Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

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The availability of 12 complete genomes of various species of genus Drosophila provides a unique opportunity to analyze genome-scale chromosomal rearrangements among a group of closely related species. This article reports on the comparison of gene order between these 12 species and on the fixed rearrangement events that disrupt gene order. Three major themes are addressed: the conservation of syntenic blocks across species, the disruption of syntenic blocks (via chromosomal inversion events) and its relationship to the phylogenetic distribution of these species, and the rate of rearrangement events over evolutionary time. Comparison of syntenic blocks across this large genomic data set confirms that genetic elements are largely (95%) localized to the same Muller element across genus Drosophila species and paracentric inversions serve as the dominant mechanism for shuffling the order of genes along a chromosome. Gene-order scrambling between species is in accordance with the estimated evolutionary distances between them and we find it to approximate a linear process over time (linear to exponential with alternate divergence time estimates). We find the distribution of synteny segment sizes to be biased by a large number of small segments with comparatively fewer large segments. Our results provide estimated chromosomal evolution rates across this set of species on the basis of whole-genome synteny analysis, which are found to be higher than those previously reported. Identification of conserved syntenic blocks across these genomes suggests a large number of conserved blocks with varying levels of embryonic expression correlation in Drosophila melanogaster. On the other hand, an analysis of the disruption of syntenic blocks between species allowed the identification of fixed inversion breakpoints and estimates of breakpoint reuse and lineage-specific breakpoint event segregation. D ROSOPHILA research has a rich history in the study of genome rearrangements that now culminates with the analysis of complete genomic sequences. Comparative genomics in Drosophila began when linkage maps of morphological traits were used to establish the homologies of six chromosomal arms in closely related species (Donald 1936;Sturtevant and Tan 1937;Muller 1940;Sturtevant and Novitski 1941). These early studies established the idea that genes are syntenic or conserved on the same chromosome arm among species. One difficulty encountered with these early comparative genomic analyses was that chromosomal arm nomenclatures varied among species (Crew and Lamy 1935;Sturtevant and Tan 1937). Muller (1940) overcame this problem when he developed a standard nomenclature that assigned a letter to each of the chromosomal arms or elements on the basis of the Drosophila melanogaster genome (chromosomal arm equals Muller element: X ¼ A, 2L ¼ B, 2R ¼ C, 3L ¼ D, 3R ¼ E, 4 ¼ F). Sturtevant and Novitski (1941) showed that the conservation of chromosomal elements extended to species across the entire genus of Drosophila.The conservation of the ...

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Variants within the human UGT1A1 gene are associated with irinotecan induced severely adverse reactions and hyperbilirubinemia. Intra-ethnic differences in the genetic variation and haplotypes of UGT1A1 gene have been analyzed in the present study. Relationship between the concentrations of total serum bilirubin (T-bil) and haplotype structure of UGT1A1 in healthy people were also evaluated. We genotyped five functional polymorphisms including À3279T4G and À3156G4A in the enhancer region, (TA)647 in the TATA box, and 211G4A (G71R), 686C4A (P229Q) in the exon1 region of UGT1A1 in three groups of healthy Chinese ethnic populations, consisting of 264 subjects of She origin, 539 of Han origin and 273 of Dong origin. The distribution of À3279T4G, (TA)647, 211G4A of UGT1A1 differed greatly as between the three ethnic groups. All of six haplotypes differed considerably between at least two of the three groups, which highlighted the need to analyze clinically irinotecan toxicity relevant SNPs and haplotypes in a variety of different racial groups within the Chinese population. Total bilirubin concentration in homozygous carriers of the À3279G and (TA)7 allele were significantly higher than those in heterozygous carriers or homozygous carriers of wild-type alleles. Carriers of the variant haplotypes (À3279G; À3156A; (TA)7; 211G; 686C) had higher serum T-Bil concentrations compared with the other groups. Our results indicate that heterogeneity among different ethnic populations is possibly the result of microevolution and is relevant to studies into the effect of tailored drug treatment.

Rare genetic variants are abundant in genomes but less tractable in genome-wide association study. Here we exploit a strategy of rare variation mapping to discover a gene essential for tendril development in cucumber (Cucumis sativus L.). In a collection of >3000 lines, we discovered a unique tendril-less line that forms branches instead of tendrils and, therefore, loses its climbing ability. We hypothesized that this unusual phenotype was caused by a rare variation and subsequently identified the causative single nucleotide polymorphism. The affected gene TEN encodes a TCP transcription factor conserved within the cucurbits and is expressed specifically in tendrils, representing a new organ identity gene. The variation occurs within a protein motif unique to the cucurbits and impairs its function as a transcriptional activator. Analyses of transcriptomes from near-isogenic lines identified downstream genes required for the tendril's capability to sense and climb a support. This study provides an example to explore rare functional variants in plant genomes.

As one of six dietary nutrients, lipid derived from different food matrices has been extensively studied and has an appropriate application in food, medicine, and cosmetic industry. Egg is a richly nutritive food, of which proteins and lipids possess excellent functional characteristics and biological activities. In recent years, egg yolk lipid has been successively separated and investigated, such as egg yolk oil, phospholipids, and fatty acids, which have anti-inflammatory activity, antioxidant activity, cardiovascular protection, and memory improvement, involving the regulation of cell function and physiological homeostatic balance. In this paper, the biological activities and underlying benefit of egg yolk lipids and fat-soluble components have been highlighted and summarized. Meanwhile, the quantitative data of egg yolk lipids needed to achieve any of the described biological effects and recommended concentrations relevant for dietary intake are reviewed. Finally, current challenges and crucial issues of high-efficiency utilization of egg yolk lipids are also discussed.

In order to illuminate the forming process of salted egg, the effects of the brine solution with different salt concentrations on the physicochemical properties, textural properties, and microstructures of duck eggs were evaluated using conventional physicochemical property determination methods. The results showed that the moisture contents of both the raw and cooked egg whites and egg yolks, the springiness of the raw egg yolks and cooked egg whites exhibited a decreasing trend with the increase in the salting time and salt concentration. The salt content, oil exudation and the hardness of the raw egg yolks showed a constantly increasing trend. Viscosity of the raw egg whites showed an overall trend in which it first deceased and then increased and decreased again, which was similar to the trend of the hardness of the cooked egg whites and egg yolks. As the salting proceeded, the pH value of the raw and cooked egg whites declined remarkably and then declined slowly, whereas the pH of the raw and cooked egg yolks did not show any noticeable changes. The effect of salting on the pH value varied significantly with the salt concentration in the brine solution. Scanning electron microscopy (SEM) revealed that salted yolks consist of spherical granules and embedded flattened porosities. It was concluded that the treatment of salt induces solidification of yolk, accompanied with higher oil exudation and the development of a gritty texture. Different salt concentrations show certain differences.