scholarly journals Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence Comparisons

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Kenro Oshima ◽  
Kenji Ueda ◽  
Teruhiko Beppu ◽  
Hiromi Nishida
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Protein Sequence ◽  
Gene Content ◽  
Functional Constraint ◽  
Specific Gene ◽  
Relaxed Selection ◽  
Sequence Comparisons ◽  
Orthologous Protein ◽  
Species Specific

Comparisons of gene content and orthologous protein sequence constitute a major strategy in whole-genome comparison studies. It is expected that horizontal gene transfer between phylogenetically distant organisms and lineage-specific gene loss have greater influence on gene content-based phylogenetic analysis than orthologous protein sequence-based phylogenetic analysis. To determine the evolution of the syntrophic bacterium Symbiobacterium thermophilum, we analyzed phylogenetic relationships among Clostridia on the basis of gene content and orthologous protein sequence comparisons. These comparisons revealed that these 2 phylogenetic relationships are topologically different. Our results suggest that each Clostridia has a species-specific gene content because frequent genetic exchanges or gene losses have occurred during evolution. Specifically, the phylogenetic positions of syntrophic Clostridia were different between these 2 phylogenetic analyses, suggesting that large diversity in the living environments may cause the observed species-specific gene content. S. thermophilum occupied the most distant position from the other syntrophic Clostridia in the gene content-based phylogenetic tree. We identified 32 genes (14 under relaxed selection and 18 under functional constraint) evolving under Symbiobacterium-specific selection on the basis of synonymous-to-nonsynonymous substitution ratios. Five of the 14 genes under relaxed selection are related to transcription. In contrast, none of the 18 genes under functional constraint is related to transcription.

scholarly journals Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins inBurkholderiaspp.

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Hui San Ong ◽  
Rahmah Mohamed ◽  
Mohd Firdaus-Raih
Keyword(s):  
Comparative Analysis ◽  
Genome Sequence ◽  
Defense Mechanisms ◽  
Surface Proteins ◽  
Ecological Niches ◽  
Specific Gene ◽  
Sequence Comparisons ◽  
Virulence Protein ◽  
Associated Proteins ◽  
Species Specific

Members of theBurkholderiafamily occupy diverse ecological niches. In pathogenic family members, glycan-associated proteins are often linked to functions that include virulence, protein conformation maintenance, surface recognition, cell adhesion, and immune system evasion. Comparative analysis of availableBurkholderiagenomes has revealed a core set of 178 glycan-associated proteins shared by allBurkholderiaof which 68 are homologous to known essential genes. The genome sequence comparisons revealed insights into species-specific gene acquisitions through gene transfers, identified an S-layer protein, and proposed that significantly reactive surface proteins are associated to sugar moieties as a potential means to circumvent host defense mechanisms. The comparative analysis using a curated database of search queries enabled us to gain insights into the extent of conservation and diversity, as well as the possible virulence-associated roles of glycan-associated proteins in members of theBurkholderiaspp. The curated list of glycan-associated proteins used can also be directed to screen other genomes for glycan-associated homologs.

scholarly journals Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships

2017 ◽  
Vol 11 ◽  
pp. 117793221769013 ◽  
Author(s):  
Luca Ambrosino ◽  
Maria Luisa Chiusano
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Function ◽  
Phylogenetic Relationships ◽  
Protein Sequence ◽  
Gene Evolution ◽  
Test Case ◽  
Messenger Rnas ◽  
Alignment Quality ◽  
Sequence Comparisons ◽  
Proteome Level

The detection of orthologs is a key approach in genomics, useful to understand gene evolution and phylogenetic relationships and essential for gene function prediction. However, a reliable annotation of the encoded protein regions is still a limiting aspect in genomics, mainly due to the lack of confirmatory experimental evidence at proteome level. Nevertheless, the current ortholog collections are generally based on protein sequence comparisons, in addition to the availability of large transcriptome sequence collections. We developed Transcriptologs, a method for the prediction of orthologs based on similarities of translated fragments from messenger RNAs of 2 species. We implemented a procedure to extend BLAST-based alignments and to define orthologs based on the Bidirectional Best Hit approach. Results from a test case on Arabidopsis thaliana and Sorghum bicolor transcript collections revealed in some cases outperformance of Transcriptologs in comparison with a classical protein-based analysis in terms of alignment quality, revealing similarities otherwise not detectable.

scholarly journals Middle Pleistocene protein sequences from the rhinoceros genusStephanorhinusand the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3033 ◽  
Author(s):  
Frido Welker ◽  
Geoff M. Smith ◽  
Jarod M. Hutson ◽  
Lutz Kindler ◽  
Alejandro Garcia-Moreno ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Phylogenetic Analysis ◽  
Late Pleistocene ◽  
Phylogenetic Relationships ◽  
Protein Sequence ◽  
Sequence Data ◽  
Protein Sequences ◽  
Middle Pleistocene ◽  
Extant Species ◽  
Protein Sequence Data

BackgroundAncient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genusStephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, includingStephanorhinusandDicerorhinus.MethodsZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genusStephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle PleistoceneStephanorhinusspecimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus,Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods.ResultsVarious ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae.Stephanorhinusis shown to be most closely related to the generaCoelodontaandDicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genusRhinoceros, opposed to forming a clade with the black and white rhinoceros species.DiscussionThe first biomolecular dataset available forStephanorhinusplaces this genus together with the extinct genusCoelodontaand the extant genusDicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genusDicerorhinusin a clade together with extantRhinocerosspecies. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals First Report of Chlamydia abortus in Farmed Fur Animals

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Zhaocai Li ◽  
Ping Liu ◽  
Xiaoan Cao ◽  
Zhongzi Lou ◽  
Kinga Zaręba-Marchewka ◽  
...  
Keyword(s):  
Economic Loss ◽  
23S Rrna ◽  
Specific Gene ◽  
First Report ◽  
Veterinary Importance ◽  
Potential Risks ◽  
Species Specific ◽  
Fur Animals ◽  
Globally Distributed ◽  
Raccoon Dogs

Chlamydia (C.) abortus, a globally distributed obligate intracellular bacterium, has attracted increasing interest according to its veterinary importance and zoonotic nature. C. abortus can infect a variety of animals and cause foetal loss in livestock resulting in economic loss. In this study, the samples collected from two farms of foxes (n=20), raccoon dogs (n=15) and minks (n=20), were investigated by Chlamydiaceae- and Chlamydia species-specific real-time PCR. The results showed that all the tested foxes (20/20) and raccoon dogs (15/15) harbored Chlamydia spp., while 5% of minks (1/20) were positive for Chlamydia spp. C. abortus was identified in all positive samples as the dominant Chlamydia species, with C. pecorum DNA coexistence in some of the rectal samples (7/20) taken from foxes. Phylogenetic analysis based on specific gene fragments of 16S rRNA, IGS-23S rRNA, and ompA revealed that all sequences obtained in this study were assigned to the Chlamydiaceae family with high similarity to C. abortus S26/3 and B577 previously identified in ruminants. This is the first report confirming that farmed foxes, raccoon dogs, and minks carry C. abortus. Further studies are needed to fully elucidate the epidemiology and pathogenicity of this pathogen in farmed fur animals as well as the potential risks to public health.

Phylogenetic analysis of the subfamily Hylodinae (Anura, Leptodactylidae) based on morphological characters

2005 ◽  
Vol 26 (2) ◽  
pp. 139-147 ◽  
Author(s):  
Francisca do Val ◽  
Paulo Nuin
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
The Other ◽  
The Family

AbstractThe systematics and phylogenetic relationships of the family Leptodactylidae are controversial as is the intrafamilial phylogeny of the leptodactylids. Here we analyze the relationships of the leptodactylid subfamily Hylodinae. This subfamily has been considered to be monophyletic and composed of three genera, Hylodes, Crossodactylus and Megaelosia. In the present study 49 characters were used, based on different studies on Leptodactylidae phylogeny. Maximum parsimony methods with unweighted and successively weighted characters were used to estimate the phylogeny of the Hylodinae. Upon analysis, the data provided further evidence of the monophyletic status of the three genera, with Megaelosia being the basal genus and the other two genera being sister taxa. The analysis with successive weighting results in a more resolved topology of the species subgroups of the genus Hylodes and separates this genus from Crossodactylus and confirms that the hylodines are monophyletic.

Profile of a mammalian sperm receptor

Development ◽  
1990 ◽  
Vol 108 (1) ◽  
pp. 1-17 ◽  
Author(s):  
P.M. Wassarman
Keyword(s):  
Gene Expression ◽  
Zona Pellucida ◽  
Specific Gene ◽  
Mammalian Development ◽  
Unique Nature ◽  
Mammalian Fertilization ◽  
Species Specific ◽  
Available Information ◽  
Mammalian Eggs ◽  
Sperm Receptor

Complementary molecules on the surface of eggs and sperm are responsible for species-specific interactions between gametes during fertilization in both plants and animals. In this essay, several aspects of current research on the mouse egg receptor for sperm, a zona pellucida glycoprotein called ZP3, are addressed. These include the structure, synthesis, and functions of the sperm receptor during oogenesis and fertilization in mice. Several conclusions are drawn from available information. These include (I) ZP3 is a member of a unique class of glycoproteins found exclusively in the extracellular coat (zona pellucida) of mammalian eggs. (II) ZP3 gene expression is an example of oocyte-specific and, therefore, sex-specific gene expression during mammalian development. (III) ZP3 is a structural glycoprotein involved in assembly of the egg extracellular coat during mammalian oogenesis. (IV) ZP3 is a sperm receptor involved in carbohydrate-mediated gamete recognition and adhesion during mammalian fertilization. (V) ZP3 is an inducer of sperm exocytosis (acrosome reaction) during mammalian fertilization. (VI) ZP3 participates in the secondary block to polyspermy following fertilization in mammals. (VII) The extracellular coat of other mammalian eggs contains a glycoprotein that is functionally analogous to mouse ZP3. The unique nature, highly restricted expression, and multiple roles of ZP3 during mammalian development make this glycoprotein a particularly attractive subject for investigation at both the cellular and molecular levels.

scholarly journals Single-cell RNA sequencing of Plasmodium vivax sporozoites reveals stage- and species-specific transcriptomic signatures

2021 ◽  
Author(s):  
Anthony A Ruberto ◽  
Caitlin Bourke ◽  
Amélie Vantaux ◽  
Steven P Maher ◽  
Aaron Jex ◽  
...  
Keyword(s):  
Single Cell ◽  
Salivary Glands ◽  
Plasmodium Vivax ◽  
Translational Regulation ◽  
Developmental Trajectory ◽  
Specific Gene ◽  
Developmental States ◽  
Usage Patterns ◽  
Gene Usage ◽  
Species Specific

Plasmodium vivax sporozoites reside in the salivary glands of a mosquito before infecting a human host. Previous transcriptome-wide studies in populations of these forms were limited in their ability to elucidate cell-to-cell variation, thereby masking cellular states potentially important in understanding transmission outcomes. In this study, we performed transcription profiling on 9,947 P. vivax sporozoites to assess the extent to which they differ at single-cell resolution. We show that sporozoites residing in the mosquito's salivary glands exist in distinct developmental states, as defined by their transcriptomic signatures. Additionally, relative to P. falciparum, P. vivax displays overlapping and unique gene usage patterns, highlighting conserved and species-specific gene programs. Notably, distinguishing P. vivax from P. falciparum were a subset of P. vivax sporozoites expressing genes associated with translational regulation and repression. Finally, our comparison of single-cell transcriptomic data from P. vivax sporozoite and erythrocytic forms reveals gene usage patterns unique to sporozoites. In defining the transcriptomic signatures of individual P. vivax sporozoites, our work provides new insights into the factors driving their developmental trajectory and lays the groundwork for a more comprehensive P. vivax cell atlas.

Albumin Immunological Relationships of Australian Marsupials. 2. The Pseudocheiridae

1990 ◽  
Vol 38 (5) ◽  
pp. 519 ◽  
Author(s):  
PR Baverstock ◽  
M Krieg ◽  
J Birrell ◽  
GM Mckay
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Position ◽  
The Family ◽  
Microcomplement Fixation

Microcomplement fixation of albumin was used to examine the phylogenetic relationships among the ringtail possums, family Pseudocheiridae. Phylogenetic analysis of the data supports the hypothesis of at least three distinct clades within the family: one containing Petauroides and Hemibelideus; a second consisting of Pseudocheirus herbertensis, Ps. forbesi, Ps. mayeri, and Ps. canescens; and a third containing Ps. archeri, Ps. corinnae, Ps. cupreus and Ps. dahli. The data have not resolved the phylogenetic position of Ps. peregrinus, which may either form a separate clade or lie close to the Ps. archeri clade.

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