scholarly journals Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa)

GigaScience ◽  
2019 ◽  
Vol 8 (7) ◽  
Author(s):  
Aki Ohdera ◽  
Cheryl L Ames ◽  
Rebecca B Dikow ◽  
Ehsan Kayal ◽  
Marta Chiodin ◽  
...  
Keyword(s):  
Life History ◽  
Evolutionary History ◽  
Life History Traits ◽  
Hox Genes ◽  
Common Ancestor ◽  
Last Common Ancestor ◽  
Valuable Resource ◽  
Genomic Features ◽  
Cassiopea Xamachana ◽  
Nuisance Species

Abstract Background Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa—the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but there are currently no published genomes within Staurozoa and Cubozoa. Findings Here we present 3 new draft genomes of Calvadosia cruxmelitensis (Staurozoa), Alatina alata (Cubozoa), and Cassiopea xamachana (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. Conclusions These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.

scholarly journals Evolutionary history and metabolic insights of ancient mammalian uricases

2014 ◽  
Vol 111 (10) ◽  
pp. 3763-3768 ◽  
Author(s):  
James T. Kratzer ◽  
Miguel A. Lanaspa ◽  
Michael N. Murphy ◽  
Christina Cicerchi ◽  
Christina L. Graves ◽  
...  
Keyword(s):  
Uric Acid ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Tumor Lysis Syndrome ◽  
Integrated Approach ◽  
Last Common Ancestor ◽  
Evolutionary Models ◽  
Monosodium Urate ◽  
Domains Of Life ◽  
History Of

Uricase is an enzyme involved in purine catabolism and is found in all three domains of life. Curiously, uricase is not functional in some organisms despite its role in converting highly insoluble uric acid into 5-hydroxyisourate. Of particular interest is the observation that apes, including humans, cannot oxidize uric acid, and it appears that multiple, independent evolutionary events led to the silencing or pseudogenization of the uricase gene in ancestral apes. Various arguments have been made to suggest why natural selection would allow the accumulation of uric acid despite the physiological consequences of crystallized monosodium urate acutely causing liver/kidney damage or chronically causing gout. We have applied evolutionary models to understand the history of primate uricases by resurrecting ancestral mammalian intermediates before the pseudogenization events of this gene family. Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history by crystallizing a mammalian uricase protein. Further, ancient and modern uricases were stably transfected into HepG2 liver cells to test one hypothesis that uricase pseudogenization allowed ancient frugivorous apes to rapidly convert fructose into fat. Finally, pharmacokinetics of an ancient uricase injected in rodents suggest that our integrated approach provides the foundation for an evolutionarily-engineered enzyme capable of treating gout and preventing tumor lysis syndrome in human patients.

scholarly journals Mycenagenomes resolve the evolution of fungal bioluminescence

2020 ◽  
Vol 117 (49) ◽  
pp. 31267-31277
Author(s):  
Huei-Mien Ke ◽  
Hsin-Han Lee ◽  
Chan-Yi Ivy Lin ◽  
Yu-Ching Liu ◽  
Min R. Lu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Developmental Stages ◽  
De Novo ◽  
Fungal Species ◽  
Last Common Ancestor ◽  
Diverse Group ◽  
Mushroom Species ◽  
Genome Assemblies

Mushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life; yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. We sequenced the genomes and transcriptomes of five bonnet mushroom species (Mycenaspp.), a diverse lineage comprising the majority of bioluminescent fungi. Two species with haploid genome assemblies ∼150 Mb are among the largest in Agaricales, and we found that a variety of repeats betweenMycenaspecies were differentially mediated by DNA methylation. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was maintained through at least 160 million years of evolution. Analyses of synteny across genomes of bioluminescent species resolved how the luciferase cluster was derived by duplication and translocation, frequently rearranged and lost in mostMycenaspecies, but conserved in theArmillarialineage. Luciferase cluster members were coexpressed across developmental stages, with the highest expression in fruiting body caps and stipes, suggesting fruiting-related adaptive functions. Our results contribute to understanding a de novo origin of bioluminescence and the corresponding gene cluster in a diverse group of enigmatic fungal species.

scholarly journals The evolutionary history of the hominin hand since the last common ancestor of Pan and Homo

2008 ◽  
Vol 212 (4) ◽  
pp. 544-562 ◽  
Author(s):  
Matthew W. Tocheri ◽  
Caley M. Orr ◽  
Marc C. Jacofsky ◽  
Mary W. Marzke
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Last Common Ancestor ◽  
History Of

scholarly journals Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species

2021 ◽  
Author(s):  
Chun Shen Lim ◽  
Brooke N Weinstein ◽  
Scott W Roy ◽  
Chris M Brown
Keyword(s):  
Ribosome Biogenesis ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Intron Loss ◽  
Fungal Species ◽  
Last Common Ancestor ◽  
Intron Evolution ◽  
Protein Coding ◽  
Genes Encoding ◽  
Fungal Genomes

Abstract Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron-exon structures, and raising the question as to why these few introns are retained. Here we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per one kbp of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and non-coding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.

scholarly journals The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Endemism, and Hybridization

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1001
Author(s):  
Zhiqing Xue ◽  
Josef Greimler ◽  
Ovidiu Paun ◽  
Kerry Ford ◽  
Michael H. J. Barfuss ◽  
...  
Keyword(s):  
New Zealand ◽  
Evolutionary History ◽  
Dna Analysis ◽  
Common Ancestor ◽  
Plastid Dna ◽  
Last Common Ancestor ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Test Species ◽  
History Of

The contrasting evolutionary histories of endemic versus related cosmopolitan species provide avenues to understand the spatial drivers and limitations of biodiversity. Here, we investigated the evolutionary history of three New Zealand endemic Deschampsia species, and how they are related to cosmopolitan D. cespitosa. We used RADseq to test species delimitations, infer a dated species tree, and investigate gene flow patterns between the New Zealand endemics and the D. cespitosa populations of New Zealand, Australia and Korea. Whole plastid DNA analysis was performed on a larger worldwide sampling. Morphometrics of selected characters were applied to New Zealand sampling. Our RADseq review of over 55 Mbp showed the endemics as genetically well-defined from each other. Their last common ancestor with D. cespitosa lived during the last ten MY. The New Zealand D. cespitosa appears in a clade with Australian and Korean samples. Whole plastid DNA analysis revealed the endemics as members of a southern hemisphere clade, excluding the extant D. cespitosa of New Zealand. Both data provided strong evidence for hybridization between D. cespitosa and D. chapmanii. Our findings provide evidence for at least two migration events of the genus Deschampsia to New Zealand and hybridization between D. cespitosa and endemic taxa.

scholarly journals Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Simone Rampelli ◽  
Silvia Turroni ◽  
Carolina Mallol ◽  
Cristo Hernandez ◽  
Bertila Galván ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Modern Human ◽  
Intestinal Microbiome ◽  
Last Common Ancestor ◽  
Human Gut ◽  
Paleolithic Site ◽  
Human Gut Microbiome ◽  
The Past

AbstractA comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

scholarly journals Genome sequences reveal divergence times of malaria parasite lineages

Parasitology ◽  
2010 ◽  
Vol 138 (13) ◽  
pp. 1737-1749 ◽  
Author(s):  
JOANA C. SILVA ◽  
AMY EGAN ◽  
ROBERT FRIEDMAN ◽  
JAMES B. MUNRO ◽  
JANE M. CARLTON ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Orthologous Gene ◽  
The Other ◽  
Divergence Times ◽  
Last Common Ancestor ◽  
Genome Sequences ◽  
Malaria Parasites ◽  
Human Malaria ◽  
History Of

SUMMARYObjectiveThe evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum.MethodsWe present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups.ResultsOur analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys.ConclusionThe results support an ancient association between malaria parasites and their primate hosts, including humans.

scholarly journals The Eukaryotic Last Common Ancestor Was Bifunctional for Hopanoid and Sterol Production

2021 ◽  
Author(s):  
Warren Francis
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Last Common Ancestor ◽  
Metabolic Demand ◽  
Anaerobic Conditions ◽  
Vertical Inheritance ◽  
Single Origin ◽  
Key Species ◽  
Facultative Aerobe ◽  
History Of

Steroid and hopanoid biomarkers can be found in ancient rocks and may give a glimpse of what life was present at that time. Sterols and hopanoids are produced by two related enzymes, though the evolutionary history of this protein family is complicated by losses and horizontal gene transfers, and appears to be widely misinterpretted. Here, I have added sequences from additional key species, and re-analysis of the phylogeny of SHC and OSC indicates a single origin of both enzymes among eukaryotes. This pattern is best explained by vertical inheritance of both enzymes from a bacterial ancestor, followed by widespread loss of SHC, and two subsequent HGT events to ferns and ascomycetes. Thus, the last common ancestor of eukaryotes would have been bifunctional for both sterol and hopanoid production. Later enzymatic innovations allowed diversification of sterols in eukaryotes. Contrary to previous interpretations, the LCA of eukaryotes potentially would have been able to produce hopanoids as a substitute for sterols in anaerobic conditions. Without invoking any other metabolic demand, the LCA of eukaryotes could have been a facultative aerobe, living in unstable conditions with respect to oxygen level.

scholarly journals Casting Light on the Adaptation Mechanisms and Evolutionary History of the Widespread Sumerlaeota

mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Yun Fang ◽  
Yang Yuan ◽  
Jun Liu ◽  
Geng Wu ◽  
Jian Yang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Rrna Gene ◽  
Gene Gain ◽  
Last Common Ancestor ◽  
Facultatively Anaerobic ◽  
Adaptation Mechanisms ◽  
Harsh Conditions

ABSTRACT Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported. As such, their physiology, ecology, and evolutionary history remain unknown. The 16S rRNA gene survey reveals that Sumerlaeota is frequently detected in diverse environments globally, especially cold arid desert soils and deep-sea basin surface sediments, where it is one dominant microbial group. Here, we retrieved four Sumerlaeota metagenome-assembled genomes (MAGs) from two hot springs and one saline lake. Including another 12 publicly available MAGs, they represent six of the nine putative Sumerlaeota subgroups/orders, as indicated by 16S rRNA gene-based phylogeny. These elusive organisms likely obtain carbon mainly through utilization of refractory organics (e.g., chitin and cellulose) and proteinaceous compounds, suggesting that Sumerlaeota act as scavengers in nature. The presence of key bidirectional enzymes involved in acetate and hydrogen metabolisms in these MAGs suggests that they are acetogenic bacteria capable of both the production and consumption of hydrogen. The capabilities of dissimilatory nitrate and sulfate reduction, nitrogen fixation, phosphate solubilization, and organic phosphorus mineralization may confer these heterotrophs great advantages to thrive under diverse harsh conditions. Ancestral state reconstruction indicated that Sumerlaeota originated from chemotrophic and facultatively anaerobic ancestors, and their smaller and variably sized genomes evolved along dynamic pathways from a sizeable common ancestor (2,342 genes), leading to their physiological divergence. Notably, large gene gain and larger loss events occurred at the branch to the last common ancestor of the order subgroup 1, likely due to niche expansion and population size effects. IMPORTANCE In recent years, the tree of life has expanded substantially. Despite this, many abundant yet uncultivated microbial groups remain to be explored. The candidate phylum Sumerlaeota is widely distributed in various harsh environments. However, their physiology, adaptation mechanisms, and evolution remain elusive due to a lack of pure cultures and limited available genomes. Here, we used genomes from uncultivated members of Sumerlaeota to disclose why these taxa can thrive under diverse harsh conditions and how they evolved from a chemotrophic and facultatively anaerobic common ancestor. This study deeply explored the biology of Sumerlaeota and provided novel insights into their possible roles in global biogeochemical cycles, adaptation mechanisms, ecological significance, and evolutionary history.

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