The Adaptive Evolution and Gigantism Mechanisms of the Hadal “Supergiant” Amphipod Alicella gigantea

Hadal trenches are commonly referred to as the deepest areas in the ocean and are characterized by extreme environmental conditions such as high hydrostatic pressures and very limited food supplies. Amphipods are considered the dominant scavengers in the hadal food web. Alicella gigantea is the largest hadal amphipod and, as such, has attracted a lot of attention. However, the adaptive evolution and gigantism mechanisms of the hadal “supergiant” remain unknown. In this study, the whole-body transcriptome analysis was conducted regarding the two hadal amphipods, one being the largest sized species A. gigantea from the New Britain Trench and another the small-sized species Bathycallisoma schellenbergi from the Marceau Trench. The size and weight measurement of the two hadal amphipods revealed that the growth of A. gigantea was comparatively much faster than that of B. schellenbergi. Phylogenetic analyses showed that A. gigantea and B. schellenbergi were clustered into a Lysianassoidea clade, and were distinct from the Gammaroidea consisting of shallow-water Gammarus species. Codon substitution analyses revealed that “response to starvation,” “glycerolipid metabolism,” and “meiosis” pathways were enriched among the positively selected genes (PSGs) of the two hadal amphipods, suggesting that hadal amphipods are subjected to intense food shortage and the pathways are the main adaptation strategies to survive in the hadal environment. To elucidate the mechanisms underlying the gigantism of A. gigantea, small-sized amphipods were used as the background for evolutionary analysis, we found the seven PSGs that were ultimately related to growth and proliferation. In addition, the evolutionary rate of the gene ontology (GO) term “growth regulation” was significantly higher in A. gigantea than in small-sized amphipods. By combining, those points might be the possible gigantism mechanisms of the hadal “supergiant” A. gigantea.

Download Full-text

LPEATs Tailor Plant Phospholipid Composition through Adjusting Substrate Preferences to Temperature

International Journal of Molecular Sciences ◽

10.3390/ijms22158137 ◽

2021 ◽

Vol 22 (15) ◽

pp. 8137

Author(s):

Sylwia Klińska ◽

Kamil Demski ◽

Katarzyna Jasieniecka-Gazarkiewicz ◽

Antoni Banaś

Keyword(s):

Growth Regulation ◽

Phylogenetic Analyses ◽

Phospholipid Composition ◽

Expression Ratio ◽

Temperature Changes ◽

Substrate Preferences ◽

Thermal Changes ◽

Biochemical Evaluation ◽

Response To Temperature ◽

Acyl Donors

Acyl-CoA:lysophosphatidylethanolamine acyltransferases (LPEATs) are known as enzymes utilizing acyl-CoAs and lysophospholipids to produce phosphatidylethanolamine. Recently, it has been discovered that they are also involved in the growth regulation of Arabidopsis thaliana. In our study we investigated expression of each Camelina sativa LPEAT isoform and their behavior in response to temperature changes. In order to conduct a more extensive biochemical evaluation we focused both on LPEAT enzymes present in microsomal fractions from C. sativa plant tissues, and on cloned CsLPEAT isoforms expressed in yeast system. Phylogenetic analyses revealed that CsLPEAT1c and CsLPEAT2c originated from Camelina hispida, whereas other isoforms originated from Camelina neglecta. The expression ratio of all CsLPEAT1 isoforms to all CsLPEAT2 isoforms was higher in seeds than in other tissues. The isoforms also displayed divergent substrate specificities in utilization of LPE; CsLPEAT1 preferred 18:1-LPE, whereas CsLPEAT2 preferred 18:2-LPE. Unlike CsLPEAT1, CsLPEAT2 isoforms were specific towards very-long-chain fatty acids. Above all, we discovered that temperature strongly regulates LPEATs activity and substrate specificity towards different acyl donors, making LPEATs sort of a sensor of external thermal changes. We observed the presented findings not only for LPEAT activity in plant-derived microsomal fractions, but also for yeast-expressed individual CsLPEAT isoforms.

Download Full-text

Evolutionary Analysis of Cystatins of Early-Emerging Metazoans Reveals a Novel Subtype in Parasitic Cnidarians

Biology ◽

10.3390/biology10020110 ◽

2021 ◽

Vol 10 (2) ◽

pp. 110

Author(s):

Pavla Bartošová-Sojková ◽

Jiří Kyslík ◽

Gema Alama-Bermejo ◽

Ashlie Hartigan ◽

Stephen D. Atkinson ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Gene Organization ◽

Gene Repertoire ◽

Evolutionary Analysis ◽

Ancestral Gene ◽

Protein Architecture ◽

Basal Metazoan ◽

Cystatin Gene ◽

Evolutionary Aspects

The evolutionary aspects of cystatins are greatly underexplored in early-emerging metazoans. Thus, we surveyed the gene organization, protein architecture, and phylogeny of cystatin homologues mined from 110 genomes and the transcriptomes of 58 basal metazoan species, encompassing free-living and parasite taxa of Porifera, Placozoa, Cnidaria (including Myxozoa), and Ctenophora. We found that the cystatin gene repertoire significantly differs among phyla, with stefins present in most of the investigated lineages but with type 2 cystatins missing in several basal metazoan groups. Similar to liver and intestinal flukes, myxozoan parasites possess atypical stefins with chimeric structure that combine motifs of classical stefins and type 2 cystatins. Other early metazoan taxa regardless of lifestyle have only the classical representation of cystatins and lack multi-domain ones. Our comprehensive phylogenetic analyses revealed that stefins and type 2 cystatins clustered into taxonomically defined clades with multiple independent paralogous groups, which probably arose due to gene duplications. The stefin clade split between the subclades of classical stefins and the atypical stefins of myxozoans and flukes. Atypical stefins represent key evolutionary innovations of the two parasite groups for which their origin might have been linked with ancestral gene chimerization, obligate parasitism, life cycle complexity, genome reduction, and host immunity.

Download Full-text

Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽

10.7717/peerj.8450 ◽

2020 ◽

Vol 8 ◽

pp. e8450 ◽

Cited By ~ 2

Author(s):

Sunan Huang ◽

Xuejun Ge ◽

Asunción Cano ◽

Betty Gaby Millán Salazar ◽

Yunfei Deng

Keyword(s):

Adaptive Evolution ◽

Phylogenetic Relationships ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Evolutionary Analysis ◽

Protein Coding ◽

Variable Regions ◽

Protein Coding Genes ◽

Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

Download Full-text

Gammaproteobacteria as essential primary symbionts in the striped shield bug, Graphosoma Lineatum (Hemiptera: Pentatomidae)

Scientific Reports ◽

10.1038/srep33168 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 24

Author(s):

Naeime Karamipour ◽

Yaghoub Fathipour ◽

Mohammad Mehrabadi

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Adult Stage ◽

Phylogenetic Analyses ◽

Light And Electron Microscopy ◽

Pcr Analysis ◽

Evolutionary Analysis ◽

Bacterial Cells ◽

Stink Bug ◽

Surface Sterilization

Abstract Many members of suborder Heteroptra harbor heritable symbiotic bacteria. Here we characterize the gut symbiotic bacterium in Graphosoma lineatum (Hemiptera: Pentatomidae) by using molecular phylogeny, real-time PCR analysis as well as light and electron microscopy observations. The microscopy observations revealed the presence of a large number of rod-shaped bacterial cells in the crypts. A very high prevalence (98 to 100%) of the symbiont infection was found in the insect populations that strongly supports an intimate association between these two organisms. Real-time PCR analysis also showed that the Gammaproteobacteria dominated the crypts. The sequences of 16sr RNA and groEL genes of symbiont showed high levels of similarity (93 to 95%) to Pantoea agglomeranse and Erwinia herbicola Gammaproteobacteria. Phylogenetic analyses placed G. lineatum symbiont in a well-defined branch, divergent from other stink bug bacterial symbionts. Co-evolutionary analysis showed lack of host-symbiont phylogenetic congruence. Surface sterilization of eggs resulted in increased pre-adult stage in the offspring (aposymbionts) in comparison to the normal. Also, fecundity, longevity, and adult stage were significantly decreased in the aposymbionts. Therefore, it seems that the symbiont might play a vital function in the host biology, in which host optimal development depends on the symbiont.

Download Full-text

A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Molecular Biology and Evolution ◽

10.1093/molbev/msaa265 ◽

2020 ◽

Author(s):

Nicolas Rodrigue ◽

Thibault Latrille ◽

Nicolas Lartillot

Keyword(s):

Adaptive Evolution ◽

Real Data ◽

Data Sets ◽

Protein Coding ◽

Site Specific ◽

Protein Coding Genes ◽

Codon Substitution ◽

Selection Framework ◽

Dna Alignment ◽

The Impact

Abstract In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.

Download Full-text

Phylogenetic Characterization of Arboviruses in Patients Suffering from Acute Fever in Rondônia, Brazil

Viruses ◽

10.3390/v12080889 ◽

2020 ◽

Vol 12 (8) ◽

pp. 889

Author(s):

Jackson Alves da Silva Queiroz ◽

Luan Felipo Botelho-Souza ◽

Felipe Souza Nogueira-Lima ◽

Rita de Cássia Pontello Rampazzo ◽

Marco Aurélio Krieger ◽

...

Keyword(s):

Viral Load ◽

Phylogenetic Analyses ◽

Metropolitan Region ◽

Evolutionary Analysis ◽

Detectable Viral Load ◽

Conventional Pcr ◽

Serum Samples ◽

Phylogenetic Characterization ◽

Genotype V ◽

Genotype Ii

The purpose of the study was to classify, through phylogenetic analyses, the main arboviruses that have been isolated in the metropolitan region of Porto Velho, Rondônia, Brazil. Serum samples from patients with symptoms suggesting arboviruses were collected and tested by One Step RT-qPCR for Zika, Dengue (serotypes 1–4), Chikungunya, Mayaro and Oropouche viruses. Positive samples were amplified by conventional PCR and sequenced utilizing the Sanger method. The obtained sequences were aligned, and an evolutionary analysis was carried out using Bayesian inference. A total of 308 samples were tested. Of this total, 20 had a detectable viral load for Dengue, being detected DENV1 (18/20), co-infection DENV1 and DENV2 (1/20) and DENV4 (1/20). For Dengue serotype 3 and for the CHIKV, ZIKV, MAYV and OROV viruses, no individuals with a detectable viral load were found. A total of 9 of these samples were magnified by conventional PCR for sequencing. Of these, 6 were successfully sequenced and, according to the evolutionary profile, 5 corresponded to serotype DENV-1 genotype V, and 1 to serotype DENV-4 genotype II. In the study, we demonstrate co-circulation of the DENV-1 genotype V and the DENV-4 genotype II. Co-circulation of several DENV serotypes in the same city poses a risk to the population and is correlated with the increase of the most severe forms of the disease. Similarly, co-circulation of genetically distinct DENV and the occurrence of simultaneous infections can affect recombination events and lead to the emergence of more virulent isolates.

Download Full-text

Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1916786117 ◽

2020 ◽

Vol 117 (11) ◽

pp. 5977-5986 ◽

Cited By ~ 1

Author(s):

Greg Slodkowicz ◽

Nick Goldman

Keyword(s):

Positive Selection ◽

Adaptive Evolution ◽

Evolutionary Biology ◽

Molecular Mechanisms ◽

Structural Information ◽

Protein Structures ◽

Unexpected Finding ◽

Evolutionary Analysis ◽

Genomic Scale ◽

Evolution Of Mammals

Understanding the molecular basis of adaptation to the environment is a central question in evolutionary biology, yet linking detected signatures of positive selection to molecular mechanisms remains challenging. Here we demonstrate that combining sequence-based phylogenetic methods with structural information assists in making such mechanistic interpretations on a genomic scale. Our integrative analysis shows that positively selected sites tend to colocalize on protein structures and that positively selected clusters are found in functionally important regions of proteins, indicating that positive selection can contravene the well-known principle of evolutionary conservation of functionally important regions. This unexpected finding, along with our discovery that positive selection acts on structural clusters, opens previously unexplored strategies for the development of better models of protein evolution. Remarkably, proteins where we detect the strongest evidence of clustering belong to just two functional groups: Components of immune response and metabolic enzymes. This gives a coherent picture of pathogens and xenobiotics as important drivers of adaptive evolution of mammals.

Download Full-text

Molecular Footprint of Drug-Selective Pressure in a Human Immunodeficiency Virus Transmission Chain

Journal of Virology ◽

10.1128/jvi.79.18.11981-11989.2005 ◽

2005 ◽

Vol 79 (18) ◽

pp. 11981-11989 ◽

Cited By ~ 53

Author(s):

Philippe Lemey ◽

Inge Derdelinckx ◽

Andrew Rambaut ◽

Kristel Van Laethem ◽

Stephanie Dumont ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Selective Pressure ◽

Phylogenetic Analyses ◽

Parallel Evolution ◽

Multidrug Resistant ◽

Resistance Mutations ◽

Fixation Rate ◽

Codon Substitution ◽

Transmission Chain ◽

Immunodeficiency Virus

ABSTRACT Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of phylogenetic reconstructions. Here we have characterized an HIV-1 transmission chain consisting of nine infected patients, almost all of whom were treated with antiviral drugs at later stages of infection. Partial pol and env gp41 regions of the HIV genome were directly sequenced from plasma viral RNA for at least one sample from each patient. Phylogenetic analyses in pol using likelihood methods inferred an evolutionary history not fully compatible with the known transmission history. This could be attributed to parallel evolution of drug resistance mutations resulting in the incorrect clustering of multidrug-resistant virus. On the other hand, a fully compatible phylogenetic tree was reconstructed from the env sequences. We were able to identify and quantify the molecular footprint of drug-selective pressure in pol using maximum likelihood inference under different codon substitution models. An increased fixation rate of mutations in the HIV population of the multidrug-resistant patient was demonstrated using molecular clock modeling. We show that molecular evolutionary analyses, guided by a known transmission history, can reveal the presence of confounding factors like natural selection and caution should be taken when accurate descriptions of HIV evolution are required.

Download Full-text

The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene

10.7287/peerj.preprints.27796 ◽

2019 ◽

Author(s):

Qiwen Zhong ◽

Shipeng Yang ◽

Xuemei Sun ◽

Lihui Wang ◽

Yi Li

Keyword(s):

Chloroplast Genome ◽

Adaptive Evolution ◽

Jerusalem Artichoke ◽

Single Copy ◽

Reverse Direction ◽

Evolutionary Analysis ◽

Helianthus Tuberosus ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Coding Regions

Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China which has become an emerging economic crop with rapid development. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (LSC, 83,981 bp), and a small single-copy region (SSC, 18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased towards A/T bases. 32 SSRs were distributed in the non-coding regions. Comparative analysis of the chloroplast genome sequence of Jerusalem artichoke and other species of the composite family revealed the chloroplast genome sequences of plants of the composite family to be highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. Phylogenetic analysis showed Helianthus petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution and has the potential to be used as a phylogenetic reconstruction locus in the composite family. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family, and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.

Download Full-text

Interspecies variation of larval locomotion kinematics in the genus Drosophila and its relation to habitat temperature

BMC Biology ◽

10.1186/s12915-021-01110-4 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Yuji Matsuo ◽

Akinao Nose ◽

Hiroshi Kohsaka

Keyword(s):

Bayesian Inference ◽

Environmental Factors ◽

Evolutionary History ◽

Evolutionary Rate ◽

Phylogenetic Analyses ◽

The Body ◽

Quantitative Relation ◽

Individual Species ◽

Habitat Temperature ◽

History Of

Abstract Background Speed and trajectory of locomotion are the characteristic traits of individual species. Locomotion kinematics may have been shaped during evolution towards increased survival in the habitats of each species. Although kinematics of locomotion is thought to be influenced by habitats, the quantitative relation between the kinematics and environmental factors has not been fully revealed. Here, we performed comparative analyses of larval locomotion in 11 Drosophila species. Results We found that larval locomotion kinematics are divergent among the species. The diversity is not correlated to the body length but is correlated instead to the habitat temperature of the species. Phylogenetic analyses using Bayesian inference suggest that the evolutionary rate of the kinematics is diverse among phylogenetic tree branches. Conclusions The results of this study imply that the kinematics of larval locomotion has diverged in the evolutionary history of the genus Drosophila and evolved under the effects of the ambient temperature of habitats.

Download Full-text