Genetic Diversity of Rhanterium eppaposum Oliv. Populations in Kuwait as Revealed by GBS.

Natural populations of Rhanterium eppaposum Oliv. (Arfaj), a perennial forage shrub, have depleted due to unethical human interventions and climate change in Kuwait. Therefore, there is an urgent need to conserve this native plant through the assessment of its genetic diversity and population structure. Genotyping by sequencing (GBS) has recently emerged as a powerful tool for the molecular diversity analysis of higher plants without prior knowledge of their genome. This study represents the first effort in using GBS to discover genome-wide single nucleotide polymorphisms (SNPs) of local Rhanterium plants to assess the genetic diversity present in landraces collected from six different locations in Kuwait. The study generated a novel set of 11,231 single nucleotide polymorphisms (SNPs) and indels (insertions and deletions) in 98 genotypes of Rhanterium. The analysis of molecular variance (AMOVA) revealed ~1.5% variation residing among the six populations, ~5% among the individuals within the population and 93% variation present within the populations (FST = 0.029; p = 0.0). Bayesian and UPGMA analyses identified two admixed clusters of the tested samples; however, the principal coordinates analysis returned the complete population as a single group. Mantel's test returned a very weak correlation coefficient of r2 = 0.101 (p = 0.00) between the geographic and genetic distance. These findings are useful for the native species to formulate conservation strategies for its sustainable management and desert rehabilitation.

Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz.

Acacia tree population is declining in several countries of the world especially in the Arabian peninsula due to human-induced activities. The tree has potential medicinal and economic benefits as a source of fuel and timber. It can fix nitrogen, a significant property that assists in desert rehabilitation. However, the lack of genomic information of Acacia pachyceras hampers its genetic study and breeding process. We performed paired-end sequencing of A. pachyceras at a depth of 120X to obtain raw sequences of 108.9 GB with a per base quality >Q30. Filtered raw data was assembled into a fasta file of 4 GB. The assembled genomic sequences consisted of 901,755 single sequence repeats (SSRs). In total 11,596 primer pairs were designed against these SSR motifs. The data generated provides baseline genomic information about the species and formulates a base for further sequencing of A. pachyceras through PACBio and HiC technologies. The novel developed SSR markers will facilitate genetic diversity and conservation studies for Acacia species.

Data on draft genome assembly and annotation of Haloxylon salicornicum Moq.

Haloxylon salicornicum Moq. Bunge ex Boiss (Rimth) is one of the main structural elements in Eastern Arabian vegetation associations. The plant is utilized as a food source for domestic stock, stabilizes the soil surface besides providing suitable microclimates for exotic species. It is considered one of the most promising species for re-vegetation. H. salicornicum community is under threat from overgrazing leading to a reduction in the percentage of distribution from 22.7% to 2.2% in Kuwait. Therefore, genome characterization of this important Kuwaiti plant is required to formulate strategies for its conservation. Here we report the draft of the H. salicornicum genome, which was sequenced on an Illumina HiSeq 2500 platform. BUSCO assessment revealed 69% of the genome was to be complete. Overall, 12960 gene structures, 11280 protein-coding genes, 11309 mRNAs (protein-coding), 51265 exons and 48100 CDSs were predicted. Functional annotation was carried out by interproscan-5.29-68.0. A total of 7222 protein-coding sequences were, annotated out of 11309 by at least one ontology term. All these genes were associated with 11 major biological processes branched into 60 child processes.

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait.

Kuwait is a country with a very high dust loading; in fact it bears the world's highest particulate matter concentration in the outdoor air. The airborne dust often has associated biological materials, including pathogenic microbes that pose a serious risk to the urban ecosystem and public health. This study has established the baseline taxonomic characterization of microbes associated with dust transported into Kuwait from different trajectories. A high volume air sampler with six-stage cascade impactor was deployed for sample collection at a remote as well as an urban site. Samples from three different seasons (autumn, spring and summer) were subjected to targeted amplicon sequencing. A set of ~ 50 and 60 bacterial and fungal genera, respectively, established the core air microbiome. The predominant bacterial genera (relative abundance ≥ 1%) were Brevundimonas (12.5%), Sphingobium (3.3%), Sphingopyxis (2.7%), Pseudomonas (2.5%), Sphingomonas (2.4%), Massilia (2.3%), Acidovorax (2.0%), Allorhizobium (1.8%), Halomonas (1.3%), and Mesorhizobium (1.1%), and the fungal taxa were Cryptococcus (12%) followed by Alternaria (9%), Aspergillus (7%), Candida (3%), Cladosporium (2.9%), Schizophyllum (1.6%), Fusarium (1.4%), Gleotinia (1.3%) and Penicillium (1.15%). Significant spatio-temporal variations were recorded in terms of relative abundances, α-diversities, and ß-diversities of bacterial communities. The dissimilarities were less pronounced and instead the communities were fairly homogenous. Linear discrimant analysis revealed three fungal genera known to be significantly differentially abundant with respect to different size fractions of dust. Our results shed light on the spatio-temporal distribution of airborne microbes and their implications in general health.

Genetic diversity and population structure of Haloxylon salicornicum moq. in Kuwait by ISSR markers.

Haloxylon salicornicum moq. Bunge ex Boiss (Rimth) is one of the native plants of Kuwait, extensively depleting through the anthropogenic activities. It is important to conserve Haloxylon community in Kuwait as it can tolerate extreme adverse conditions of drought and salinity to be potentially used in the desert and urban revegetation and greenery national programs. Therefore, a set of 16 inter simple sequence repeat (ISSR) markers were used to assess genetic diversity and population structure of 108 genotypes from six locations in Kuwait. The ISSR primers produced 195 unambiguous and reproducible bands out of which 167 bands were polymorphic (86.5%) with a mean PIC value of 0.31. The overall average values of Nei's gene diversity (h') and Shannon's diversity index (I) were 0.254 and 0.375, respectively. Results of AMOVA revealed high genetic variations within populations (77.8%) and low among populations (22%). The values of Fixation index (FST = 0.22; P = 0.0), Genetic differentiation (GST = 0.262; G'ST = 0.327; D = 0.335 and Gene flow (NM = 0.880) were indicative of heterozygous populations. The results of STRUCTURE and split decomposition analysis suggested that the Rimth accessions of Kuwait can be grouped into five and six subpopulations, respectively. Principal coordinate analysis (PCoA) grouped them into three clusters. The pairwise Nei's genetic distances (DS) among populations demonstrated a narrow range from 0.047 to 0.187 (Scale-0.0 to 1.0). The Mantel's test revealed a weak correlation (r2- 0.188; P-0.013) between the genetic distance and geographic distances. Our results suggest that the narrowly distributed Haloxylon community in Kuwait demonstrated a high genetic diversity within the populations however the overall population structure was weak.

Draft genome sequence of the silver pomfret fish, Pampus argenteus.

Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.

Avian influenza A virus (H5N1) outbreaks, Kuwait, 2007.

Phylogenetic analysis of influenza A viruses (H5N1) isolated from Kuwait in 2007 show that (H5N1) sublineage clade 2.2 viruses continue to spread across Europe, Africa, and the Middle East. Virus isolates were most closely related to isolates from central Asia and were likely vectored by migratory birds.