenetic Position ◽  
List Type ◽  
Genome Duplication Event ◽  
Genome Duplications ◽  
Duplication Events ◽  
Phylogenomic Analyses

SummaryMosses (Bryophyta) are a key group occupying important phylogenetic position for understanding land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage and contains more than 95% of the modern mosses, whereas the other classes are by nature species-poor. The phylogeny of mosses remains elusive at present.Recurrent whole genome duplications have shaped the evolution trajectory of angiosperms, but little is known about the genome evolutionary history in mosses. It remains to be answered if there existed a historical genome duplication event associated with the species radiation of class Bryopsida.Here, the high-confidence moss phylogeny was generated covering major moss lineages. Two episodes of ancient genomic duplication events were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida and Tetraphidopsida, with estimated ages of the gene duplications clustered around 329 and 182 million year ago, respectively.The third episode of polyploidy event (termed ψ) was tightly associated with the early diversification of Bryopsida with an estimated age of ~87 million years. By scrutinizing the phylogenetic timing of duplicated syntelogs in Physcomitrella patens, the WGD1 and WGD2 events were confidently re-recognized as the ψ event and the Funarioideae duplication event (~65 mya), respectively. Together, our findings unveiled four episodes of polyploidy events in the evolutionary past of Physcomitrella patens.

scholarly journals A new time-scale for ray-finned fish evolution

2006 ◽  
Vol 274 (1609) ◽  
pp. 489-498 ◽  
Author(s):  
Imogen A Hurley ◽  
Rachel Lockridge Mueller ◽  
Katherine A Dunn ◽  
Eric J Schmidt ◽  
Matt Friedman ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Duplication ◽  
Nuclear Data ◽  
Duplication Event ◽  
Molecular Data ◽  
Morphological Data ◽  
Crown Group ◽  
Genome Duplication Event ◽  
Evolutionary Origins ◽  
Date Estimate

The Actinopterygii (ray-finned fishes) is the largest and most diverse vertebrate group, but little is agreed about the timing of its early evolution. Estimates using mitochondrial genomic data suggest that the major actinopterygian clades are much older than divergence dates implied by fossils. Here, the timing of the evolutionary origins of these clades is reinvestigated using morphological, and nuclear and mitochondrial genetic data. Results indicate that existing fossil-based estimates of the age of the crown-group Neopterygii, including the teleosts, Lepisosteus (gar) and Amia (bowfin), are at least 40 Myr too young. We present new palaeontological evidence that the neopterygian crown radiation is a Palaeozoic event, and demonstrate that conflicts between molecular and morphological data for the age of the Neopterygii result, in part, from missing fossil data. Although our molecular data also provide an older age estimate for the teleost crown, this range extension remains unsupported by the fossil evidence. Nuclear data from all relevant clades are used to demonstrate that the actinopterygian whole-genome duplication event is teleost-specific. While the date estimate of this event overlaps the probable range of the teleost stem group, a correlation between the genome duplication and the large-scale pattern of actinopterygian phylogeny remains elusive.

scholarly journals The American Paddlefish Genome Provides Novel Insights into Chromosomal Evolution and Bone Mineralization in Early Vertebrates

2020 ◽  
Author(s):  
Peilin Cheng ◽  
Yu Huang ◽  
Yunyun Lv ◽  
Hao Du ◽  
Zhiqiang Ruan ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Calcium Binding ◽  
Bone Mineralization ◽  
Chromosomal Evolution ◽  
Duplication Event ◽  
Comparative Genomic ◽  
Evolutionary Status ◽  
Genome Duplication Event ◽  
Early Vertebrates ◽  
Species Specific

Abstract Sturgeons and paddlefishes (Acipenseriformes) occupy the basal position of ray-finned fishes, although they have cartilaginous skeletons as in Chondrichthyes. This evolutionary status and their morphological specializations make them a research focus, but their complex genomes (polyploidy and the presence of microchromosomes) bring obstacles and challenges to molecular studies. Here, we generated the first high-quality genome assembly of the American paddlefish (Polyodon spathula) at a chromosome level. Comparative genomic analyses revealed a recent species-specific whole-genome duplication event, and extensive chromosomal changes, including head-to-head fusions of pairs of intact, large ancestral chromosomes within the paddlefish. We also provide an overview of the paddlefish SCPP (secretory calcium-binding phosphoprotein) repertoire that is responsible for tissue mineralization, demonstrating that the earliest flourishing of SCPP members occurred at least before the split between Acipenseriformes and teleosts. In summary, this genome assembly provides a genetic resource for understanding chromosomal evolution in polyploid nonteleost fishes and bone mineralization in early vertebrates.

scholarly journals The divergence of alternative splicing between ohnologs in teleost fishes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuwei Wang ◽  
Baocheng Guo
Keyword(s):  
Alternative Splicing ◽  
Gene Duplication ◽  
Functional Divergence ◽  
Duplication Event ◽  
Rna Seq ◽  
Genome Duplication Event ◽  
Duplication Events ◽  
Function Sharing ◽  
Independent Model ◽  
Rule Out

Abstract Background Gene duplication and alternative splicing (AS) are two distinct mechanisms generating new materials for genetic innovations. The evolutionary link between gene duplication and AS is still controversial, due to utilizing duplicates from inconsistent ages of duplication events in earlier studies. With the aid of RNA-seq data, we explored evolutionary scenario of AS divergence between duplicates with ohnologs that resulted from the teleost genome duplication event in zebrafish, medaka, and stickleback. Results Ohnologs in zebrafish have fewer AS forms compared to their singleton orthologs, supporting the function-sharing model of AS divergence between duplicates. Ohnologs in stickleback have more AS forms compared to their singleton orthologs, which supports the accelerated model of AS divergence between duplicates. The evolution of AS in ohnologs in medaka supports a combined scenario of the function-sharing and the accelerated model of AS divergence between duplicates. We also found a small number of ohnolog pairs in each of the three teleosts showed significantly asymmetric AS divergence. For example, the well-known ovary-factor gene cyp19a1a has no AS form but its ohnolog cyp19a1b has multiple AS forms in medaka, suggesting that functional divergence between duplicates might have result from AS divergence. Conclusions We found that a combined scenario of function-sharing and accelerated models for AS evolution in ohnologs in teleosts and rule out the independent model that assumes a lack of correlation between gene duplication and AS. Our study thus provided insights into the link between gene duplication and AS in general and ohnolog divergence in teleosts from AS perspective in particular.

scholarly journals Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Francesco Monticolo ◽  
Emanuela Palomba ◽  
Maria Luisa Chiusano
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Death ◽  
Acetic Acid ◽  
Programmed Cell Death ◽  
Differential Expression ◽  
Ribosomal Proteins ◽  
Relative Proportion ◽  
Duplication Event ◽  
Genome Duplication Event ◽  
Cell Death Pathway

AbstractProgrammed cell death involves complex molecular pathways in both eukaryotes and prokaryotes. In Escherichia coli, the toxin–antitoxin system (TA-system) has been described as a programmed cell death pathway in which mRNA and ribosome organizations are modified, favoring the production of specific death-related proteins, but also of a minor portion of survival proteins, determining the destiny of the cell population. In the eukaryote Saccharomyces cerevisiae, the ribosome was shown to change its stoichiometry in terms of ribosomal protein content during stress response, affecting the relative proportion between ohnologs, i.e., the couple of paralogs derived by a whole genome duplication event. Here, we confirm the differential expression of ribosomal proteins in yeast also during programmed cell death induced by acetic acid, and we highlight that also in this case pairs of ohnologs are involved. We also show that there are different trends in cytosolic and mitochondrial ribosomal proteins gene expression during the process. Moreover, we show that the exposure to acetic acid induces the differential expression of further genes coding for products related to translation processes and to rRNA post-transcriptional maturation, involving mRNA decapping, affecting translation accuracy, and snoRNA synthesis. Our results suggest that the reprogramming of the overall translation apparatus, including the cytosolic ribosome reorganization, are relevant events in yeast programmed cell death induced by acetic acid.

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