scholarly journals Extreme Genomic Makeover: Evolutionary History of Maternally-transmitted Clam Symbionts

2020 ◽  
Author(s):  
M Perez ◽  
C Breusing ◽  
B Angers ◽  
YJ Won ◽  
CR Young
Keyword(s):  
Genome Evolution ◽  
Evolutionary History ◽  
Free Living ◽  
Genome Wide ◽  
A Genome ◽  
Chemosynthetic Bacteria ◽  
History Of ◽  
Vesicomyid Clam ◽  
Do So

AbstractGiven their recent switch to a vertically-transmitted intracellular lifestyle, the chemosynthetic bacteria associated with deep-sea vesicomyid clams are an excellent model system to study the processes underlying reductive genome evolution. In this study, we provide the first estimates of the relative contributions of drift, recombination and selection in shaping the ongoing reductive genome evolution in these symbionts. To do so, we compared the genomes of endosymbionts associated with 11 vesicomyid clam species to that of closely related free-living bacteria and their respective hosts’ mitochondria. Our investigation confirmed that neutral evolutionary processes were the dominant driver of reductive genome evolution in this group and highlighted the important role of horizontal gene transfer in mitigating genome erosion. Finally, a genome-wide screen for episodic positive selection across the symbiont phylogeny revealed the pervasive role of selective processes in maintaining symbiont functional integrity.

scholarly journals Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dayana E. Salas-Leiva ◽  
Eelco C. Tromer ◽  
Bruce A. Curtis ◽  
Jon Jerlström-Hultqvist ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Origin Recognition Complex ◽  
Common Ancestor ◽  
Genomic Analysis ◽  
Free Living ◽  
A Genome ◽  
History Of ◽  
Eukaryotic Dna ◽  
Comparative Genomics Analysis ◽  
Dna Processing

AbstractCells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

scholarly journals A genome‐wide linkage map for the house sparrow ( Passer domesticus ) provides insights into the evolutionary history of the avian genome

2020 ◽  
Vol 20 (2) ◽  
pp. 544-559 ◽  
Author(s):  
Ingerid J. Hagen ◽  
Sigbjørn Lien ◽  
Anna M. Billing ◽  
Tore O. Elgvin ◽  
Cassandra Trier ◽  
...  
Keyword(s):  
Linkage Map ◽  
Evolutionary History ◽  
House Sparrow ◽  
Passer Domesticus ◽  
Genome Wide ◽  
A Genome ◽  
Avian Genome ◽  
History Of

scholarly journals Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria

2010 ◽  
Vol 278 (1713) ◽  
pp. 1814-1822 ◽  
Author(s):  
Matías J. Cafaro ◽  
Michael Poulsen ◽  
Ainslie E. F. Little ◽  
Shauna L. Price ◽  
Nicole M. Gerardo ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Antibiotic Production ◽  
Symbiotic Association ◽  
Free Living ◽  
Ant Colonies ◽  
History Of ◽  
Fungus Growing Ants ◽  
Related Fungus

Fungus-growing ants (tribe Attini) engage in a mutualism with a fungus that serves as the ants' primary food source, but successful fungus cultivation is threatened by microfungal parasites (genus Escovopsis ). Actinobacteria (genus Pseudonocardia ) associate with most of the phylogenetic diversity of fungus-growing ants; are typically maintained on the cuticle of workers; and infection experiments, bioassay challenges and chemical analyses support a role of Pseudonocardia in defence against Escovopsis through antibiotic production. Here we generate a two-gene phylogeny for Pseudonocardia associated with 124 fungus-growing ant colonies, evaluate patterns of ant– Pseudonocardia specificity and test Pseudonocardia antibiotic activity towards Escovopsis . We show that Pseudonocardia associated with fungus-growing ants are not monophyletic: the ants have acquired free-living strains over the evolutionary history of the association. Nevertheless, our analysis reveals a significant pattern of specificity between clades of Pseudonocardia and groups of related fungus-growing ants. Furthermore, antibiotic assays suggest that despite Escovopsis being generally susceptible to inhibition by diverse Actinobacteria, the ant-derived Pseudonocardia inhibit Escovopsis more strongly than they inhibit other fungi, and are better at inhibiting this pathogen than most environmental Pseudonocardia strains tested. Our findings support a model that many fungus-growing ants maintain specialized Pseudonocardia symbionts that help with garden defence.

scholarly journals Reconstructing the Evolutionary History of Chromosomal Races on Islands: A Genome-Wide Analysis of Natural House Mouse Populations

2020 ◽  
Vol 37 (10) ◽  
pp. 2825-2837 ◽  
Author(s):  
Paolo Franchini ◽  
Andreas F Kautt ◽  
Alexander Nater ◽  
Gloria Antonini ◽  
Riccardo Castiglia ◽  
...  
Keyword(s):  
House Mouse ◽  
Regulatory Networks ◽  
Evolutionary History ◽  
Large Scale ◽  
Chromosomal Races ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Demographic Patterns ◽  
Aeolian Archipelago

Abstract Chromosomal evolution is widely considered to be an important driver of speciation, as karyotypic reorganization can bring about the establishment of reproductive barriers between incipient species. One textbook example for genetic mechanisms of speciation are large-scale chromosomal rearrangements such as Robertsonian (Rb) fusions, a common class of structural variants that can drastically change the recombination landscape by suppressing crossing-over and influence gene expression by altering regulatory networks. Here, we explore the population structure and demographic patterns of a well-known house mouse Rb system in the Aeolian archipelago in Southern Italy using genome-wide data. By analyzing chromosomal regions characterized by different levels of recombination, we trace the evolutionary history of a set of Rb chromosomes occurring in different geographical locations and test whether chromosomal fusions have a single shared origin or occurred multiple times. Using a combination of phylogenetic and population genetic approaches, we find support for multiple, independent origins of three focal Rb chromosomes. The elucidation of the demographic patterns of the mouse populations within the Aeolian archipelago shows that an interplay between fixation of newly formed Rb chromosomes and hybridization events has contributed to shaping their current karyotypic distribution. Overall, our results illustrate that chromosome structure is much more dynamic than anticipated and emphasize the importance of large-scale chromosomal translocations in speciation.

scholarly journals Origin Recognition Complex (ORC) Evolution Is Influenced by Global Gene Duplication/Loss Patterns in Eukaryotic Genomes

2020 ◽  
Vol 12 (2) ◽  
pp. 3878-3889 ◽  
Author(s):  
Eduard Ocaña-Pallarès ◽  
Zaida Vergara ◽  
Bénédicte Desvoyes ◽  
Manuel Tejada-Jimenez ◽  
Ainoa Romero-Jurado ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Origin Recognition Complex ◽  
Free Living ◽  
Data Set ◽  
Genome Duplications ◽  
History Of ◽  
Eukaryotic Genomes ◽  
Eukaryotic Feature ◽  
Origin Recognition

Abstract The conservation of orthologs of most subunits of the origin recognition complex (ORC) has served to propose that the whole complex is common to all eukaryotes. However, various uncertainties have arisen concerning ORC subunit composition in a variety of lineages. Also, it is unclear whether the ancestral diversification of ORC in eukaryotes was accompanied by the neofunctionalization of some subunits, for example, role of ORC1 in centriole homeostasis. We have addressed these questions by reconstructing the distribution and evolutionary history of ORC1-5/CDC6 in a taxon-rich eukaryotic data set. First, we identified ORC subunits previously undetected in divergent lineages, which allowed us to propose a series of parsimonious scenarios for the origin of this multiprotein complex. Contrary to previous expectations, we found a global tendency in eukaryotes to increase or decrease the number of subunits as a consequence of genome duplications or streamlining, respectively. Interestingly, parasites show significantly lower number of subunits than free-living eukaryotes, especially those with the lowest genome size and gene content metrics. We also investigated the evolutionary origin of the ORC1 role in centriole homeostasis mediated by the PACT region in human cells. In particular, we tested the consequences of reducing ORC1 levels in the centriole-containing green alga Chlamydomonas reinhardtii. We found that the proportion of centrioles to flagella and nuclei was not dramatically affected. This, together with the PACT region not being significantly more conserved in centriole-bearing eukaryotes, supports the notion that this neofunctionalization of ORC1 would be a recent acquisition rather than an ancestral eukaryotic feature.

scholarly journals The essential genome of the crenarchaeal model Sulfolobus islandicus

2018 ◽  
Author(s):  
Changyi Zhang ◽  
Alex P. R. Phillips ◽  
Rebecca L. Wipfler ◽  
Gary J. Olsen ◽  
Rachel J. Whitaker
Keyword(s):  
Cell Biology ◽  
Evolutionary History ◽  
Experimental System ◽  
Essential Genes ◽  
Future Research ◽  
Sulfolobus Islandicus ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Gene Knockouts

AbstractSulfolobus islandicus is a model experimental system in the TACK superphylum of the Archaea, a key lineage in the evolutionary history of cell biology. Here we report a genome-wide identification of the repertoire of genes essential to S. islandicus growth in culture. We confirm previous targeted gene knockouts, uncover the non-essentiality of functions assumed to be essential to the Sulfolobus cell, including the proteinaceous S-layer, and highlight key essential genes whose functions are yet to be determined. Phyletic distributions illustrate the potential transitions that have occurred during the evolution of this contemporary archaeal cell and highlight the sets of genes that may have been associated with each transition. We use this comparative context as a lens to focus future research on archaea-specific uncharacterized essential genes for which future functional data would provide valuable insights into the evolutionary history of the contemporary cell.

scholarly journals A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids

2011 ◽  
Vol 21 (8) ◽  
pp. 1294-1305 ◽  
Author(s):  
Bridgett M. vonHoldt ◽  
John P. Pollinger ◽  
Dent A. Earl ◽  
James C. Knowles ◽  
Adam R. Boyko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Wide Perspective

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

scholarly journals A Genome-Wide Analysis of Pathogenesis-Related Protein-1 (PR-1) Genes from Piper nigrum Reveals Its Critical Role during Phytophthora capsici Infection

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1007
Author(s):  
Divya Kattupalli ◽  
Asha Sreenivasan ◽  
Eppurathu Vasudevan Soniya
Keyword(s):  
Phytophthora Capsici ◽  
Regulatory Elements ◽  
Piper Nigrum ◽  
Binding Motif ◽  
Altered Expression ◽  
Genome Wide ◽  
A Genome ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related

Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related (PR) proteins. Through a genome-wide survey, eleven PR-1 genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from P. nigrum. Despite the critical functional domains, PnPR-1 homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of PnPR-1 proteins were identified using MEME. Most of the PnPR-1 proteins were basic in nature. Secondary and 3D structure analyses of the PnPR-1 proteins were also predicted, which may be linked to a functional role in P. nigrum. The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed PnPR-1 genes mapped to the P. nigrum-P. capsici interaction pathway. An altered expression pattern was detected for PnPR-1 transcripts among which a significant upregulation was noted for basic PnPR-1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of PnPR-1 genes. This is the first genome-wide study that identified the role of PR-1 genes during P. nigrum-P. capsici interactions. The detailed in silico experimental analysis revealed the vital role of PnPR-1 genes in regulating the first layer of defense towards a P. capsici infection in Panniyur-1 plants.

scholarly journals Gut bacteria are essential for normal cuticle development in herbivorous turtle ants

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christophe Duplais ◽  
Vincent Sarou-Kanian ◽  
Dominique Massiot ◽  
Alia Hassan ◽  
Barbara Perrone ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Nitrogen Assimilation ◽  
Isotope Ratio Mass Spectrometry ◽  
Gut Bacteria ◽  
Resonance Spectroscopy ◽  
Nitrogen Flow ◽  
Isotopic Enrichment ◽  
History Of ◽  
Cuticle Development

AbstractAcross the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to the formation of proteins, catecholamine cross-linkers, and chitin in the cuticle. This study identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution, and provides a framework for understanding the nitrogen flow from nutrients through bacteria into the insect cuticle.

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