High Sequence Divergence but Limited Architectural Rearrangements in Organelle Genomes of Cyanophora (Glaucophyta) Species

2020 ◽  
Author(s):  
Sarah Russell ◽  
Christopher Jackson ◽  
Adrian Reyes‐Prieto
Keyword(s):  
Sequence Divergence ◽  
High Sequence Divergence ◽  
Organelle Genomes

scholarly journals Structural characterization and duplication modes of pseudogenes in plants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Flavia Mascagni ◽  
Gabriele Usai ◽  
Andrea Cavallini ◽  
Andrea Porceddu
Keyword(s):  
Evolutionary Rate ◽  
Populus Trichocarpa ◽  
Sequence Divergence ◽  
Strand Break ◽  
Whole Genome ◽  
Flanking Sequence ◽  
Plant Genomes ◽  
High Sequence Divergence ◽  
Flanking Regions

AbstractWe identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

Strong genetic subdivision in Leptobrachium hendricksoni (Anura: Megophryidae) in Southeast Asia

2018 ◽  
Vol 39 (1) ◽  
pp. 99-111
Author(s):  
Gordon Draškić ◽  
Sansareeya Wangkulangkul ◽  
Iñigo Martínez-Solano ◽  
Judit Vörös
Keyword(s):  
Southeast Asia ◽  
Sequence Divergence ◽  
Population Divergence ◽  
Geological History ◽  
Base Pairs ◽  
Sea Levels ◽  
Phylogenetic Studies ◽  
High Sequence Divergence ◽  
Southern Thailand ◽  
Rising Sea Levels

Many biodiversity hotspots are located in areas with a complex geological history, like Southeast Asia, where species diversity may still be far underestimated, especially in morphologically conservative groups like amphibians. Recent phylogenetic studies on the frog genusLeptobrachiumfrom Southeast Asia revealed the presence of deeply divergent mitochondrial clades inLeptobrachium hendricksonifrom Malaysia and Sumatra but populations from Thailand have not been studied so far. In this study, we re-evaluate patterns of intraspecific genetic diversity inL. hendricksonibased on the analysis of combined sequences of mitochondrial 12S and 16S genes (1310 base pairs) including for the first time samples from southern Thailand. Thai populations ofL. hendricksoniformed a distinct clade with respect to populations from central and southern Malaysia and Sumatra. High sequence divergence between lineages from Thailand, Malaysia and Sumatra suggests the possible presence of cryptic species inL. hendricksoni. Divergence withinL. hendricksonidates back to the late Miocene, around 6 Mya, when lineages from Thailand, north Malaysia and Sumatra split from a lineage in south Malaysia, at about the same time as rising sea levels isolated the Thai-Malay peninsula. Subsequent splits took place later in the Pliocene, around 4.5 and 2.6 Mya. Our results highlight the role of geological history in promoting population divergence and speciation.

scholarly journals Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks

Heredity ◽  
2009 ◽  
Vol 104 (6) ◽  
pp. 543-551 ◽  
Author(s):  
M Plohl ◽  
V Petrović ◽  
A Luchetti ◽  
A Ricci ◽  
E Šatović ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Sequence Divergence ◽  
Bivalve Mollusks ◽  
High Sequence Divergence

Morphological and molecular evidence for the recognition of Caloglossa fonticola sp. nov. (Delesseriaceae, Rhodophyta) from an underground spring in Guangxi, China

Phytotaxa ◽  
2021 ◽  
Vol 522 (1) ◽  
pp. 15-26
Author(s):  
KUN-PENG FANG ◽  
FANG-RU NAN ◽  
JIA FENG ◽  
QI LIU ◽  
XU-DONG LIU ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Molecular Evidence ◽  
Unique Combination ◽  
High Sequence Divergence ◽  
Molecular Phylogenetic ◽  
Freshwater Habitats ◽  
Globally Distributed ◽  
Lateral Axis

Caloglossa (Ceramiales, Rhodophyta) is a globally distributed euryhaline red macroalgal genus. However, only a few Caloglossa species have been documented in permanent freshwater habitats. Here, a new Caloglossa species, Caloglossa fonticola sp. nov., is described and illustrated from an underground spring in Bama County, Guangxi, China, based on morphological observations and molecular phylogenetic analysis. The new species is morphologically distinguishable from other species in the genus by a unique combination of character states, including thallus internodal blades linear, hardly or slightly constricted at nodes, adventitious branches and endogenous branches both absent, and unicellular rhizoids forming from clusters of wing cells arising from the first three axial cells of the main axis and lateral axis. Phylogenetic analysis based on rbcL and LSU rRNA DNA sequences indicated that Caloglossa fonticola was nested in a well-supported clade with Caloglossa bengalensis (Bootstrap supports for ML/posterior probabilities for BI: rbcL-98/1.00, LSU-100/1.00), with high sequence divergence between these two species (8.2–8.4% for rbcL and 3.2% for LSU), supporting its specific status. This is the first species of the genus Caloglossa reported in spring water habitats. The description of C. fonticola expands the known diversity of Caloglossa.

scholarly journals Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil’s Disease

2021 ◽  
Vol 22 (24) ◽  
pp. 13434
Author(s):  
Eric Olo Ndela ◽  
François Enault ◽  
Ariane Toussaint
Keyword(s):  
Gene Transfer ◽  
Genomic Organization ◽  
Sequence Divergence ◽  
Specific Gene ◽  
Diverse Group ◽  
High Sequence Divergence ◽  
Causative Agents ◽  
Weil’S Disease ◽  
Weil's Disease ◽  
Model Strain

The virome associated with the corkscrew shaped bacterium Leptospira, responsible for Weil’s disease, is scarcely known, and genetic tools available for these bacteria remain limited. To reduce these two issues, potential transposable prophages were searched in Leptospiraceae genomes. The 236 predicted transposable prophages were particularly abundant in the most pathogenic leptospiral clade, being potentially involved in the acquisition of virulent traits. According to genomic similarities and phylogenies, these prophages are distantly related to known transposable phages and are organized into six groups, one of them encompassing prophages with unusual TA-TA ends. Interestingly, structural and transposition proteins reconstruct different relationships between groups, suggesting ancestral recombinations. Based on the baseplate phylogeny, two large clades emerge, with specific gene-contents and high sequence divergence reflecting their ancient origin. Despite their high divergence, the size and overall genomic organization of all prophages are very conserved, a testimony to the highly constrained nature of their genomes. Finally, similarities between these prophages and the three known non-transposable phages infecting L. biflexa, suggest gene transfer between different Caudovirales inside their leptospiral host, and the possibility to use some of the transposable prophages in that model strain.

scholarly journals Two Distinct Lysosomal Targeting Strategies Afford Trojan Horse Antibodies With Pan-Filovirus Activity

2021 ◽  
Vol 12 ◽  
Author(s):  
Ariel S. Wirchnianski ◽  
Anna Z. Wec ◽  
Elisabeth K. Nyakatura ◽  
Andrew S. Herbert ◽  
Megan M. Slough ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Sequence Divergence ◽  
Proteolytic Cleavage ◽  
Trojan Horse ◽  
Viral Glycoprotein ◽  
High Sequence Divergence ◽  
Niemann Pick ◽  
Sites Of Action ◽  
A Site ◽  
Blocking Antibodies

Multiple agents in the family Filoviridae (filoviruses) are associated with sporadic human outbreaks of highly lethal disease, while others, including several recently identified agents, possess strong zoonotic potential. Although viral glycoprotein (GP)-specific monoclonal antibodies have demonstrated therapeutic utility against filovirus disease, currently FDA-approved molecules lack antiviral breadth. The development of broadly neutralizing antibodies has been challenged by the high sequence divergence among filovirus GPs and the complex GP proteolytic cleavage cascade that accompanies filovirus entry. Despite this variability in the antigenic surface of GP, all filoviruses share a site of vulnerability—the binding site for the universal filovirus entry receptor, Niemann-Pick C1 (NPC1). Unfortunately, this site is shielded in extracellular GP and only uncovered by proteolytic cleavage by host proteases in late endosomes and lysosomes, which are generally inaccessible to antibodies. To overcome this obstacle, we previously developed a ‘Trojan horse’ therapeutic approach in which engineered bispecific antibodies (bsAbs) coopt viral particles to deliver GP:NPC1 interaction-blocking antibodies to their endo/lysosomal sites of action. This approach afforded broad protection against members of the genus Ebolavirus but could not neutralize more divergent filoviruses. Here, we describe next-generation Trojan horse bsAbs that target the endo/lysosomal GP:NPC1 interface with pan-filovirus breadth by exploiting the conserved and widely expressed host cation-independent mannose-6-phosphate receptor for intracellular delivery. Our work highlights a new avenue for the development of single therapeutics protecting against all known and newly emerging filoviruses.

scholarly journals Sequence analysis of the equid herpesvirus 2 chemokine receptor homologues E1, ORF74 and E6 demonstrates high sequence divergence between field isolates

2007 ◽  
Vol 88 (9) ◽  
pp. 2450-2462 ◽  
Author(s):  
Emma L. Sharp ◽  
Helen E. Farrell ◽  
Kerstin Borchers ◽  
Edward C. Holmes ◽  
Nicholas J. Davis-Poynter
Keyword(s):  
Chemokine Receptors ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Gene Families ◽  
Open Reading Frames ◽  
Amino Acid Difference ◽  
Transmembrane Receptors ◽  
Equid Herpesvirus ◽  
High Sequence Divergence ◽  
Reading Frames

Equid herpesvirus 2 (EHV-2), in common with other members of the subfamily Gammaherpesvirinae, encodes homologues of cellular seven-transmembrane receptors (7TMR), namely open reading frames (ORFs) E1, 74 and E6, which each show some similarity to cellular chemokine receptors. Whereas ORF74 and E6 are members of gammaherpesvirus-conserved 7TMR gene families, E1 is currently unique to EHV-2. To investigate their genetic variability, EHV-2 7TMRs from a panel of equine gammaherpesvirus isolates were sequenced. A region of gB was sequenced to provide comparative sequence data. Phylogenetic analysis revealed six ‘genogroups’ for E1 and four for ORF74, which exhibited approximately 10–38 and 11–27 % amino acid difference between groups, respectively. In contrast, E6 was highly conserved, with two genogroups identified. The greatest variation was observed within the N-terminal domains and other extracellular regions. Nevertheless, analysis of the number of non-synonymous (d N) and synonymous (d S) substitutions per site generally supported the hypothesis that the 7TMRs are under negative selective pressure to retain functionally important residues, although some site-specific positive selection (d N>d S) was also observed. Collectively, these data are consistent with transmembrane and cytoplasmic domains being less tolerant of mutations with adverse effects upon function. Finally, there was no evidence for genetic linkage between the different gB, E1, ORF74 and E6 genotypes, suggesting frequent intergenic recombination between different EHV-2 strains.

scholarly journals Aborting meiosis overcomes hybrid sterility

2020 ◽  
Author(s):  
Simone Mozzachiodi ◽  
Lorenzo Tattini ◽  
Agnes Llored ◽  
Agurtzane Irizar ◽  
Neža Škofljanc ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Hybrid Sterility ◽  
Sequence Divergence ◽  
Association Analyses ◽  
Phenotypic Differences ◽  
Recombination Hotspots ◽  
High Sequence Divergence ◽  
Local Sequence ◽  
Genome Analyses ◽  
Sterile Hybrids

AbstractHybrids between species or diverged lineages contain fundamentally novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explored to what extent and how an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 yeast diploid backgrounds with different genomic structures and levels of sterility. Genome analyses of 284 clones revealed that RTG promoted recombination and generated extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination was reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially occurred in regions with local sequence homology and in meiotic recombination hotspots. The loss-of-heterozygosity had a profound impact on sexual and asexual fitness, and enabled genetic mapping of phenotypic differences in sterile lineages where linkage or association analyses failed. We propose that RTG gives sterile hybrids access to a natural route for genome recombination and adaptation.One sentence summaryAborting meiosis followed by a return to mitotic growth promotes evolution by genome wide-recombination in sterile yeast hybrids.

scholarly journals Aborting meiosis allows recombination in sterile diploid yeast hybrids

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Simone Mozzachiodi ◽  
Lorenzo Tattini ◽  
Agnes Llored ◽  
Agurtzane Irizar ◽  
Neža Škofljanc ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Meiotic Recombination ◽  
Sequence Divergence ◽  
Phenotypic Differences ◽  
Recombination Hotspots ◽  
Genome Recombination ◽  
High Sequence Divergence ◽  
Genome Analyses ◽  
Meiotic Recombination Hotspots ◽  
Sterile Hybrids

AbstractHybrids between diverged lineages contain novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explore to what extent an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 Saccharomyces cerevisiae and S. paradoxus diploid hybrids with different genomic structures and levels of sterility. Genome analyses of 275 clones reveal that RTG promotes recombination and generates extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination is reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially arises in regions with low local heterozygosity and near meiotic recombination hotspots. The loss-of-heterozygosity has a profound impact on sexual and asexual fitness, and enables genetic mapping of phenotypic differences in sterile lineages where linkage analysis would fail. We propose that RTG gives sterile yeast hybrids access to a natural route for genome recombination and adaptation.

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