Complete Genome Sequences of African Salmonella enterica Serovar Enteritidis Clinical Isolates Associated with Bloodstream Infection

ABSTRACT We report the complete genome sequencing and annotation of four Salmonella enterica serovar Enteritidis isolates, two that are representative of the Central/Eastern African clade (CP255 and D7795) and two of the Global Epidemic clade (A1636 and P125109).

Althenia tzvelevii (Potamogetonaceae), a new species from SW Western Australia with bilocular anthers: morphology and molecular phylogenetic relationships

A new species Althenia tzvelevii is described from south western Australia. This is the second species after A. bilocularis described with bilocular anthers. Illustrations of plant morphology are provided by means of SEM images and habitat photographs are included. The phylogenetic relationships of the new species were investigated using five plastid DNA markers (matK, ndhF, rbcL, rpoB, and rpoC1), with published sequences augmented by several new sequences resulting in coverage of all described species in the genus. Althenia tzvelevii forms a clade with A. patentifolia and A. bilocularis and other relationships within the genus are clarified. The Western Australian Althenia hearnii is strongly supported as sister to the Eurasian-African clade composed by A. filiformis and A. orientalis.

Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse

Genetic diversity and maternal ancestry line relationships amongst a sample of 96 Cleveland Bay horses were investigated using a 479bp length of mitochondrial D-loop sequence. The analysis yielded at total of 11 haplotypes with 27 variable positions, all of which have been described in previous equine mitochondrial DNA d-loop studies. Four main haplotype clusters were present in the Cleveland Bay breed describing 89% of the total sample. This suggests that only four principal maternal ancestry lines exist in the present-day global Cleveland Bay population. Comparison of these sequences with other domestic horse haplotypes shows a close association of the Cleveland Bay horse with Northern European (Clade C), Iberian (Clade A) and North African (Clade B) horse breeds. This indicates that the Cleveland Bay horse may not have evolved exclusively from the now extinct Chapman horse, as previous work as suggested. The Cleveland Bay horse remains one of only fivedomestic horse breeds classified as Critical on the Rare Breeds Survival Trust (UK) Watchlist and our results provide important information on the origins of this breed and represent a valuable tool for conservation purposes.

Human Infections Caused by Clonally Related African Clade (Clade III) Strains of Candida auris in the Greater Houston Region

ABSTRACT Candida auris is a pathogen of considerable public health importance. It was first reported in 2009. Five clades, determined by genomic analysis and named by the distinct regions where they were initially identified, have been defined. We previously completed a draft genome sequence of an African clade (clade III) strain cultured from the urine of a patient hospitalized in the greater Houston metropolitan region (strain LOM). Although initially uncommon, reports of the African clade in the United States have grown to include a recent cluster in California. Here, we describe a second human C. auris infection in the Houston area. Whole-genome sequence analysis demonstrated the Houston patient isolates to be clonally related to one another but distantly related to other African clade organisms recovered in the United States or elsewhere. Infections in these patients were present on admission to the hospital and occurred several months apart. Taken together, the data demonstrate the emergence and persistence of a clonal C. auris population and highlights the importance of routine high-resolution genomic surveillance of emerging human pathogens in the clinical laboratory.

Phylogenomics and biogeography of the world's thrushes (Aves, Turdus ): new evidence for a more parsimonious evolutionary history

To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescent phylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to the Palaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.

Three new species and a new combination among Southern African Schoenus (Cyperaceae, tribe Schoeneae)

Schoenus is a morphologically complex, predominately austral genus. The taxonomy of the southern African clade of Schoenus has received recent attention with the transfer of 24 southern African species into Schoenus from Tetraria and Epischoenus in 2017. A taxonomic revision in early 2018 both revised the taxonomy of the Schoenus compar—Schoenus pictus and allies group, as well as described three new species endemic to the Cape Floristic Region of South Africa. In addition, seven new species were described in early 2019 as part of a revision of the Schoenus cuspidatus group. Here, we build on this recent taxonomic work by providing descriptions for three new species (Schoenus bracteosus, Schoenus comparoides and Schoenus triticoides). We also provide a new name at species rank for a taxon previously named as a variety of Tetraria sylvatica. We present detailed species descriptions, distribution maps and an updated identification key.

A record of Notostraca on Socotra Island and the importance of local conservation of the habitat

The first record of Triops Schrank, 1803 (Crustacea: Branchiopoda: Notostraca: Triopsidae) from Socotra Island is presented herein. Besides Madagascar and the current note, the genus is unknown from Indian Ocean islands. A brief morphological exploration indicates that the Socotran Triops cf. granarius (Lucas, 1864) (trachyaspis form) belongs to an African clade within this widespread Old World species complex and not to T. granarius s.str. from East Asia. Detailed morphological and molecular revision of the poorly studied Middle Eastern and Northern African populations in comparison to East Asian populations are needed to understand this group and the phylogenetic position and status of the Socotran tadpole shrimp. Found in a single locality (the archeological site Eriosh) in the rapidly changing coastal plains on Socotra, together with other large branchiopods (endemic Anostraca and unidentified Spinicaudata), the insular Triops population and the regionally neglected temporary lake habitat deserve a special protection status from a biodiversity conservation perspective. Triops cf. granarius is hereby suggested as a local flagship species for the conservation of temporary pool habitats on the island.

Phylogenetic analysis of Histoplasma capsulatum var duboisii in baboons from archived formalin-fixed, paraffin embedded tissues

Histoplasma capsulatum var. duboisii (Hcd) infections have been well documented to cause chronic granulomatous disease, mainly involving the skin of baboons and humans in African countries primarily. This retrospective study classified the subspecies of Histoplasma and developed a phylogenetic tree utilizing DNA sequences extracted from formalin-fixed, paraffin embedded (FFPE) tissues from 9 baboons from a research colony in Texas histologically diagnosed with Hcd. Based on sequence analysis of ITS-2, Tub-1, and ARF, Hcd isolated from the archived samples closely aligns with the African clade and has 88% sequence homology with a sample isolated from an individual in Senegal.

Molecular phylogeny and evolutionary history ofMoricandiaDC (Brassicaceae)

BackgroundThe phylogeny of tribe Brassiceae (Brassicaceae) has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genusMoricandiaDC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species ofMoricandiahave been used in several phylogenetic studies, the phylogeny of this genus is not well established.MethodsHere we present a phylogenetic analysis of the genusMoricandiausing a nuclear (the internal transcribed spacers of the ribosomal DNA) and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and thetrnT-trnF region). We also included in the analyses members of their sister genusRytidocarpusand from the close genusEruca.ResultsThe phylogenetic analyses showed a clear and robust phylogeny of the genusMoricandia. The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genusMoricandiaappears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plusM. arvensis.DiscussionWe dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed toRytidocarpus moricandioidesis indeed aMoricandiaspecies, and we propose to name it asM. rytidocarpoidessp. nov. In addition, in all the phylogenetic analyses,M. foleyiappeared outside theMoricandialineage but within the genusEruca. Therefore,M. foleyishould be excluded from the genusMoricandiaand be ascribed, at least provisionally, to the genusEruca.

Complete Genome Sequence of the African Strain AXO1947 of Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae is the etiological agent of bacterial rice blight. Three distinct clades of X. oryzae pv. oryzae are known. We present the complete annotated genome of the African clade strain AXO194 using long-read single-molecule PacBio sequencing technology. The genome comprises a single chromosome of 4,674,975 bp and encodes for nine transcriptional activator-like (TAL) effectors. The approach and data presented in this announcement provide information for complex bacterial genome organization and the discovery of new virulence effectors, and they facilitate target characterization of TAL effectors.