scholarly journals Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum

2020 ◽  
Vol 37 (9) ◽  
pp. 2601-2615 ◽  
Author(s):  
Rosa Fernández ◽  
Marina Marcet-Houben ◽  
Fabrice Legeai ◽  
Gautier Richard ◽  
Stéphanie Robin ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Acyrthosiphon Pisum ◽  
High Capacity ◽  
Chromatin Accessibility ◽  
Pea Aphid ◽  
Specific Gene ◽  
Gene Duplications ◽  
Evolutionary Mechanisms ◽  
Ancestral Gene ◽  
Species Specific

Abstract Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host–symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.

scholarly journals Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum

2019 ◽  
Author(s):  
Rosa Fernández ◽  
Marina Marcet-Houben ◽  
Fabrice Legeai ◽  
Gautier Richard ◽  
Stéphanie Robin ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Acyrthosiphon Pisum ◽  
High Capacity ◽  
Chromatin Accessibility ◽  
Pea Aphid ◽  
Specific Gene ◽  
Gene Duplications ◽  
Evolutionary Mechanisms ◽  
Ancestral Gene ◽  
Species Specific

AbstractEcology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem-sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there is a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed to tackle the history of duplicated genes to pave the road towards understanding the role of gene duplication in ecological adaptation.

MULTITROPHIC MODELS OF PREDATOR–PREY ENERGETICS: III. A CASE STUDY IN AN ALFALFA ECOSYSTEM

1984 ◽  
Vol 116 (7) ◽  
pp. 950-963 ◽  
Author(s):  
A. P. Gutierrez ◽  
J. U. Baumgaertner ◽  
C. G. Summers
Keyword(s):  
Population Dynamics ◽  
Acyrthosiphon Pisum ◽  
Pea Aphid ◽  
Predator Prey ◽  
Pool Model ◽  
Metabolic Pool ◽  
Species Specific ◽  
Hypera Brunneipennis ◽  
Aphid Populations

AbstractThe field population dynamics of pea aphid (Acyrthosiphon pisum) and blue alfalfa aphid (A. kondoi) in alfalfa (Medicago sativa), as influenced by weather, competitors (Egyptian alfalfa weevil = EAW, Hypera brunneipennis), predation from coccinellids (Hippodamia convergens) and harvesting practices, are examined with a stochastic multitrophic level simulation model. The model incorporates a demand-driven functional-response model to estimate prey consumption, and a metabolic pool model to determine the rates and priorities of food allocation to respiration, growth, reproduction, and egestion.The model results compare favorably with field data, and are used to examine the effects of removal of each of the above factors on the dynamics of the aphids. The model shows that the observed density of EAW did not affect the aphid dynamics, but did reduce the standing crop of alfalfa. The predator H. convergens had a significant effect on the population dynamics of the aphids and the plant. Harvesting greatly affected the aphid population dynamics, as well as the dynamics of plant growth and reserve accumulation. However, high temperatures mediated through species-specific respiration costs and possibly a fungal pathogen were responsible for the observed dominance of blue aphid populations in the cool parts of the year and pea aphid populations during warmer parts of the year.

scholarly journals Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream

2019 ◽  
Author(s):  
Jaume Pérez-Sánchez ◽  
Fernando Naya-Català ◽  
Beatriz Soriano ◽  
M. Carla Piazzon ◽  
Ahmed Hafez ◽  
...  
Keyword(s):  
Genome Size ◽  
Transcriptional Analysis ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Gene Duplications ◽  
Dna Transposons ◽  
Species Specific

AbstractGilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding towards more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds (∼732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreambrowser. Homology-based functional annotation, supported by RNA-seq transcripts, identified 55,423 actively transcribed genes corresponding to 21,275 unique descriptions with more than 55% of duplicated genes. The mobilome accounts for the 75% of the full genome size and it is mostly constituted by introns (599 Mb), whereas the rest is represented by low complexity repeats, RNA retrotransposons, DNA transposons and non-coding RNAs. This mobilome also contains a large number of chimeric/composite genes (i. e. loci presenting fragments or exons mostly surrounded by LINEs and Tc1/mariner DNA transposons), whose analysis revealed an enrichment in immune-related functions and processes. Analysis of synteny and gene phylogenies uncovered a high rate of species-specific duplications, resulting from recent independent duplications rather than from genome polyploidization (2.024 duplications per gene; 0.385 excluding gene expansions). These species-specific duplications were enriched in gene families functionally related to genome transposition, immune response and sensory responses. Additionally, transcriptional analysis of liver, skeletal muscle, intestine, gills and spleen supported a high number of functionally specialized paralogs under tissue-exclusive regulation. Altogether, these findings suggest a role of recent large-scale gene duplications coupled to tissue expression diversification in the evolution of gilthead sea bream genome during its successful adaptation to a changing and pathogen-rich environment. This issue also underscores a role of evolutionary routes for rapid increase of the gene repertoire in teleost fish that are independent of polyploidization. Since gilthead sea bream has a well-recognized plasticity, the current study will advance our understanding of fish biology and how organisms of this taxon interact with the environment.

scholarly journals Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection

2021 ◽  
Author(s):  
Yuan Huang ◽  
Jiahui Chen ◽  
Chuan Dong ◽  
Dylan Sosa ◽  
Shengqian Xia ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Duplication ◽  
Positive Selection ◽  
Specific Gene ◽  
Phenotypic Evolution ◽  
New Genes ◽  
Parental Gene ◽  
New Gene ◽  
Species Specific ◽  
Partial Gene Duplication

Abstract Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana. EXOV is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNA-seq analyses revealed that, despite its young age, EXOV has acquired many novel direct and indirect interactions in which the parental gene does not engage. This observation is consistent with the high, selection-driven substitution rate of its encoded protein, in contrast to the slowly evolving EXOVL, suggesting an important role for EXOV in phenotypic evolution. We observed significant differentiation of morphological changes for all phenotypes assessed in genome-edited and T-DNA insertional single mutants and in double T-DNA insertion mutants in EXOV and EXOVL. We discovered a substantial divergence of phenotypic effects by principal component analyses, suggesting neofunctionalization of the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological evolution in A. thaliana.

scholarly journals Cloning and Functional Characterisation of the Duplicated RDL Subunits from the Pea Aphid, Acyrthosiphon pisum

2018 ◽  
Vol 19 (8) ◽  
pp. 2235 ◽  
Author(s):  
Silvia del Villar ◽  
Andrew Jones
Keyword(s):  
Gene Duplication ◽  
Gaba Receptor ◽  
Acyrthosiphon Pisum ◽  
Antagonistic Activity ◽  
Pea Aphid ◽  
Crop Damage ◽  
Xenopus Laevis Oocytes ◽  
Recent Gene Duplication ◽  
Functional Characterisation ◽  
Natural Insecticides

The insect GABA receptor, RDL (resistance to dieldrin), is a cys-loop ligand-gated ion channel (cysLGIC) that plays a central role in neuronal signaling, and is the target of several classes of insecticides. Many insects studied to date possess one Rdl gene; however, there is evidence of two Rdls in aphids. To characterise further this insecticide target from pests that cause millions of dollars’ worth of crop damage each year, we identified the complete cysLGIC gene superfamily of the pea aphid, Acyrthosiphon pisum, using BLAST analysis. This confirmed the presence of two Rdl-like genes (RDL1 and RDL2) that likely arose from a recent gene duplication. When expressed individually in Xenopus laevis oocytes, both subunits formed functional ion channels gated by GABA. Alternative splicing of RDL1 influenced the potency of GABA, and the potency of fipronil was different on the RDL1bd splice variant and RDL2. Imidacloprid and clothianidin showed no antagonistic activity on RDL1, whilst 100 μM thiacloprid reduced the GABA responses of RDL1 and RDL2 to 55% and 62%, respectively. It was concluded that gene duplication of Rdl may have conferred increased tolerance to natural insecticides, and played a role in the evolution of insect cysLGICs.

scholarly journals ARABIDILLO gene homologues in basal land plants: species-specific gene duplication and likely functional redundancy

Planta ◽  
2012 ◽  
Vol 236 (6) ◽  
pp. 1927-1941 ◽  
Author(s):  
Laura A. Moody ◽  
Younousse Saidi ◽  
Emma J. Smiles ◽  
Susan J. Bradshaw ◽  
Matthew Meddings ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Redundancy ◽  
Land Plants ◽  
Specific Gene ◽  
Species Specific

scholarly journals Isolation of botulinolysin, a thiol-activated hemolysin, from serotype D Clostridium botulinum : A species-specific gene duplication in Clostridia

2016 ◽  
Vol 193 ◽  
pp. 20-29
Author(s):  
Tomonori Suzuki ◽  
Thomas Nagano ◽  
Koichi Niwa ◽  
Shingo Mutoh ◽  
Masataka Uchino ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Clostridium Botulinum ◽  
Specific Gene ◽  
Species Specific

scholarly journals Comparative Analysis of Intra- and Inter-Specific Genomic Variability in the Peach Potato Aphid, Myzus persicae

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 368 ◽  
Author(s):  
Mandrioli ◽  
Salvatore ◽  
Ferrari ◽  
Patelli ◽  
Manicardi
Keyword(s):  
Myzus Persicae ◽  
Acyrthosiphon Pisum ◽  
Aphid Species ◽  
Comparative Approach ◽  
Specific Gene ◽  
Gene Duplications ◽  
Potato Aphid ◽  
Genomic Variability ◽  
Peach Potato Aphid

The availability of genomic data in the last decade relating to different aphid species has allowed the analysis of the genomic variability occurring among such species, whereas intra-specific variability has hitherto very largely been neglected. In order to analyse the intra-genomic variability in the peach potato aphid, Myzus persicae, comparative analyses were performed revealing several clone-specific gene duplications, together with numerous deletions/rearrangements. Our comparative approach also allowed us to evaluate the synteny existing between the two M. persicae clones tested and between the peach potato aphid and the pea aphid, Acyrthosiphon pisum. Even if part of the observed rearrangements are related to a low quality of some assembled contigs and/or to the high number of contigs present in these aphid genomes, our evidence reveals that aphid clones are genetically more different than expected. These results suggest that the choice of performing genomes sequencing combining different biotypes/populations, as revealed in the case of the soybean aphid, Aphis glycines, is unlikely to be very informative in aphids. Interestingly, it is possible that the holocentric nature of aphid chromosomes favours genome rearrangements that can be successively inherited transgenerationally via the aphid’s apomictic (parthenogenetic) mode of reproduction. Lastly, we evaluated the structure of the cluster of genes coding for the five histones (H1, H2A, H2B, H3 and H4) in order to better understand the quality of the two M. persicae genomes and thereby to improve our knowledge of this functionally important gene family.

scholarly journals MHC class I evolution; from Northern pike to salmonids

2020 ◽  
Author(s):  
Unni Grimholt ◽  
Morten Lukacs
Keyword(s):  
Immune System ◽  
Mhc Class I ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Northern Pike ◽  
Class I ◽  
Specific Gene ◽  
Whole Genome ◽  
Gene Duplications ◽  
Species Specific

Abstract Background: Salmonids are of major importance both as farmed and wild animals. With the changing environment comes changes in pathogenic pressures so understanding the immune system of all salmonid species is of essence. Major histocompatibility complex (MHC) genes are key players in the adaptive immune system signalling infection to responding T-cells populations. Classical MHC class I (MHCI) genes, defined by high polymorphism, broad expression patterns and peptide binding ability, have a key role in inducing immunity. In salmonids, the fourth whole genome duplication that occurred 94 million years ago has provided salmonids with duplicate MHCI regions, while Northern Pike, a basal sister clade to salmonids, represent a species which has not experienced this whole genome duplication. Results: Comparing the gene organization and evolution of MHC class I gene sequences in Northern pike versus salmonids displays a complex picture of how many of these genes evolved. Regional salmonid Ia and Ib Z lineage gene duplicates are not orthologs to the Northern pike Z lineage sequences. Instead, salmonids have experienced unique gene duplications in both duplicate regions as well as in the Salmo and Oncorhynchus branch. Species-specific gene duplications are even more pronounced for some L lineage genes. Conclusions: Although both Northern pike as well as salmonids have expanded their U and Z lineage genes, these gene duplications occurred separately in pike and in salmonids. However, the similarity between these duplications suggest the transposable machinery was present in a common ancestor. The salmonid MHCIa and MHCIb regions were formed during the 94 MYA since the split from pike and before the Oncorhynchus and Salmo branch separated. As seen in tetrapods, the non-classical U lineage genes are diversified duplicates of their classical counterpart. One MHCI lineage, the L lineage, experienced massive species-specific gene duplications after Oncorhynchus and Salmo split approximately 25 MYA. Based on what we currently know about L lineage genes, this large variation in number of L lineage genes also signals a large functional diversity in salmonids.

Sign in / Sign up

Export Citation Format

Share Document