Genomics

Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within a single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme  geographical variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasize how the interplay between genomic architecture and local scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

Here we report a benchmark of the effect of bootstrap cut-off values of the RDP Classifier tool in terms of data retention along the different taxonomic ranks by using Illumina reads. Results provide guidelines for planning sequencing depths and selection of bootstrap cut-off in taxonomic assignments.

The 19 chromosomal pairs of the swine karyotype are resolved into 18 peaks denoted A to Q and Y by dual-beam flow cytometry. The chromosomal content of six peaks has previously been determined by analyzing male/female differences, karyotypes of animals carrying translocations, and PCR studies of genes with known assignments. For the remaining chromosomes, putative assignments to flow peaks were deduced from comparison of DNA contents, determined by flow cytometry, and chromosomal size. We present here the complete characterization of the pig bivariate flow karyotype using the PARM-PCR technique combined with fluorescence in situ hybridization. Chromosome-specific probes were generated by PCR amplification of 300 sorted chromosomes with primers under nonspecific conditions and used to paint chromosomes by FISH. The chromosomal content of each peak was identified: peaks A (chromosome 1), B (13), C (6), D (2), E (14), F (3), G (7), H (9,4,X), H1 (9), I (15), J (8), K (5), L (10), M (12), N (16), O (11), P (17), Q (18), Y (Y). We were able to characterize perfectly the pig bivariate flow karyotype. Such techniques could be applied to any other species.