scholarly journals Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta)

2020 ◽  
Author(s):  
Chung Hyun Cho ◽  
Seung In Park ◽  
Claudia Ciniglia ◽  
Eun Chan Yang ◽  
Louis Graf ◽  
...  
Keyword(s):  
Hot Springs ◽  
Rapid Evolution ◽  
Extreme Environments ◽  
Gc Content ◽  
Protein Size ◽  
Protein Properties ◽  
Red Algal ◽  
History Of ◽  
Heterotrophic Metabolism ◽  
Mitochondrial Genome Evolution

Abstract The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the evolutionary history of their mitochondrial genomes. To fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes. This high divergence was likely driven by natural selection in the multiple extreme environments Galdieria species inhabit, their highly flexible heterotrophic metabolism, and the impacts of population size reduction. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.

scholarly journals Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta)

2020 ◽  
Author(s):  
Chung Hyun Cho ◽  
Seung In Park ◽  
Claudia Ciniglia ◽  
Eun Chan Yang ◽  
Louis Graf ◽  
...  
Keyword(s):  
Hot Springs ◽  
Rapid Evolution ◽  
Extreme Environments ◽  
Gc Content ◽  
Protein Size ◽  
Gc Skew ◽  
Protein Properties ◽  
Red Algal ◽  
Heterotrophic Metabolism ◽  
Mitochondrial Genome Evolution

Abstract BackgroundThe Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes). ResultsTo fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes. ConclusionsThis high divergence was likely driven by natural selection in the multiple extreme environments that Galdieria species inhabit combined with their highly flexible heterotrophic metabolism. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.

scholarly journals Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Chung Hyun Cho ◽  
Seung In Park ◽  
Claudia Ciniglia ◽  
Eun Chan Yang ◽  
Louis Graf ◽  
...  
Keyword(s):  
Hot Springs ◽  
Rapid Evolution ◽  
Extreme Environments ◽  
Gc Content ◽  
Protein Size ◽  
Gc Skew ◽  
Protein Properties ◽  
Red Algal ◽  
Heterotrophic Metabolism ◽  
Mitochondrial Genome Evolution

Abstract Background The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes). Results To fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes. Conclusions The high divergence of G-type mitogenomes was likely driven by natural selection in the multiple extreme environments that Galdieria species inhabit combined with their highly flexible heterotrophic metabolism. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.

scholarly journals Phycobiliproteins from extreme environments and their potential applications

2020 ◽  
Vol 71 (13) ◽  
pp. 3827-3842 ◽  
Author(s):  
Anton Puzorjov ◽  
Alistair J McCormick
Keyword(s):  
Hot Springs ◽  
Elevated Temperatures ◽  
Algal Species ◽  
Extreme Environments ◽  
Fundamental Understanding ◽  
Thermophilic Species ◽  
Red Algal ◽  
Potential Applications ◽  
Thermophilic Organisms ◽  
Photosynthetic Adaptation

Abstract The light-harvesting phycobilisome complex is an important component of photosynthesis in cyanobacteria and red algae. Phycobilisomes are composed of phycobiliproteins, including the blue phycobiliprotein phycocyanin, that are considered high-value products with applications in several industries. Remarkably, several cyanobacteria and red algal species retain the capacity to harvest light and photosynthesise under highly selective environments such as hot springs, and flourish in extremes of pH and elevated temperatures. These thermophilic organisms produce thermostable phycobiliproteins, which have superior qualities much needed for wider adoption of these natural pigment–proteins in the food, textile, and other industries. Here we review the available literature on the thermostability of phycobilisome components from thermophilic species and discuss how a better appreciation of phycobiliproteins from extreme environments will benefit our fundamental understanding of photosynthetic adaptation and could provide a sustainable resource for several industrial processes.

scholarly journals Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1169
Author(s):  
Xin Li ◽  
Xiaocen Wang ◽  
Pengtao Gong ◽  
Nan Zhang ◽  
Xichen Zhang ◽  
...  
Keyword(s):  
Codon Usage ◽  
Genetic Manipulation ◽  
Molecular Genetic ◽  
Gc Content ◽  
Giardia Duodenalis ◽  
Codon Usage Pattern ◽  
Protein Size ◽  
New Genes ◽  
Optimal Codons ◽  
Usage Patterns

Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.

scholarly journals Extremophilic Exopolysaccharides: Biotechnologies and Wastewater Remediation

2021 ◽  
Vol 12 ◽  
Author(s):  
Aparna Banerjee ◽  
Shrabana Sarkar ◽  
Tanvi Govil ◽  
Patricio González-Faune ◽  
Gustavo Cabrera-Barjas ◽  
...  
Keyword(s):  
Hydrothermal Vents ◽  
Hot Springs ◽  
Mine Drainage ◽  
Oil Spills ◽  
Extreme Environments ◽  
Substantial Part ◽  
Wastewater Remediation ◽  
Water Contaminants ◽  
Chemical Groups ◽  
Trace And Toxic Metals

Various microorganisms thrive under extreme environments, like hot springs, hydrothermal vents, deep marine ecosystems, hyperacid lakes, acid mine drainage, high UV exposure, and more. To survive against the deleterious effect of these extreme circumstances, they form a network of biofilm where exopolysaccharides (EPSs) comprise a substantial part. The EPSs are often polyanionic due to different functional groups in their structural backbone, including uronic acids, sulfated units, and phosphate groups. Altogether, these chemical groups provide EPSs with a negative charge allowing them to (a) act as ligands toward dissolved cations as well as trace, and toxic metals; (b) be tolerant to the presence of salts, surfactants, and alpha-hydroxyl acids; and (c) interface the solubilization of hydrocarbons. Owing to their unique structural and functional characteristics, EPSs are anticipated to be utilized industrially to remediation of metals, crude oil, and hydrocarbons from contaminated wastewaters, mines, and oil spills. The biotechnological advantages of extremophilic EPSs are more diverse than traditional biopolymers. The present review aims at discussing the mechanisms and strategies for using EPSs from extremophiles in industries and environment bioremediation. Additionally, the potential of EPSs as fascinating biomaterials to mediate biogenic nanoparticles synthesis and treat multicomponent water contaminants is discussed.

scholarly journals Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India

2021 ◽  
Author(s):  
VISHNU PRASOODANAN P K ◽  
Shruti S. Menon ◽  
Rituja Saxena ◽  
Prashant Waiker ◽  
Vineet K Sharma
Keyword(s):  
Hot Springs ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Central India ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Protein Coding ◽  
Protein Coding Genes

Discovery of novel thermophiles has shown promising applications in the field of biotechnology. Due to their thermal stability, they can survive the harsh processes in the industries, which make them important to be characterized and studied. Members of Anoxybacillus are alkaline tolerant thermophiles and have been extensively isolated from manure, dairy-processed plants, and geothermal hot springs. This article reports the assembled data of an aerobic bacterium Anoxybacillus sp. strain MB8, isolated from the Tattapani hot springs in Central India, where the 16S rRNA gene shares an identity of 97% (99% coverage) with Anoxybacillus kamchatkensis strain G10. The de novo assembly and annotation performed on the genome of Anoxybacillus sp. strain MB8 comprises of 2,898,780 bp (in 190 contigs) with a GC content of 41.8% and includes 2,976 protein-coding genes,1 rRNA operon, 73 tRNAs, 1 tm-RNA and 10 CRISPR arrays. The predicted protein-coding genes have been classified into 21 eggNOG categories. The KEGG Automated Annotation Server (KAAS) analysis indicated the presence of assimilatory sulfate reduction pathway, nitrate reducing pathway, and genes for glycoside hydrolases (GHs) and glycoside transferase (GTs). GHs and GTs hold widespread applications, in the baking and food industry for bread manufacturing, and in the paper, detergent and cosmetic industry. Hence, Anoxybacillus sp. strain MB8 holds the potential to be screened and characterized for such commercially relevant enzymes.

Surface and Subsurface Quality Evaluation of Engineered Wood Products by Ultrasonic Means

2014 ◽  
pp. 182-220
Author(s):  
Frank C. Beall ◽  
Henrique Reis
Keyword(s):  
Product Development ◽  
Material Properties ◽  
Rapid Evolution ◽  
Solid Wood ◽  
Wood Products ◽  
Assessment And Evaluation ◽  
Engineered Wood Products ◽  
Engineered Wood ◽  
History Of ◽  
Ultrasonic Techniques

The use of ultrasonic techniques to evaluate the properties of engineered wood-based materials is discussed with respect to research to date and the use of more advanced techniques. The latter is critical because of the rapid evolution from solid wood to reconstituted structural materials. In addition, although considerable research has been done, there have been few introductions into manufacturing. This chapter traces the history of the use and latest developments of ultrasonics in several key areas, particularly the measurement of adhesive curing and quality in composites and laminates, and detection of flaws in solid wood materials. The techniques reviewed apply to product development, material properties, process control, product quality assessment, and evaluation of products in service.

scholarly journals An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
João PL Castro ◽  
Michelle N Yancoskie ◽  
Marta Marchini ◽  
Stefanie Belohlavy ◽  
Layla Hiramatsu ◽  
...  
Keyword(s):  
Bone Growth ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Selection Response ◽  
Major Effect ◽  
Selection Experiment ◽  
Genomic Analyses ◽  
Selection Experiments ◽  
Polygenic Adaptation ◽  
History Of

Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

scholarly journals Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature

2020 ◽  
Vol 8 (6) ◽  
pp. 906 ◽  
Author(s):  
Francisco L. Massello ◽  
Chia Sing Chan ◽  
Kok-Gan Chan ◽  
Kian Mau Goh ◽  
Edgardo Donati ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metabolic Profile ◽  
Hot Springs ◽  
Meta Analysis ◽  
Extreme Environments ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Phylogenetic Distance ◽  
Microbial Profile ◽  
The World

The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities’ profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.

The Triassic U–Pb age for the aquatic long-necked protorosaur of Guizhou, China

2014 ◽  
Vol 151 (4) ◽  
pp. 749-754 ◽  
Author(s):  
YANBIN WANG ◽  
DETING YANG ◽  
JUAN HAN ◽  
LITING WANG ◽  
JIANXIN YAO ◽  
...  
Keyword(s):  
Middle Triassic ◽  
Rapid Evolution ◽  
Guizhou Province ◽  
Ion Microprobe ◽  
Isotopic Age ◽  
Zircon Age ◽  
Marine Reptiles ◽  
Wide Range ◽  
History Of ◽  
Permian Mass Extinction

AbstractThe ancient marine limestone beds of the upper part of the Guanling Formation, Panxian County, Guizhou Province, SW China, yielded a wide range of high-diversity well-preserved marine reptiles such as the fully aquatic protorosaur with an extremely long neckDinocephalosaurus orientalis, the oldest mixosaurid ichthyosaurs and lariosaurs. However, there is no precise isotopic age to study the intriguing origin, evolution and emigration history of the important fauna. We report a sensitive high-resolution ion microprobe (SHRIMP) U–Pb zircon age for a volcanic tuff bed within the upper part of the Guanling Formation. The result indicates that the age of the fossil horizon is 244.0±1.3 Ma, 14 Ma earlier than the previously estimated age based on conodont evidence. We consider that the marine reptiles had a relatively rapid evolution during Middle Triassic time, some 8 Ma after the end-Permian mass extinction.

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