Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition

Comparative evolutionary analyses of 26 Streptococcus genomes show that recombination and positive selection have both had important roles in the adaptation of different species to different hosts

Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae

<p>Abstract</p> <p>Background</p> <p><it>Staphylococcus </it>belongs to the Gram-positive low G + C content group of the Firmicutes division of bacteria. <it>Staphylococcus aureus </it>is an important human and veterinary pathogen that causes a broad spectrum of diseases, and has developed important multidrug resistant forms such as methicillin-resistant <it>S. aureus </it>(MRSA). <it>Staphylococcus simiae </it>was isolated from South American squirrel monkeys in 2000, and is a coagulase-negative bacterium, closely related, and possibly the sister group, to <it>S. aureus</it>. Comparative genomic analyses of closely related bacteria with different phenotypes can provide information relevant to understanding adaptation to host environment and mechanisms of pathogenicity.</p> <p>Results</p> <p>We determined a Roche/454 draft genome sequence for <it>S. simiae </it>and included it in comparative genomic analyses with 11 other <it>Staphylococcus </it>species including <it>S. aureus</it>. A genome based phylogeny of the genus confirms that <it>S. simiae </it>is the sister group to <it>S. aureus </it>and indicates that the most basal <it>Staphylococcus </it>lineage is <it>Staphylococcus pseudintermedius</it>, followed by <it>Staphylococcus carnosus</it>. Given the primary niche of these two latter taxa, compared to the other species in the genus, this phylogeny suggests that human adaptation evolved after the split of <it>S. carnosus</it>. The two coagulase-positive species (<it>S. aureus </it>and <it>S. pseudintermedius</it>) are not phylogenetically closest but share many virulence factors exclusively, suggesting that these genes were acquired by horizontal transfer. Enrichment in genes related to mobile elements such as prophage in <it>S. aureus </it>relative to <it>S. simiae </it>suggests that pathogenesis in the <it>S. aureus </it>group has developed by gene gain through horizontal transfer, after the split of <it>S. aureus </it>and <it>S. simiae </it>from their common ancestor.</p> <p>Conclusions</p> <p>Comparative genomic analyses across 12 <it>Staphylococcus </it>species provide hypotheses about lineages in which human adaptation has taken place and contributions of horizontal transfer in pathogenesis.</p

Characterization of the Heart Transcriptome of the White Shark (Carcharodon carcharias)

Background: The white shark (Carcharodon carcharias) is a globally distributed, apex predator possessing physical, physiological, and behavioral traits that have garnered it significant public attention. In addition to interest in the genetic basis of its form and function, as a representative of the oldest extant jawed vertebrate lineage, white sharks are also of conservation concern due to their small population size and threat from overfishing. Despite this, surprisingly little is known about the biology of white sharks, and genomic resources are unavailable. To address this deficit, we combined Roche-454 and Illumina sequencing technologies to characterize the first transcriptome of any tissue for this species. Results: From white shark heart cDNA we generated 665,399 Roche 454 reads (median length 387-bp) that were assembled into 141,626 contigs (mean length 503-bp). We also generated 78,566,588 Illumina reads, which we aligned to the 454 contigs producing 105,014 454/Illumina consensus sequences. To these, we added 3,432 non-singleton 454 contigs. By comparing these sequences to the UniProtKB/Swiss-Prot database we were able to annotate 21,019 translated open reading frames (ORFs) of ≥ 20 amino acids. Of these, 19,277 were additionally assigned Gene Ontology (GO) functional annotations. While acknowledging the limitations of our single tissue transcriptome, Fisher tests showed the white shark transcriptome to be significantly enriched for numerous metabolic GO terms compared to the zebra fish and human transcriptomes, with white shark showing more similarity to human than to zebra fish (i.e. fewer terms were significantly different). We also compared the transcriptome to other available elasmobranch sequences, for signatures of positive selection and identified several genes of putative adaptive significance on the white shark lineage. The white shark transcriptome also contained 8,404 microsatellites (dinucleotide, trinucleotide, or tetranucleotide motifs ≥ five perfect repeats). Detailed characterization of these microsatellites showed that ORFs with trinucleotide repeats, were significantly enriched for transcription regulatory roles and that trinucleotide frequency within ORFs was lower than for a wide range of taxonomic groups including other vertebrates. Conclusion: The white shark heart transcriptome represents a valuable resource for future elasmobranch functional and comparative genomic studies, as well as for population and other biological studies vital for effective conservation of this globally vulnerable species

Transcriptome Derived Microsatellites Demonstrate Strong Genetic Differentiation in Pacific White Sharks

Recent advances in genome-scale sequencing technology have allowed the development of high resolution genetic markers for the study of non-model taxa. In particular, transcriptome sequencing has proven to be highly useful in generating genomic markers for use in population genetic studies, allowing for insight into species connectivity, as well as local adaptive processes as many transcriptome-derived markers are found within or associated with functional genes. Herein, we developed a set of 30 microsatellite markers from a heart transcriptome for the white shark (Carcharodon carcharias), a widely distributed and globally vulnerable marine predator. Using these markers as well as ten published anonymous genomic microsatellite loci, we provide (i) the first nuclear genetic assessment of the cross-Pacific connectivity of white sharks, and (ii) a comparison of the levels of inferred differentiation across microsatellite marker sets (i.e., transcriptome versus anonymous) to assess their respective utility to elucidate the population genetic dynamics of white sharks. Significant (FST = 0.083, P = 0.05; G”ST = 0.200; P = 0.001) genetic differentiation was found between Southwestern Pacific (n = 19) and Northeastern Pacific (n = 20) white sharks, indicating restricted, cross Pacific gene flow in this species. Transcriptome-derived microsatellite marker sets identified much higher (up to 2X) levels of genetic differentiation than anonymous genomic markers, underscoring potential utility of transcriptome markers in identifying subtle population genetic differences within highly vagile, globally distributed marine species

Genetic Connectivity in the Florida Reef System: Comparative Phylogeography of Commensal Invertebrates With Contrasting Reproductive Strategies

Effective spatial management of coral reefs including design of marine protected areas requires an understanding of interpopulation genetic connectivity. We assessed gene flow along 355 km of the Florida reef system and between Florida and Belize in three commensal invertebrates occupying the same host sponge (Callyspongia vaginalis) but displaying contrasting reproductive dispersal strategies: the broadcast-spawning brittle star Ophiothrix lineata and two brooding amphipods Leucothoe kensleyi and Leucothoe ashleyae. Multiple analytical approaches to sequence variation in the mitochondrial COI gene demonstrated a high degree of overall connectivity for all three species along the Florida reef system. Ophiothrix lineata showed significant genetic structuring between Florida and Belize, and a pattern of isolation by distance but no significant genetic structuring along the Florida coastline. Bayesian estimates of migration detected a strong southerly dispersal bias for O. lineata along the Florida reef system, contrary to the general assumption of northerly gene flow in this region based on the direction of the Florida Current. Both amphipods, despite direct development, also showed high gene flow along the Florida reef system. Multiple inferences of long-distance dispersal from a nested clade analysis support the hypothesis that amphipod transport, possibly in detached sponge fragments, could generate the high levels of overall gene flow observed. However, this transport mechanism appears much less effective across deep water as connectivity between Florida and Belize (1072 km) is highly restricted

Mitochondrial genome of an Atlantic white shark (Carcharodon carcharias)

Here we report the first full mitochondrial genome sequence for a white shark caught in the Atlantic Ocean. The mitochondrial genome is 16,745 bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region. The base composition of this mtDNA lineage is A: 30.7%, C: 26.9%, G: 13.8%, and T: 28.6%. In concordance with previous population genetic studies, the Atlantic caught individual forms a separate lineage from individuals caught on either side of the Pacific Ocean

A Streamlined, Bi-Organelle, Multiplex PCR Approach to Species Identification: Application to Global Conservation and Trade Monitoring of the Great White Shark, Carcharodon carcharias

The great white shark, Carcharodon carcharias, is the most widely protected elasmobranch in the world, and is classified as Vulnerable by the IUCN and listed on Appendix III of CITES. Monitoring of trade in white shark products and enforcement of harvest and trade prohibitions is problematic, however, in large part due to difficulties in identifying marketed shark parts (e.g., dried fins, meat and processed carcasses) to species level. To address these conservation and management problems, we have developed a rapid, molecular diagnostic assay based on species-specific PCR primer design for accurate identification of white shark body parts, including dried fins. The assay is novel in several respects: It employs a multiplex PCR assay utilizing both nuclear (ribosomal internal transcribed spacer 2) and mitochondrial (cytochrome b) loci simultaneously to achieve a highly robust measure of diagnostic accuracy; it is very sensitive, detecting the presence of white shark DNA in a mixture of genomic DNAs from up to ten different commercially fished shark species pooled together in a single PCR tube; and it successfully identifies white shark DNA from globally distributed animals. In addition to its utility for white shark trade monitoring and conservation applications, this highly streamlined, bi-organelle, multiplex PCR assay may prove useful as a general model for the design of genetic assays aimed at detecting body parts from other protected and threatened species

Genome content and phylogenomics reveal both ancestral and lateral evolutionary pathways in plant-pathogenic Streptomyces species

© 2016, American Society for Microbiology. All Rights Reserved. Streptomyces spp. are highly differentiated actinomycetes with large, linear chromosomes that encode an arsenal of biologically active molecules and catabolic enzymes. Members of this genus are well equipped for life in nutrient-limited environments and are common soil saprophytes. Out of the hundreds of species in the genus Streptomyces, a small group has evolved the ability to infect plants. The recent availability of Streptomyces genome sequences, including four genomes of pathogenic species, provided an opportunity to characterize the gene content specific to these pathogens and to study phylogenetic relationships among them. Genome sequencing, comparative genomics, and phylogenetic analysis enabled us to discriminate pathogenic from saprophytic Streptomyces strains; moreover, we calculated that the pathogen-specific genome contains 4,662 orthologs. Phylogenetic reconstruction suggested that Streptomyces scabies and S. ipomoeae share an ancestor but that their biosynthetic clusters encoding the required virulence factor thaxtomin have diverged. In contrast, S. turgidiscabies and S. acidiscabies, two relatively unrelated pathogens, possess highly similar thaxtomin biosynthesis clusters, which suggests that the acquisition of these genes was through lateral gene transfer

White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated with Wound Healing and the Maintenance of Genome Stability

The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability in white and whale sharks may reflect the combined selective pressure of large genome sizes, high repeat content, high long-interspersed element retrotransposon representation, large body size, and long lifespans, represented across these two species. Molecular adaptation for wound healing was also evident, with positive selection in key genes involved in the wound-healing process, as well as Gene Ontology enrichments in fundamental wound-healing pathways. Sharks, particularly apex predators such as the white shark, are believed to have an acute sense of smell. However, we found very few olfactory receptor genes, very few trace amine-associated receptors, and extremely low numbers of G protein-coupled receptors. We did however, identify 13 copies of vomeronasal type 2 (V2R) genes in white shark and 10 in whale shark; this, combined with the over 30 V2Rs reported previously for elephant shark, suggests this gene family may underlie the keen odorant reception of chondrichthyans

Blastocystis Mitochondrial Genomes Appear to Show Multiple Independent Gains and Losses of Start and Stop Codons.

Complete mitochondrion-related organelle (MRO) genomes of several subtypes (STs) of the unicellular stramenopile Blastocystis are presented. Complete conservation of gene content and synteny in gene order is observed across all MRO genomes, comprising 27 protein coding genes, 2 ribosomal RNA genes, and 16 transfer RNA (tRNA) genes. Despite the synteny, differences in the degree of overlap between genes were observed between subtypes and also between isolates within the same subtype. Other notable features include unusual base-pairing mismatches in the predicted secondary structures of some tRNAs. Intriguingly, the rps4 gene in some MRO genomes is missing a start codon and, based on phylogenetic relationships among STs, this loss has happened twice independently. One unidentified open reading frame (orf160) is present in all MRO genomes. However, with the exception of ST4 where the feature has been lost secondarily, orf160 contains variously one or two in-frame stop codons. The overall evidence suggests that both the orf160 and rps4 genes are functional in all STs, but how they are expressed remains unclear