PyEvolve: a toolkit for statistical modelling of molecular evolution

Butterfield, Andrew; Vedagiri, Vivek; Lang, Edward; Lawrence, Catherine; Wakefield, Matthew J.; Isaev, Alexander; Huttley, Gavin A.

doi:10.1186/1471-2105-5-1

Cited by 426 publications

(197 citation statements)

References 18 publications

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“…The sequences within each clade were then aligned with muscle (Edgar, 2004), trimmed to equal length, and only sequences with a length ≥ 90% of all reads were retained. Remaining sequences were clustered at 0.03 cut‐off following the pipeline detailed in Arif et al .…”

Section: Methodsmentioning

confidence: 99%

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Ziegler

Arif

Burt

et al. 2017

Journal of Biogeography

140

130

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AimCoral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth.LocationShallow water coral reefs throughout the Red Sea (RS), Sea of Oman (SO), and Persian/Arabian Gulf (PAG).MethodsNext‐generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera.ResultsCorals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C‐ to D‐dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)‐based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera.Main conclusionsOur study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host–symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing ‘Future Ocean’ conditions.

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Section: Methodsmentioning

confidence: 99%

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Ziegler

Arif

Burt

et al. 2017

Journal of Biogeography

140

130

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“…A reciprocal allversus-all BLASTp search was performed (threshold E value of Յ1eϪ10) (45), and orthologous groups were determined by orthAgogue and MCL (ignoring E values, percent match lengths of Ն80%, and inflation values of 5 [46,47]). The groups of orthologues (GOs) were then aligned by using MUSCLE and back-translated to the nucleotide sequence by using Translatorx Perl script (48)(49)(50). Maximum likelihood phylogenetic reconstruction of each GO was performed in MEGA6.06 (51), using the Kimura two-parameter model as the nucleotide substitution model and a discrete gamma distribution (4 categories) to model evolutionary rate differences among sites.…”

Section: Methodsmentioning

confidence: 99%

Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides

et al. 2016

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Despite the importance of lipooligosaccharides (LOSs) in the pathogenicity of campylobacteriosis, little is known about the genetic and phenotypic diversity of LOS in Campylobacter coli. In this study, we investigated the distribution of LOS locus classes among a large collection of unrelated C. coli isolates sampled from several different host species. Furthermore, we paired C. coli genomic information and LOS chemical composition for the first time to investigate possible associations between LOS locus class sequence diversity and biochemical heterogeneity. After identifying three new LOS locus classes, only 85% of the 144 isolates tested were assigned to a class, suggesting higher genetic diversity than previously thought. This genetic diversity is at the basis of a completely unexplored LOS structural heterogeneity. Mass spectrometry analysis of the LOSs of nine isolates, representing four different LOS classes, identified two features distinguishing C. coli LOS from that of Campylobacter jejuni. 2-Amino-2-deoxy-D-glucose (GlcN)-GlcN disaccharides were present in the lipid A backbone, in contrast to the ␤-1=-6-linked 3-diamino-2,3-dideoxy-D-glucopyranose (GlcN3N)-GlcN backbone observed in C. jejuni. Moreover, despite the fact that many of the genes putatively involved in 3-acylamino-3,6-dideoxy-D-glucose (Quip3NAcyl) were apparently absent from the genomes of various isolates, this rare sugar was found in the outer core of all C. coli isolates. Therefore, regardless of the high genetic diversity of the LOS biosynthesis locus in C. coli, we identified species-specific phenotypic features of C. coli LOS that might explain differences between C. jejuni and C. coli in terms of population dynamics and host adaptation. IMPORTANCEDespite the importance of C. coli to human health and its controversial role as a causative agent of Guillain-Barré syndrome, little is known about the genetic and phenotypic diversity of C. coli LOSs. Therefore, we paired C. coli genomic information and LOS chemical composition for the first time to address this paucity of information. We identified two species-specific phenotypic features of C. coli LOS, which might contribute to elucidating the reasons behind the differences between C. jejuni and C. coli in terms of population dynamics and host adaptation. C ampylobacteriosis is the most common bacterial foodborne disease in developed countries, with over 200,000 human cases being reported annually in the European Union alone (1). The true burden of the disease in the population is likely underestimated, as many infections result in mild gastroenteritis (1). Approximately 80% of reported infections are caused by Campylobacter jejuni, and 7 to 18% of cases are attributed to C. coli. Therefore, C. coli is among the five most important bacterial etiological agents of human gastroenteritis (2, 3).As in other Gram-negative bacteria, Campylobacter species cell surface glycoconjugates, including lipooligosaccharides (LOSs), play an important role in serum and bile resistance; resistanc...

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“…The B204 amino acid sequence was queried against the metagenome database using tblastn to identify contigs that shared 30% or higher identity to STIV B204. The sequences were aligned using MUSCLE (34).…”

Section: Methodsmentioning

confidence: 99%

Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase

Dellas

Snyder

Dills

et al. 2016

J Virol

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Sulfolobus turreted icosahedral virus (STIV), an archaeal virus that infects the hyperthermoacidophile Sulfolobus solfataricus, is one of the most well-studied viruses of the domain Archaea. STIV shares structural, morphological, and sequence similarities with viruses from other domains of life, all of which are thought to belong to the same viral lineage. Several of these common features include a conserved coat protein fold, an internal lipid membrane, and a DNA-packaging ATPase. B204 is the ATPase encoded by STIV and is thought to drive packaging of viral DNA during the replication process. Here, we report the crystal structure of B204 along with the biochemical analysis of B204 mutants chosen based on structural information and sequence conservation patterns observed among members of the same viral lineage and the larger FtsK/HerA superfamily to which B204 belongs. Both in vitro ATPase activity assays and transfection assays with mutant forms of B204 confirmed the essentiality of conserved and nonconserved positions. We also have identified two distinct particle morphologies during an STIV infection that differ in the presence or absence of the B204 protein. The biochemical and structural data presented here are not only informative for the STIV replication process but also can be useful in deciphering DNA-packaging mechanisms for other viruses belonging to this lineage. IMPORTANCE STIV is a virus that infects a host from the domainArchaea that replicates in high-temperature, acidic environments. While STIV has many unique features, there exist several striking similarities between this virus and others that replicate in different environments and infect a broad range of hosts from Bacteria and Eukarya. Aside from structural features shared by viruses from this lineage, there exists a significant level of sequence similarity between the ATPase genes carried by these different viruses; this gene encodes an enzyme thought to provide energy that drives DNA packaging into the virion during infection. The experiments described here highlight the elements of this enzyme that are essential for proper function and also provide supporting evidence that B204 is present in the mature STIV virion. In Sulfolobus turreted icosahedral virus (STIV), the open reading frame B204 (previously described as B164) (1, 2) encodes a putative ATPase that is predicted to function as the molecular motor driving viral DNA packaging during infection (3). Interestingly, it has been demonstrated that viruses harboring ATPases homologous to B204 share other common features, such as a spherical morphology, an internal lipid membrane, and a structurally homologous coat protein fold (termed the double ␤-barrel or double jelly roll fold) (4). The structural and functional assessment of viruses belonging to this putative viral lineage can provide insights on viral infection strategies across the three domains of life. In the case of B204, understanding its function has implications for mechanisms by which an ancient molecular motor may h...

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PyEvolve: a toolkit for statistical modelling of molecular evolution

Cited by 426 publications

References 18 publications

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides

Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase

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