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Similarity between the human genome and archea genome in deep sea hydrothermal vents?

Similarity between the human genome and archea genome in deep sea hydrothermal vents?



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I'm trying to find some reference that shows what percentage of the human genome is similar to some organism from the domain Archea that lives near or on deep sea hydrothermal vents.

Can someone points me out in the right direction?


To achieve whole genome alignment between a genome as large as a human, and as small as an archea organism, is possible, but in the end, you'll have to strain your eyes to see patterns. The archea genome is about 1-5 million bp long, whereas the human genome is about 3.3 billion bp long (that's a thousand times too large).

In practice what this means is that you may or may not have small islands of similarity, in vast regions of emptiness.

Nevertheless, you can align whole genomes using the MUMer tool (http://mummer.sourceforge.net/). The white paper is here Delcher, Arthur L., et al. "Alignment of whole genomes." Nucleic acids research 27.11 (1999): 2369-2376.

You might also be interested in reading this:

Wei, Liping, et al. "Comparative genomics approaches to study organism similarities and differences." Journal of biomedical informatics 35.2 (2002): 142-150.


Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes

The genomes of the 21 completely sequenced Thermococcales display a characteristic high level of rearrangements. As a result, the prediction of their origin and termination of replication on the sole basis of chromosomal DNA composition or skew is inoperative. Using a different approach based on biologically relevant sequences, we were able to determine oriC position in all 21 genomes. The position of dif, the site where chromosome dimers are resolved before DNA segregation could be predicted in 19 genomes. Computation of the core genome uncovered a number of essential gene clusters with a remarkably stable chromosomal position across species, in sharp contrast with the scrambled nature of their genomes. The active chromosomal reorganization of numerous genes acquired by horizontal transfer, mainly from mobile elements, could explain this phenomenon.


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Pál C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet. 200537:1372–5.

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Yanai I, Lercher M. The society of genes. Cambridge: Harvard University Press 2016.


Introduction

Members of the domain Archaea are now known to have diversified and radiated into a variety of disparate habitats in both aquatic freshwater, marine, and terrestrial environments. When the Archaea were first recognized via phylogenetic analyses of ribosomal RNA sequences of pure cultures (Woese and Fox, 1977 Woese, 1987), they appeared at first to be a narrowly distributed group found in only a few specific, often extreme habitats, including hydrothermal springs and vents, hypersaline ponds, and anoxic niches. Their considerable phylogenetic and habitat diversity, global abundance, and widespread distribution in marine plankton and elsewhere have recently been recognized over the past several decades (DeLong, 1998, 2003 Santoro et al., 2019 Baker et al., 2020). Ongoing discoveries of archaeal ubiquity that first occurred the 1990s were originally propelled by logical extensions of rRNA-based, cultivation-independent survey approach pioneered by Pace et al. in the mid-1980s (Pace et al., 1985, 1986 Pace, 1997).

The ubiquity of planktonic Archaea was first realized in the early 1990s, when two new groups of planktonic Archaea were initially reported. One new clade was peripherally related to the Crenarchaeota (DeLong, 1992 Fuhrman et al., 1992), and was dubbed Marine Group I Archaea (DeLong, 1992). Marine Group I Archaea have recently been proposed to be assigned to the new phylum Thermoproteota (Parks et al., 2020 Rinke et al., 2020). The other new archaeal clade (Marine Group II Archaea) was found to be affiliated with the euryarchaeotal Thermoplasma lineage (DeLong, 1992). Marine Group II have recently been assigned to the phylum Thermoplasmatota in the order Poseidoniales. Two phylotypes called Marine Group IIa and IIb Archaea (Massana et al., 2000) have been placed within the new families Ca. Poseidoniaceae and Ca. Thalassarchaeaceae, respectively (Rinke et al., 2019, 2020). Soon after the discovery of Group I and Group II planktonic Archaea, two other new lineages of planktonic Archaea were also discovered during cultivation independent surveys in marine environments (Fuhrman and Davis, 1997 López-Garc໚ et al., 2001b).

Several excellent reviews and articles focussed on marine planktonic Archaea have recently been published (Stahl and de la Torre, 2012 Zhang et al., 2015 Haro-Moreno et al., 2017 Pereira et al., 2019 Santoro et al., 2019 Baker et al., 2020), so readers are referred to those for more comprehensive overviews. This short Perspective deliberately focuses on a brief historical account of own my lab’s adventures in studying marine planktonic Archaea over the past 30 years. The intent of this brief account is to provide some context and historical perspective on past, current, and ongoing work on marine planktonic Archaea (reported in this collection and elsewhere), as new discoveries about archaeal denizens of the oceans continue to emerge. Apologies in advance to the many excellent contributors to the marine archaeal field, whose work may not be cited herein due to the brevity of this Perspective.


Elusive Asgard Archaea Finally Cultured in Lab

Nicoletta Lanese
Aug 12, 2019

ABOVE: Scientists collected deep-sea mud from Omine Ridge off the Japanese coast using the manned submersible Shinkai 6500.
OAR/NATIONAL UNDERSEA RESEARCH PROGRAM (NURP), JAMSTEC

A n elusive marine microbe, once known only by its DNA, has finally been cultured in the lab and could grant hints as to how eukaryotic life originated, researchers reported August 8 in a preprint posted to bioRxiv. The single-cell organism grows branching appendages and contains eukaryote-like genes, though it belongs to the domain Archaea.

“This is a monumental paper that reflects a tremendous amount of work and perseverance,” says Thijs Ettema, an evolutionary microbiologist at Wageningen University in the Netherlands who was not involved in this study, in an interview with Nature. “We’ve learnt a lot from the genome, but without a lab culture, we can only learn so much.”

In 2015, Ettema and his colleagues spotted samples of the mysterious microbes in mud collected near Loki’s Castle, a sea-floor hydrothermal vent field off the Greenland coast. They recovered an archaean genome speckled with eukaryote-like genes, and soon were followed by other labs that uncovered similar archaea. Many scientists now believe that an ancestor of these Asgard archaea, as they’re collectively known, gave rise to eukaryotic life. They propose that, about 2 billion years ago, an Asgard relative enveloped a passing bacterium that later evolved into a mitochondrion, according to Nature.

See “Archaea Family Tree Blossoms, Thanks to Genomics”

Until now, scientists have pieced together this narrative from isolated genetic fragments of the Asgard lineage. The new study from Japan began long before the ancient archaea captured everyone’s attention, in 2006, and represents a new chapter in the study of these organisms’ evolution, being the first time they have been cultured.

“It’s a tremendous effort, and it’s a really nice story because they started out before the Asgard frenzy even started. Halfway through their experiment they must’ve realized they had gold in their hands,” Simonetta Gribaldo, an evolutionary microbiologist at the Pasteur Institute in Paris, tells Nature.

The strange organism was first plucked from the 2,500-meter-deep Omine Ridge off the coast of Japan, where it was buried in deep-sea mud, according to Science. To mimic the harsh conditions of the seabed, microbiologist Hiroyuki Imachi of the Japan Agency for Marine-Earth Science and Technology and his colleagues built a bioreactor to contain the seafloor muck and continually bathe it in methane gas. Five years later, they scraped samples into glass tubes filled with various nutrients and waited.

A year later, they detected microbes growing in one of the samples that resembled bacteria, superficially, but were genetically distinct. These were the Asgard archaea they had hoped for. Over the next six years, they worked to isolate and culture pure samples of the organism, which they found takes between 14 and 25 days to double its cells in culture. In comparison, most bacteria double in under an hour.

Finally, the researchers produced a pure sample of Prometheoarchaeum syntrophicum, which they named for the Greek god Prometheus who sculpted humans from mud. Although not yet published in a peer-reviewed journal, the paper has already earned praise from prominent leaders in the field.

“It’s one of the slowest-dividing organisms I know of,” says Ettema. Ettema also shared his excitement over the groundbreaking experiment on Twitter and unpacked the significance of the study.

Loki decloacked! https://t.co/BDzAWt92s3 The amount of work described in manuscript represents a monumental effort, of which the importance cannot be understated! A thread. pic.twitter.com/hou1q9OR2P

— Thijs J. G. Ettema . (@Ettema_lab) August 6, 2019

With the cultured microbe in hand, the researchers sequenced its full genome and confirmed the existence of eukaryote-like genes. They also observed that the microbe usually grows in tandem with a second, methane-producing archaeon, with whom it fosters a symbiotic relationship. Prometheoarchaeum breaks down amino acids and supplies its partner with energy in the form of hydrogen, which might otherwise impede the Asgard’s growth, according to Science.

Images captured with an electron microscope revealed that Prometheoarchaeum develops lengthy appendages with multiple branches, according to Nature. The authors suggest the microbe may have used the tentacles to grab hold of oxygen-producing organisms.

“This is exactly what we predicted,” says David Baum, an evolutionary biologist at the University of Wisconsin-Madison, in an interview with Science. In 2014, Baum and a colleague proposed an “inside-out origin” of eukaryotic evolution: internal organelles did not evolve from components drawn into simpler cells, but rather from extensions of the cell membrane that latched onto beneficial partners.

Ettema notes that other known archaea more closely resemble eukaryotes than Prometheoarchaeum, so it remains unclear which stood as the immediate precursor to complex life as we know it. But he expects follow-up studies should now be much easier to pursue. “I’m sure it will not take 12 years to get the next Asgard into culture,” he tells Science.

The preprint authors declined requests for interviews with Nature while their paper is being reviewed by a journal.

“Opinion: Archaea Is Our Evolutionary Sister, Not Mother”

Correction (August 26): Scientists propose that an Asgard relative enveloped a bacterium that evolved into a mitochondrion about 2 billion years ago, not 2 million as previously stated. The Scientist regrets the error.


Wood on the seafloor: An oasis for deep-sea life

Sunken woods promote the dispersal of rare deep-sea animals, forming hotspots of biodiversity at the deep seafloor.

Trees do not grow in the deep sea, nevertheless sunken pieces of wood can develop into oases for deep-sea life -- at least temporarily until the wood is fully degraded. A team of Max Planck researchers from Germany now showed how sunken wood can develop into attractive habitats for a variety of microorganisms and invertebrates. By using underwater robot technology, they confirmed their hypothesis that animals from hot and cold seeps would be attracted to the wood due to the activity of bacteria, which produce hydrogen sulfide during wood degradation.

Many of the animals thriving at hydrothermal vents and cold seeps require special forms of energy such as methane and hydrogen sulfide emerging from the ocean floor. They carry bacterial symbionts in their body, which convert the energy from these compounds into food. The vents and seeps are often separated by hundreds of kilometers of deep-sea desert, with no connection between them.

For a long time it was an unsolved mystery how animals can disperse between those rare oases of energy in the deep sea. One hypothesis was that sunken whale carcasses, large dead algae, and also sunken woods could serve as food source and temporary habitat for deep-sea animals, but only if bacteria were able to produce methane and sulfur compounds from it.

To tackle this question, the team deposited wood logs on the Eastern Mediterranean seafloor at depths of 1700 meters and returned after one year to study the fauna, bacteria, and chemical microgradients.

"We were surprised how many animals had populated the wood already after one year. The main colonizers were wood-boring bivalves of the genus Xylophaga, also named "shipworms" after their shallow-water counterparts. The wood-boring Xylophaga essentially constitute the vanguard and prepare the habitat for other followers," Bienhold said. &bdquoBut they also need assistance from bacteria, namely to make use of the cellulose from the wood, which is difficult to digest."

The team of researchers observed that the wood-boring bivalves had cut large parts of the wood into smaller chips, which were further degraded by many other organisms. This activity led to the consumption of oxygen, enabling the production of hydrogen sulfide by sulfate-reducing microorganisms. And indeed, the researchers also found a mussel, which is typically only found at cold seeps or similar environments where it uses sulfur compounds as an energy source. "It is amazing to see how deep-sea bacteria can transform foreign substances such as wood to provide energy for cold-seep mussels on their journey through the deep ocean," said Antje Boetius, chief scientist of the expedition. Furthermore, the researchers discovered unknown species of deep-sea worms, which have been described by taxonomic experts in Germany and the USA. Thus, sunken woods do not only promote the dispersal of rare deep-sea animals, but also form hotspots of biodiversity at the deep seafloor.


Seafloor Processes

Donato Giovannelli , Roy E. Price , in Encyclopedia of Ocean Sciences (Third Edition) , 2019

Pure Culture Isolates From Shallow-Water Hydrothermal Vents

Much of the microbiology of marine thermophiles started in the early 1980s with pioneering culturing efforts carried out by Karl Stetter in the shallow-water vents off Volcano Island (Eolian Island, Sicily). There, Stetter and colleagues isolated Pyrodictium, the first organism to grow optimally above 100°C (the boiling temperature of water at sea-level), and Pyrolobus, which has a maximum growth temperature of 113°C—spurring a wealth of interest in the isolation of thermophiles and hyperthermophiles from shallow-water hydrothermal vents ( Stetter et al., 1983 , 1987 ). Since then, a number of mesophilic and (hyper)thermophilic heterotrophs and obligate fermenters have been isolated from numerous shallow-water hydrothermal vents ( Table 1 ).

In the hyperthermophilic range, members of the Archaea phyla Crenarchaeota and Euryarchaeota are numerically dominant among isolated strains, and appear to be either obligate aerobes or microaerophiles (members of the genus Acidianus, Pyrobaculum, and Thermococcus), or obligate anaerobes capable of elemental sulfur reduction (members of the genus Pyrodictium, Staphylothermus, Stetteria, Pyrococcus, and Thermococcus). These strains were isolated from shallow-water hydrothermal vents from all over the world, representing settings characterized by different lithologies and geochemistries, suggesting an important role of hyperthermophilic Archaea in the cycling of organic matter at high temperatures regardless of setting. Representatives of the Thermotogae phylum and a single member of the Bacteroidetes were also isolated in the hyperthermophilic range from shallow-water vents in southern Italy and Tachibana Bay, Japan, respectively. In the thermophilic and mesophilic range, isolated pure cultures represent a wider array of phyla, with members of the Gammaproteobacteria, Deltaproteobacteria, Firmicutes, Planctomycetes, Deferribacteres, Bacteroidetes, Chloroflexi, and Thermotogae. Members isolated in this range cover the entire spectrum of possible chemoheterotrophic metabolisms, with obligate fermenters, aerobes and anaerobes capable of S 0 , NO3 − or Fe(III) reduction. Culture-dependent diversity surveys also isolated a high number of heterotrophic Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Firmicutes from shallow-water vents worldwide.

Several phylotypes of obligate and facultative chemolithoautotrophic Bacteria and Archaea have been also isolated from shallow-water hydrothermal vents ( Table 1 ). The majority of these isolates have optimal growth temperatures in the thermophilic and hyperthermophilic range, with representatives of the Euryarchaeota genera Archaeoglobus, Ferroglobus, methanogenic genera Methanopyrus, Methanococcus, and Methanotorris, and representatives of the Crenarchaeota genera Acidianus and Ignicoccus in the Archaea. The majority are capable of oxidizing hydrogen with the exception of Acidianus infernus and Ferroglobus placidus, which oxidize elemental sulfur and Fe(II), respectively. The only Archaea isolate with optimum growth temperatures in the mesophilic range is Methanococcus aeolicus, a methanogen isolated from the Eolian Island shallow-water hydrothermal vents and capable of using both hydrogen and formate as an energy source.

Among the Bacteria isolates, members of the Aquificae phylum and the Delta and Gammaproteobacteria class of the Proteobacteria have been isolated from shallow-water hydrothermal vents worldwide ( Table 1 ). All the Deltaproteobacteria and Aquificae strains are hydrogen oxidizers, with the exception of Hydrogenivirga caldilitoris, which is an obligate sulfur oxidizer. Oxygen is respired by all the Aquificae isolates belonging to the Aquificaceae and Hydrogenothermaceae families, while the only isolate from the Desulfurobacteriaceae, Thermovibrio ruber, is able to respire either nitrate or elemental sulfur, in line with the physiology of the group. Isolates belonging to the Deltaproteobacteria show the higher versatility in term of terminal electron acceptor, being able to use different sulfur compounds (elemental sulfur, thiosulfate, sulfite, sulfate), Fe(III), Mn(IV), and selenate. Strains belonging to the Gammaproteobacteria are the only chemolithoautotrophic isolates described in the mesophilic range ( Table 1 ), and together with the Gammaproteobacteria isolates in the thermophilic range, are obligate aerobes. One exception is Marinobacter santoriniensis, isolated from the hydrothermal sediments of Santorini (Greece), which is capable of aerobic and anaerobic respiration of nitrate and arsenate. Such trends in the use of different electron donors by different taxa may give clues to the geochemical variability of the environmental niche occupied in situ. There is a clear need to increase our efforts to isolate pure cultures of chemolithoautotrophic prokaryotes representing numerically dominant and ecologically significant taxa from these ecosystems.

Based on this information it is clear that the microbial diversity associated with shallow-water vents is poorly constrained. While the similarities between deep-sea and shallow-water vents are evident, differences between the microbial assemblages in the two ecosystems are more subtle, and may be linked to the influence of the organic matter inputs and other dynamic geodrivers present at shallow depths.


The MIxS environmental packages

Fourteen environmental packages provide a wealth of environmental and epidemiological contextual data fields for a complete description of sampling environments. The environmental packages can be combined with any of the GSC checklists ( Fig. 1 and Supplementary Results 2). Researchers within The Human Microbiome Project 26 contributed the host-associated and all human packages. The Terragenome Consortium contributed sediment and soil packages. Finally, ICoMM, Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites and the Max Planck Institute for Marine Microbiology contributed the water package. The MIMARKS working group developed the remaining packages (air, microbial mat/biofilm, miscellaneous natural or artificial environment, plant-associated and wastewater/sludge). The package names describe high-level habitat terms in order to be exhaustive. The miscellaneous natural or artificial environment package contains a generic set of parameters, and is included for any other habitat that does not fall into the other thirteen categories. Whenever needed, multiple packages may be used for the description of the environment.


Genomics

The genomics section embraces studies of whole genome structure, function and evolution. This includes the genomic research of specific life forms as well as metaorganisms and particular habitats. Papers considered for publication include methodology contributions dealing with the sequencing, assembly and annotation of genomic data, studies of whole genome or metagenome composition, organization and function, as well as evolutionary genomics.

Cancer predictive studies

The identification of individual or clusters of predictive genetic alterations might help in defining the outcome of cancer treatment, allowing for the stratification of patients into distinct cohorts for sele.

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Authors: Alejandro R. Walker and Susmita Datta

Citation: Biology Direct 2019 14 :11

Published on: 24 July 2019

Profiling microbial strains in urban environments using metagenomic sequencing data

The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a .

Authors: Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett and Nicola Segata

Citation: Biology Direct 2018 13 :9

Conservation of the separase regulatory domain

We report a protein sequence analysis of the cell cycle regulatory protease, separase. The sequence and structural conservation of the C-terminal protease domain has long been recognized, whereas the N-termina.

Authors: Michael Melesse, Joshua N. Bembenek and Igor B. Zhulin

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Content type: Discovery notes

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Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not.

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Published on: 4 August 2016

Conservation and divergence of the histone code in nucleomorphs

Nucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved in.

Authors: Georgi K. Marinov and Michael Lynch

Citation: Biology Direct 2016 11 :18

Published on: 5 April 2016

Nucleic acids delivery methods for genome editing in zygotes and embryos: the old, the new, and the old-new

In the recent years, sequence-specific nucleases such as ZFNs, TALENs, and CRISPR/Cas9 have revolutionzed the fields of animal genome editing and transgenesis. However, these new techniques require microinject.

Authors: Masahiro Sato, Masato Ohtsuka, Satoshi Watanabe and Channabasavaiah B. Gurumurthy

Citation: Biology Direct 2016 11 :16

Published on: 31 March 2016

Preservation of methylated CpG dinucleotides in human CpG islands

CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cyto.

Authors: Alexander Y. Panchin, Vsevolod J. Makeev and Yulia A. Medvedeva

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Published on: 22 March 2016

A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution

The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their .

Authors: Marek Eliáš, Vladimír Klimeš, Romain Derelle, Romana Petrželková and Jan Tachezy

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Published on: 2 February 2016

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

Next-generation sequencing (NGS) enables the recovery of pathogen genomes from clinical samples without the need for culturing. Depletion of host/microbiota components (e.g., ribosomal RNA and poly-A RNA) and .

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Content type: Discovery notes

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Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm

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A new rhesus macaque assembly and annotation for next-generation sequencing analyses

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Mycobacteriophage-drived diversification of Mycobacterium abscessus

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Authors: Mohamed Sassi, Philippe Gouret, Olivier Chabrol, Pierre Pontarotti and Michel Drancourt

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Parallel universes of Black Six biology

Creation of lethal and synthetic lethal mutations in an experimental organism is a cornerstone of genetic dissection of gene function, and is related to the concept of an essential gene. Common inbred mouse st.

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Published on: 19 July 2014

Midichlorians - the biomeme hypothesis: is there a microbial component to religious rituals?

Cutting edge research of human microbiome diversity has led to the development of the microbiome-gut-brain axis concept, based on the idea that gut microbes may have an impact on the behavior of their human ho.

Authors: Alexander Y Panchin, Alexander I Tuzhikov and Yuri V Panchin

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Faster evolving Drosophilaparalogs lose expression rate and ubiquity and accumulate more non-synonymous SNPs

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Recognizing short coding sequences of prokaryotic genome using a novel iteratively adaptive sparse partial least squares algorithm

Significant efforts have been made to address the problem of identifying short genes in prokaryotic genomes. However, most known methods are not effective in detecting short genes. Because of the limited infor.

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Circularity and self-cleavage as a strategy for the emergence of a chromosome in the RNA-based protocell

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How protein targeting to primary plastids via the endomembrane system could have evolved? A new hypothesis based on phylogenetic studies

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The mechanistic and evolutionary aspects of the 2′- and 3′-OH paradigm in biosynthetic machinery

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RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction

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Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxi.

Authors: Vivek Anantharaman, Kira S Makarova, A Maxwell Burroughs, Eugene V Koonin and L Aravind

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Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes

The PIWI module, found in the PIWI/AGO superfamily of proteins, is a critical component of several cellular pathways including germline maintenance, chromatin organization, regulation of splicing, RNA interfer.

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Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers

MicroRNAs (miRNAs) are non-uniformly distributed in genomes and

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Published on: 22 April 2013

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Published on: 4 April 2013

Invariance and optimality in the regulation of an enzyme

The Michaelis-Menten equation, proposed a century ago, describes the kinetics of enzyme-catalyzed biochemical reactions. Since then, this equation has been used in countless, increasingly complex models of cel.

Authors: Ed Reznik, Stefan Yohe and Daniel Segrè

Citation: Biology Direct 2013 8 :7

Published on: 22 March 2013

Next-generation phylogenomics

Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimagin.

Authors: Cheong Xin Chan and Mark A Ragan

Citation: Biology Direct 2013 8 :3

Published on: 22 January 2013

Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability

Alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the Pacific Ocean. Living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions.

Authors: Thomas Holder, Claire Basquin, Judith Ebert, Nadine Randel, Didier Jollivet, Elena Conti, Gáspár Jékely and Fulvia Bono

Citation: Biology Direct 2013 8 :2

Published on: 16 January 2013

Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of .

Citation: Biology Direct 2013 8 :1

Published on: 16 January 2013

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made.

Authors: Yuri I Wolf, Kira S Makarova, Natalya Yutin and Eugene V Koonin

Citation: Biology Direct 2012 7 :46

Published on: 14 December 2012

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reaso.

Authors: Frank Emmert-Streib, Shailesh Tripathi and Ricardo de Matos Simoes

Citation: Biology Direct 2012 7 :44

Published on: 10 December 2012

Bioinformatics clouds for big data manipulation

As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computin.

Authors: Lin Dai, Xin Gao, Yan Guo, Jingfa Xiao and Zhang Zhang

Citation: Biology Direct 2012 7 :43

Published on: 28 November 2012

The origin of life is a spatially localized stochastic transition

Life depends on biopolymer sequences as catalysts and as genetic material. A key step in the Origin of Life is the emergence of an autocatalytic system of biopolymers. Here we study computational models that a.

Authors: Meng Wu and Paul G Higgs

Citation: Biology Direct 2012 7 :42

Published on: 24 November 2012

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune system.

Authors: Kira S Makarova, Vivek Anantharaman, L Aravind and Eugene V Koonin

Citation: Biology Direct 2012 7 :40

Published on: 14 November 2012

Early evolution of efficient enzymes and genome organization

Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specifici.

Authors: András Szilágyi, Ádám Kun and Eörs Szathmáry

Citation: Biology Direct 2012 7 :38

Published on: 31 October 2012

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX

The dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes. Annotation methods vary considerably and may fail to identi.

Authors: Derrick E Wood, Henry Lin, Ami Levy-Moonshine, Rajiswari Swaminathan, Yi-Chien Chang, Brian P Anton, Lais Osmani, Martin Steffen, Simon Kasif and Steven L Salzberg

Citation: Biology Direct 2012 7 :37

Published on: 30 October 2012

Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates

Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive fam.

Authors: Jerzy Jurka, Weidong Bao, Kenji K Kojima, Oleksiy Kohany and Matthew G Yurka

Citation: Biology Direct 2012 7 :36

Published on: 25 October 2012

Constructive neutral evolution: exploring evolutionary theory’s curious disconnect

Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation.

Citation: Biology Direct 2012 7 :35

Published on: 13 October 2012

Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with functi.

Authors: Valérie de Crécy-Lagard, Farhad Forouhar, Céline Brochier-Armanet, Liang Tong and John F Hunt

Citation: Biology Direct 2012 7 :32

Published on: 26 September 2012

Stop codons in bacteria are not selectively equivalent

The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of st.

Authors: Inna S Povolotskaya, Fyodor A Kondrashov, Alice Ledda and Peter K Vlasov

Citation: Biology Direct 2012 7 :30

Published on: 13 September 2012

Identifying the mechanisms of intron gain: progress and trends

Continued improvements in Next-Generation DNA/RNA sequencing coupled with advances in gene annotation have provided researchers access to a plethora of annotated genomes. Subsequent analyses of orthologous gen.

Authors: Paul Yenerall and Leming Zhou

Citation: Biology Direct 2012 7 :29

Published on: 10 September 2012

Does the central dogma still stand?

Prions are agents of analog, protein conformation-based inheritance that can confer beneficial phenotypes to cells, especially under stress. Combined with genetic variation, prion-mediated inheritance can be c.

Citation: Biology Direct 2012 7 :27

Published on: 23 August 2012

CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs

CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated sequences) is a recently discovered prokaryotic defense system against foreign DNA, including viruses and plasmids. CRISP.

Authors: Marko Djordjevic, Magdalena Djordjevic and Konstantin Severinov

Citation: Biology Direct 2012 7 :24

Published on: 31 July 2012

The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others) a

The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems.

Authors: Harold S Bernhardt

Citation: Biology Direct 2012 7 :23

Published on: 13 July 2012

The manoeuvrability hypothesis to explain the maintenance of bilateral symmetry in animal evolution

The overwhelming majority of animal species exhibit bilateral symmetry. However, the precise evolutionary importance of bilateral symmetry is unknown, although elements of the understanding of the phenomenon h.

Authors: Gábor Holló and Mihály Novák

Citation: Biology Direct 2012 7 :22

Published on: 12 July 2012

CRISPR loci reveal networks of gene exchange in archaea

CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and.

Authors: Avital Brodt, Mor N Lurie-Weinberger and Uri Gophna

Citation: Biology Direct 2011 6 :65

Published on: 21 December 2011

Purine biosynthesis in archaea: variations on a theme

The ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukary.

Authors: Anne M Brown, Samantha L Hoopes, Robert H White and Catherine A Sarisky

Citation: Biology Direct 2011 6 :63

Published on: 14 December 2011

The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations

Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be .


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Keywords: community structure, cultivation, biodegradation, marine actinobacteria, microbial diversity, pyrosequencing, Southwest Indian Ridge

Citation: Chen P, Zhang L, Guo X, Dai X, Liu L, Xi L, Wang J, Song L, Wang Y, Zhu Y, Huang L and Huang Y (2016) Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge. Front. Microbiol. 7:1340. doi: 10.3389/fmicb.2016.01340

Received: 22 May 2016 Accepted: 15 August 2016
Published: 29 August 2016.

William D. Orsi, L࿍wig-Maximilians University of Munich, Germany
Sean Patrick Jungbluth, University of Southern California, USA

Copyright © 2016 Chen, Zhang, Guo, Dai, Liu, Xi, Wang, Song, Wang, Zhu, Huang and Huang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Ying Huang, [email protected]

† Present Address: Lijun Xi, State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum, Qingdao, China