scholarly journals Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

2020 ◽  
Author(s):  
Yang Liu ◽  
Kira S. Makarova ◽  
Wen-Cong Huang ◽  
Yuri I. Wolf ◽  
Anastasia Nikolskaya ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Gene Loss ◽  
Protein Domain ◽  
Dynamic Evolution ◽  
Archaeal Diversity ◽  
Metabolic Diversity ◽  
Complete Genomes ◽  
Conserved Core ◽  
Origin Of Eukaryotes

AbstractComparative analysis of 162 (nearly) complete genomes of Asgard archaea, including 75 not reported previously, substantially expands the phylogenetic and metabolic diversity of the Asgard superphylum, with six additional phyla proposed. Phylogenetic analysis does not strongly support origin of eukaryotes from within Asgard, leaning instead towards a three-domain topology, with eukaryotes branching outside archaea. Comprehensive protein domain analysis in the 162 Asgard genomes results in a major expansion of the set of eukaryote signature proteins (ESPs). The Asgard ESPs show variable phyletic distributions and domain architectures, suggestive of dynamic evolution via horizontal gene transfer (HGT), gene loss, gene duplication and domain shuffling. The results appear best compatible with the origin of the conserved core of eukaryote genes from an unknown ancestral lineage deep within or outside the extant archaeal diversity. Such hypothetical ancestors would accumulate components of the mobile archaeal ‘eukaryome’ via extensive HGT, eventually, giving rise to eukaryote-like cells.

scholarly journals Phylogenetic analysis of perfect repeats in the genomes of unicellular cyanobacteria

2005 ◽  
Vol 3 (2) ◽  
pp. 15-21
Author(s):  
Lidia E Mikheeva ◽  
Yuri L Orlov ◽  
Nikolay A Kolchanov ◽  
Sergey V Shestakov
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Molecular Phylogeny ◽  
Genome Organization ◽  
Whole Genome ◽  
Ecological Genomics ◽  
Close Phylogenetic Relationship ◽  
Complete Genomes ◽  
Relationship Of ◽  
Close Genetic Relationship

We have fulfilled in silico research of number, structure, distribution and location of direct and inverted repeated sequences in eight complete genomes of unicellular cyanobacteria. Analysis of whole genome repeats has shown utility of this approach for purposes of molecular phylogeny and ecological genomics. Comparative analysis of nonrandom repeats patterns has allowed: 1) to confirm the close genetic relationship of two Prochlorococcus marinus strains (MED4 and SS120) that have reduced genomes and inhabit the econiches with different light intensities; 2) to suggest the close phylogenetic relationship of genomes Prochlorococcus marinus MIT9313 and Synechococcus WH8102 that significantly differ by sets of lightharvesting photosystem; 3) to  reveal specific differences in genome organization between marine and freshwater cyanobacteria.

scholarly journals Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes

2018 ◽  
Author(s):  
Mingwei Cai ◽  
Yang Liu ◽  
Zhichao Zhou ◽  
Yuchun Yang ◽  
Jie Pan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Analysis ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Group D ◽  
Origin Of Eukaryotes

AbstractAsgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.

scholarly journals Frequency of Detection and Phylogenetic Analysis of Porcine circovirus 3 (PCV-3) in Healthy Primiparous and Multiparous Sows and Their Mummified Fetuses and Stillborn

Pathogens ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 533 ◽  
Author(s):  
Viviane Saporiti ◽  
Susanna Martorell ◽  
Taís F. Cruz ◽  
Francini Klaumann ◽  
Florencia Correa-Fiz ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Porcine Circovirus ◽  
Reproductive Parameters ◽  
Reproductive Disorders ◽  
Time Points ◽  
Lack Of Information ◽  
Complete Genomes ◽  
Reproductive Disease ◽  
Porcine Circovirus 3 ◽  
Intrauterine Infections

Porcine circovirus 3 (PCV-3) has been suggested as a putative causal agent of swine reproductive disease. A number of different studies have pointed out this association, but there is still a lack of information regarding the normal rates of PCV-3 infection in farms with normal reproductive parameters. The objective of the present study was to assess the frequency of PCV-3 detection in primiparous and multiparous sows and in tissues from their respective fetuses from farms with average reproductive parameters. Sera from 57 primiparous and 64 multiparous sows from 3 different farms were collected at two time points. Brain and lung tissues from 49 mummies and 206 stillborn were collected at farrowing. Samples were tested by PCR, and when positive, quantified by quantitative PCR. Thirty-nine complete genomes were obtained and phylogenetically analyzed. All sera from multiparous sows were negative, while 19/57 (33.3%) primiparous sows were PCV-3 PCR positive. From the 255 tested fetuses, 86 (33.7%) had at least one tissue positive to PCV-3. The frequency of detection in fetuses from primiparous sows (73/91, 80.2%) was significantly higher than those from multiparous ones (13/164, 7.9%). It can be concluded that PCV-3 is able to cause intrauterine infections in absence of overt reproductive disorders.

Gene loss in plants: Evidence from genome-wide phylogenetic analysis of thiamine pyrophosphate-dependent enzymes

2014 ◽  
Vol 53 (3) ◽  
pp. 221-227
Author(s):  
Xin-Min Tian ◽  
Peng Wang ◽  
Wen-Bin Hu ◽  
Da-Hai Gao ◽  
Qiong Li
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Loss ◽  
Thiamine Pyrophosphate ◽  
Genome Wide

scholarly journals CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

2007 ◽  
Vol 36 (Supplement_1) ◽  
pp. D504-D511 ◽  
Author(s):  
Yi Huang ◽  
Susanna K. P. Lau ◽  
Patrick C. Y. Woo ◽  
Kwok-yung Yuen
Keyword(s):  
Comparative Analysis ◽  
Comparative Sequence Analysis ◽  
Nomenclature System ◽  
Comprehensive Database ◽  
Representative Sequence ◽  
Phylogenetic Studies ◽  
Complete Genomes ◽  
Downstream Analysis ◽  
Bat Coronavirus ◽  
Group 1

Abstract The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.

Comparative analysis of the complete chloroplast genomic sequence and chemical components of Cinnamomum micranthum and Cinnamomum kanehirae

Holzforschung ◽  
2017 ◽  
Vol 71 (3) ◽  
pp. 189-197 ◽  
Author(s):  
Chia-Chen Wu ◽  
Fang-Hua Chu ◽  
Cheng-Kuen Ho ◽  
Chia-Hsuan Sung ◽  
Shu-Hwa Chang
Keyword(s):  
Phylogenetic Analysis ◽  
Liquid Chromatography ◽  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Genomic Sequence ◽  
Ultra Performance Liquid Chromatography ◽  
Chemical Components ◽  
Complete Chloroplast Genome ◽  
Medicinal Fungus ◽  
Indel Markers

Abstract Cinnamomum micranthum (Hayata) Hayata is a tree species that is often confused with Cinnamomum kanehirae Hayata, which is an endemic species in Taiwan and the sole natural host of the valuable medicinal fungus Antrodia cinnamomea. However, the two species are highly similar in morphology and difficult to distinguish based on traditional vegetative structures or wood anatomical methods. The aim of the present study was to identify of these two species by DNA and chemical analysis. The complete chloroplast genome of C. micranthum has been determined and compared with that of C. kanehirae. The leaf methanol extracts of these species were also analyzed by ultra-performance liquid chromatography (UPLC). The length of the C. micranthum chloroplast genome was 152675 bp, i.e. 25 bp shorter than that of C. kanehirae. In phylogenetic analysis, C. micranthum was more closely related to C. kanehirae than other six Lauracea species. Six validated insertion/deletions of bases in the DNA (InDels) are suitable for differentiation of the two species. Moreover, high amounts of linalool and sesamin were present in the leaves of C. kanehirae, but not in C. micranthum. Overall, this study provided new insight for distinguishing the two species on the basis of the chemical composition of the leaves and the InDel markers.

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