scholarly journals Pinpointing the PRDM9-PRDM7 Gene Duplication Event During Primate Divergence

2021 ◽  
Vol 12 ◽  
Author(s):  
Sacha Heerschop ◽  
Zahra Fagrouch ◽  
Ernst J. Verschoor ◽  
Hans Zischler
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Mechanisms ◽  
Zinc Fingers ◽  
Hybrid Sterility ◽  
Duplication Event ◽  
Model Systems ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Evolutionary Consequences ◽  
Exon 10

Studies on the function of PRDM9 in model systems and its evolution during vertebrate divergence shed light on the basic molecular mechanisms of hybrid sterility and its evolutionary consequences. However, information regarding PRDM9-homolog, PRDM7, whose origin is placed in the primate evolutionary tree, as well as information about the fast-evolving DNA-binding zinc finger array of strepsirrhine PRDM9 are scarce. Thus, we aimed to narrow down the date of the duplication event leading to the emergence of PRDM7 during primate evolution by comparing the phylogenetic tree reconstructions of representative primate samples of PRDM orthologs and paralogs. To confirm our PRDM7 paralogization pattern, database-deposited sequences were used to test the presence/absence patterns expected from the paralogization timing. In addition, we extended the existing phylogenetic tree of haplorrhine PRDM9 zinc fingers with their strepsirrhine counterparts. The inclusion of strepsirrhine zinc fingers completes the PRDM9 primate phylogeny. Moreover, the updated phylogeny of PRDM9 zinc fingers showed distinct clusters of strepsirrhine, tarsier, and anthropoid degenerated zinc fingers. Here, we show that PRDM7 emerged on the branch leading to the most recent common ancestor of catarrhines; therefore, its origin is more recent than previously expected. A more detailed character evolutionary study suggests that PRDM7 may have evolved differently in Cercopithecoidea as compared to Hominoidea: it lacks the first four exons in Old World monkeys orthologs and exon 10 in Papionini orthologs. Dating the origin of PRDM7 is essential for further studies investigating why Hominoidea representatives need another putative histone methyltransferase in the testis.

scholarly journals Early Archean origin of heterodimeric Photosystem I

2017 ◽  
Author(s):  
Tanai Cardona
Keyword(s):  
Gene Duplication ◽  
Photosystem I ◽  
Water Oxidation ◽  
Duplication Event ◽  
Oxygenic Photosynthesis ◽  
Recent Common Ancestor ◽  
Type I ◽  
Reaction Centre ◽  
Gene Duplication Event ◽  
Most Recent Common Ancestor

AbstractWhen and how oxygenic photosynthesis originated remains controversial. Wide uncertainties exist for the earliest detection of biogenic oxygen in the geochemical record or the origin of water oxidation in ancestral lineages of the phylum Cyanobacteria. A unique trait of oxygenic photosynthesis is that the process uses a Type I reaction centre with a heterodimeric core, also known as Photosystem I, made of two distinct but homologous subunits, PsaA and PsaB. In contrast, all other known Type I reaction centres in anoxygenic phototrophs have a homodimeric core. A compelling hypothesis for the evolution of a heterodimeric Type I reaction centre is that the gene duplication that allowed the divergence of PsaA and PsaB was an adaptation to incorporate photoprotective mechanisms against the formation of reactive oxygen species, therefore occurring after the origin of water oxidation to oxygen. Here I show, using sequence comparisons and Bayesian relaxed molecular clocks that this gene duplication event may have occurred in the early Archean more than 3.4 billion years ago, long before the most recent common ancestor of crown group Cyanobacteria and the Great Oxidation Event. If the origin of water oxidation predated this gene duplication event, then that would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

scholarly journals Dual Role of Metallic Trace Elements in Stress Biology—From Negative to Beneficial Impact on Plants

2019 ◽  
Vol 20 (13) ◽  
pp. 3117 ◽  
Author(s):  
Ewa Muszyńska ◽  
Mateusz Labudda
Keyword(s):  
Trace Elements ◽  
Molecular Mechanisms ◽  
Plant Protection ◽  
Model Systems ◽  
Elevated Concentration ◽  
Metallic Ions ◽  
Beneficial Effects ◽  
Metallic Trace Elements ◽  
Beneficial Impact ◽  
Evolutionary Consequences

Heavy metals are an interesting group of trace elements (TEs). Some of them are minutely required for normal plant growth and development, while others have unknown biological actions. They may cause injury when they are applied in an elevated concentration, regardless of the importance for the plant functioning. On the other hand, their application may help to alleviate various abiotic stresses. In this review, both the deleterious and beneficial effects of metallic trace elements from their uptake by roots and leaves, through toxicity, up to the regulation of physiological and molecular mechanisms that are associated with plant protection against stress conditions have been briefly discussed. We have highlighted the involvement of metallic ions in mitigating oxidative stress by the activation of various antioxidant enzymes and emphasized the phenomenon of low-dose stimulation that is caused by non-essential, potentially poisonous elements called hormesis, which is recently one of the most studied issues. Finally, we have described the evolutionary consequences of long-term exposure to metallic elements, resulting in the development of unique assemblages of vegetation, classified as metallophytes, which constitute excellent model systems for research on metal accumulation and tolerance. Taken together, the paper can provide a novel insight into the toxicity concept, since both dose- and genotype-dependent response to the presence of metallic trace elements has been comprehensively explained.

scholarly journals Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus

2020 ◽  
Author(s):  
Armin Scheben ◽  
Olivia Mendivil Ramos ◽  
Melissa Kramer ◽  
Sara Goodwin ◽  
Sara Oppenheim ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Gene Annotation ◽  
Rapid Evolution ◽  
Recent Common Ancestor ◽  
Specific Gene ◽  
Cancer Resistance ◽  
Base Level ◽  
Most Recent Common Ancestor ◽  
Fruit Bat ◽  
Artibeus Jamaicensis

AbstractBats are exceptional among mammals for harbouring diverse pathogens and for their robust immune systems. In addition, bats are unusually long-lived and show low rates of cancer. Contiguous and complete reference genomes are needed to determine the genetic basis of these adaptations and establish bats as models for research into mammalian health. Here we sequenced and analysed the genomes of the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus). We sequenced these two species using a mix of Illumina and Oxford Nanopore Technologies (ONT), assembling draft genomes with some of the highest contig N50s (28-29Mb) of bat genomes to date. Work is in progress to increase the base-level accuracies of these genomes. We conducted gene annotation and identified a set of 10,928 orthologs from bats and mammalian outgroups including humans, rodents, horses, pigs, and dogs. To detect positively selected genes as well as lineage-specific gene gains and losses, we carried out comprehensive branch-site likelihood ratio tests and gene family size analyses. Our analysis found signatures of rapid evolution in the innate immune response genes of bats, and evidence of past infections with diverse viral clades in Artibeus jamaicensis and Pteronotus mesoamericanus. We additionally found evidence of positive selection of tumor suppressors, which may play a role in the low cancer rates, in the most recent common ancestor of bats. These new genomic resources enable insights into the extraordinary adaptations of bats, with implications for mammalian evolutionary studies and public health.

scholarly journals Rediscovering a Forgotten System of Symbiosis: Historical Perspective and Future Potential

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1063
Author(s):  
Vincent G. Martinson
Keyword(s):  
Historical Perspective ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Model Systems ◽  
Recent Common Ancestor ◽  
Comparative Genomic ◽  
Human Populations ◽  
Candida Auris ◽  
Most Recent Common Ancestor ◽  
Recent Emergence

While the majority of symbiosis research is focused on bacteria, microbial eukaryotes play important roles in the microbiota and as pathogens, especially the incredibly diverse Fungi kingdom. The recent emergence of widespread pathogens in wildlife (bats, amphibians, snakes) and multidrug-resistant opportunists in human populations (Candida auris) has highlighted the importance of better understanding animal–fungus interactions. Regardless of their prominence there are few animal–fungus symbiosis models, but modern technological advances are allowing researchers to utilize novel organisms and systems. Here, I review a forgotten system of animal–fungus interactions: the beetle–fungus symbioses of Drugstore and Cigarette beetles with their symbiont Symbiotaphrina. As pioneering systems for the study of mutualistic symbioses, they were heavily researched between 1920 and 1970, but have received only sporadic attention in the past 40 years. Several features make them unique research organisms, including (1) the symbiont is both extracellular and intracellular during the life cycle of the host, and (2) both beetle and fungus can be cultured in isolation. Specifically, fungal symbionts intracellularly infect cells in the larval and adult beetle gut, while accessory glands in adult females harbor extracellular fungi. In this way, research on the microbiota, pathogenesis/infection, and mutualism can be performed. Furthermore, these beetles are economically important stored-product pests found worldwide. In addition to providing a historical perspective of the research undertaken and an overview of beetle biology and their symbiosis with Symbiotaphrina, I performed two analyses on publicly available genomic data. First, in a preliminary comparative genomic analysis of the fungal symbionts, I found striking differences in the pathways for the biosynthesis of two B vitamins important for the host beetle, thiamine and biotin. Second, I estimated the most recent common ancestor for Drugstore and Cigarette beetles at 8.8–13.5 Mya using sequence divergence (CO1 gene). Together, these analyses demonstrate that modern methods and data (genomics, transcriptomes, etc.) have great potential to transform these beetle–fungus systems into model systems again.

scholarly journals Cladogram misreading of undergraduate students in understanding evolutionary

2021 ◽  
Vol 7 (2) ◽  
pp. 179-187
Author(s):  
Sa'diatul Fuadiyah ◽  
Topik Hidayat ◽  
Didik Priyandoko
Keyword(s):  
Phylogenetic Tree ◽  
Undergraduate Students ◽  
Reading Ability ◽  
Common Ancestor ◽  
Monophyletic Group ◽  
Recent Common Ancestor ◽  
Difficulty Level ◽  
Multiple Choice Questions ◽  
Most Recent Common Ancestor ◽  
Data Collection Instrument

The student's ability to understand evolutionary studies is determined by representing a phylogenetic tree or cladogram. This study aims to determine the tree thinking ability, especially the students' reading ability in interpreting the cladogram. This descriptive study involved 29 students as subjects. Students are selected by purposive random sampling, only students who have attended and studied evolution courses. The data collection instrument used tests and interview guidelines. The test questions consist of 20 multiple choice questions with five answer choices. The difficulty level of the questions used includes understanding, applying, analyzing, and evaluating. The phylogenetic tree interpretation refers to four indicators, including the most recent common ancestor (MRCA), monophyletic group, branch proximity, contemporary descendant, and counting the branch or nodes position. The data obtained were analyzed using Microsoft Excel 2013 and Anates-V4, then presented in percentage form. The results showed that many students misinterpreted the cladogram. Furthermore, errors in cladogram interpretation occurred in monophyletic group indicators (38%), most common ancestor (59%), branch proximity (41%), contemporary ancestry (39%), and branch position calculations (53%). These results indicate that misreading of analysis in cladogram interpretation is moderate to high, so it is necessary to formulate the most appropriate way to teach phylogenetic studies in evolution.

scholarly journals Consequences of Recombination on Traditional Phylogenetic Analysis

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 879-891 ◽  
Author(s):  
Mikkel H Schierup ◽  
Jotun Hein
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Population Data ◽  
Recent Common Ancestor ◽  
Data Sets ◽  
Data Set ◽  
Most Recent Common Ancestor ◽  
Total Branch Length ◽  
Viral Sequences

Abstract We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.

scholarly journals The reconstructed ancestral subunit a functions as both V-ATPase isoforms Vph1p and Stv1p inSaccharomyces cerevisiae

2011 ◽  
Vol 22 (17) ◽  
pp. 3176-3191 ◽  
Author(s):  
Gregory C. Finnigan ◽  
Victor Hanson-Smith ◽  
Benjamin D. Houser ◽  
Hae J. Park ◽  
Tom H. Stevens
Keyword(s):  
Common Ancestor ◽  
Evolutionary Model ◽  
Retrograde Transport ◽  
Duplication Event ◽  
Recent Common Ancestor ◽  
Anterograde Transport ◽  
Atpase Subunit ◽  
Ancestral Gene ◽  
Subunit A ◽  
Most Recent Common Ancestor

The vacuolar-type, proton-translocating ATPase (V-ATPase) is a multisubunit enzyme responsible for organelle acidification in eukaryotic cells. Many organisms have evolved V-ATPase subunit isoforms that allow for increased specialization of this critical enzyme. Differential targeting of the V-ATPase to specific subcellular organelles occurs in eukaryotes from humans to budding yeast. In Saccharomyces cerevisiae, the two subunit a isoforms are the only difference between the two V-ATPase populations. Incorporation of Vph1p or Stv1p into the V-ATPase dictates the localization of the V-ATPase to the vacuole or late Golgi/endosome, respectively. A duplication event within fungi gave rise to two subunit a genes. We used ancestral gene reconstruction to generate the most recent common ancestor of Vph1p and Stv1p (Anc.a) and tested its function in yeast. Anc.a localized to both the Golgi/endosomal network and vacuolar membrane and acidified these compartments as part of a hybrid V-ATPase complex. Trafficking of Anc.a did not require retrograde transport from the late endosome to the Golgi that has evolved for retrieval of the Stv1p isoform. Rather, Anc.a localized to both structures through slowed anterograde transport en route to the vacuole. Our results suggest an evolutionary model that describes the differential localization of the two yeast V-ATPase isoforms.

scholarly journals xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

2017 ◽  
Author(s):  
Eliot C Bush ◽  
Anne E Clark ◽  
Carissa A DeRanek ◽  
Alexander Eng ◽  
Juliet Forman ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Genomic Island ◽  
Gene Families ◽  
Enteric Bacteria ◽  
Genomic Islands ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
A Genome ◽  
History Of ◽  
Multiple Strains

AbstractBackgroundGenomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based and comparative have been developed to identify them. Some of these methods are explicitly designed to work in single strains, while others make use of multiple strains. In general, existing methods do not identify islands in the context of the phylogeny in which they evolved. Even multiple strain approaches are best suited to identifying genomic islands that are present in one strain but absent in others. They do not automatically recognize islands which are shared between some strains in the clade or determine the branch on which these islands inserted within the phylogenetic tree.ResultsWe have developed a software package, xenoGI, that identifies genomic islands and maps their origin within a clade of closely related bacteria, determining which branch they inserted on. It takes as input a set of sequenced genomes and a tree specifying their phylogenetic relationships. Making heavy use of synteny information, the package builds gene families in a species-tree-aware way, and then attempts to combine into islands those families whose members are adjacent and whose most recent common ancestor is shared. The package provides a variety of text-based analysis functions, as well as the ability to export genomic islands into formats suitable for viewing in a genome browser. We demonstrate the capabilities of the package with several examples from enteric bacteria, including an examination of the evolution of the acid fitness island in the genus Escherichia. In addition we use output from simulations and a set of known genomic islands from the literature to show that xenoGI can accurately identify genomic islands and place them on a phylogenetic tree.ConclusionsxenoGI is an effective tool for studying the history of genomic island insertions in a clade of microbes. It identifies genomic islands, and determines which branch they inserted on within the phylogenetic tree for the clade. Such information is valuable because it helps us understand the adaptive path that has produced living species. Given the large and growing number of sequenced microbial genomes, this sort of analysis will become increasingly useful in the future.

scholarly journals Research Methodology to Define the Introduction of the SARS-CoV-2 B.1.429 Variant in Hawaii

2021 ◽  
Author(s):  
David P Maison ◽  
Vivek R Nerurkar
Keyword(s):  
Public Health ◽  
Phylogenetic Tree ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Recent Common Ancestor ◽  
Nucleotide Polymorphisms ◽  
Multiple Sequence ◽  
Most Recent Common Ancestor ◽  
Control And Prevention ◽  
Public Health Officials

Abstract Here, we present a methodology to define the origin of SARS-CoV-2 variants as exemplified by defining the introduction of the B.1.429 variant in Hawaii. We used 187 B.1.429 variant sequences from Hawai’i deposited in the GenBank and GISAID as of March 20, 2021, as an example to develop the methodology. Briefly, i) acquire sequences, ii) perform multiple sequence alignment, iii) trim the alignment, iv) remove incomplete sequences, v) remove duplicates, and vi) generate a phylogenetic tree. The tree defined the most recent common ancestor as the origin. Further, the multiple sequence alignment used to generate the phylogenetic tree identified 20 single nucleotide polymorphisms in the B.1.429 variant genome. The Centers for Disease Control and Prevention defines B.1.429 as a variant initially found in California. This variant was introduced in Hawai'i multiple times in early 2021. Based on the phylogenetic tree, we conclude that the B.1.429 variant has entered Hawai’i at different timepoints from at least seven different states in the continental United States. This information provides a tool for policy makers and public health officials in applying precision public health genomics.

Regulation of microRNAs in Inflammation-Associated Colorectal Cancer: A Mechanistic Approach

2020 ◽  
Vol 20 ◽  
Author(s):  
Sridhar Muthusami ◽  
Ilangovan Ramachandran ◽  
Sneha Krishnamoorthy ◽  
Yuvaraj Sambandam ◽  
Satish Ramalingam ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Molecular Mechanisms ◽  
Colorectal Carcinogenesis ◽  
Model Systems ◽  
Necrosis Factor Alpha ◽  
Multi Stage ◽  
Mechanistic Approach ◽  
Tnf Α ◽  
Factor Alpha

: The development of colorectal cancer (CRC) is a multi-stage process. The inflammation of the colon as in inflammatory bowel disease (IBD) such as ulcerative colitis (UC) or Crohn’s disease (CD) is often regarded as the initial trigger for the development of CRC. Many cytokines such as tumor necrosis factor alpha (TNF-α) and several interleukins (ILs) are known to exert proinflammatory actions, and inflammation initiates or promotes tumorigenesis of various cancers, including CRC through differential regulation of microRNAs (miRNAs/miRs). miRNAs can be oncogenic miRNAs (oncomiRs) or anti-oncomiRs/tumor suppressor miRNAs, and they play key roles during colorectal carcinogenesis. However, the functions and molecular mechanisms of regulation of miRNAs involved in inflammation-associated CRC are still anecdotal and largely unknown. Consolidating the published results and offering perspective solutions to circumvent CRC, the current review is focused on the role of miRNAs and their regulation in the development of CRC. We have also discussed the model systems adapted by researchers to delineate the role of miRNAs in inflammation-associated CRC.

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