Draft Genome Sequences of Seven Vibrio cholerae Isolates from Adult Patients in Qatar.

We report the draft genome sequences of seven Vibrio cholerae isolates from patients. Four isolates were profiled as multilocus sequence type 69, serogroup O1, a subset of seventh-pandemic El Tor clonal isolates. Presented here are genome assemblies and evidence for major pathogenicity islands, virulence factors, and antimicrobial resistance genes.

Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf.

Strain B66T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 6.5-8) and with 0-6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66T was affiliated with the family Alteromonadaceae, sharing the highest sequence similarities to the genera Alteromonas (93.7-95.4 %), Aestuariibacter (94.0-95.1 %), Agaribacter (93.3-93.7 %), Glaciecola (92.0-93.7 %), Marisendiminitalea (93.2-93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium. Major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c/iso-C15 : 0 2-OH and iso-C15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66T (=QCC B003/17T=LMG 30288 T=CCUG 70703T).

Toxicocladosporium aquimarinum sp. nov. and Toxicocladosporium qatarense sp. nov., isolated from marine waters of the Arabian Gulf surrounding Qatar.

The Arabian Gulf surrounding Qatar is distinct from other marine ecosystems due to its high salinity (35-75 PSU) and extreme water temperature fluctuations (11-40 °C). Furthermore, in the last decade, Qatar has been witnessing an industrial boom as well as extensive infrastructure construction activities. Marine micro-organisms, including fungi, remain largely unexplored in the Arabian Gulf. During a 3 year study, we investigated the diversity of marine fungi in coastal waters around Qatar. As a result, two new Toxicocladosporium species were isolated from the Qatari marine environment. Molecular and phylogenetic analyses of rRNA gene sequences of five loci, namely the internal transcribed spacer 1 and 2 regions and the D1/D2 domains of the large subunit rRNA, actin, RNA polymerase second largest subunit and beta-tubulin genes, were used to confirm the identity of the novel species for which we propose the names Toxicocladosporium aquimarinum sp. nov. and Toxicocladosporium qatarense sp. nov.

Kondoa qatarensis f.a., sp. nov., a novel yeast species isolated from marine water in Qatar.

During a study of yeast diversity in marine waters of the Arabian Gulf surrounding Qatar, 30 strains were isolated that represent a novel species of Kondoa. The isolates were obtained from five locations along the Qatari coast. Species identifications were based on sequence analysis of the internal transcribed spacer (ITS) regions and D1/D2 domains of the large subunit (LSU) rRNA gene. Five strains were selected for further study. The novel species was closely related to Kondoa aeria (CBS 8352T) and Kondoa malvinella (CBS 6082T) but differed from the two species by 5.6 % sequence divergence (16 substitutions and 14 gaps) in the ITS region. On the basis of D1/D2 domains of the LSU rRNA gene, the novel species differed from K. aeria by only >0.35 % sequence divergence (2 substitutions and 0 gaps) and 1.5 % sequence divergence (9 substitutions and 1 gap) to that of K. malvinella. Although the novel species showed a close similarity in the D1/D2 domains to K. aeria (CBS 8352T), based on the significant differences (16 substitutions) in ITS regions and on the basis of physiological and biochemical tests, viz ability to grow at 35 °C, and inability to assimilate, sucrose, raffinose, d,l-lactate, succinate, citrate and nitrite, these strains are considered as novel species of Kondoa. The species name of Kondoa qatarensis f.a., sp. nov. is proposed with specimen 2Y109 as the holotype.

A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms.

BACKGROUND: The date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified. RESULTS: Here we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome. CONCLUSIONS: Based on a modified genotyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms.

Whale sharks, Rhincodon typus, aggregate around offshore platforms in Qatari waters of the Arabian Gulf to feed on fish spawn.

Whale sharks, Rhincodon typus, are known to aggregate to feed in a small number of locations in tropical and subtropical waters. Here we document a newly discovered major aggregation site for whale sharks within the Al Shaheen oil field, 90 km off the coast of Qatar in the Arabian Gulf. Whale sharks were observed between April and September, with peak numbers observed between May and August. Density estimates of up to 100 sharks within an area of 1 km(2) were recorded. Sharks ranged between four and eight metres' estimated total length (mean 6.92 ± 1.53 m). Most animals observed were actively feeding on surface zooplankton, consisting primarily of mackerel tuna, Euthynnus affinis, eggs.