Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of "living fossils." As arthropods, they belong to the Ecdysozoa}, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes, and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses. Here we use a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers and 5,775 candidate conserved protein coding genes. Comparison to other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications (WGDs) ~ 300 MYA, followed by extensive chromosome fusion

Complete genome sequence of Planctomyces limnophilus type strain (Mü 290).

Planctomyces limnophilus Hirsch and Müller 1986 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. Besides Pirellula staleyi, this is the second completed genome sequence of the family Planctomycetaceae. P. limnophilus is of interest because it differs from Pirellula by the presence of a stalk and its structure of fibril bundles, its cell shape and size, the formation of multicellular rosettes, low salt tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304 protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project

Fine mapping of a QTL for white markings on chromosome 23 in Scandinavian Fjord horses.

In Fjord horses, it is undesirable to have extensive white markings on the head or legs. White markings tended to be multifactorial pleitropic traits with phenotypic effects not solely restricted to coat colour but a variety of other syndromes which could have a negative impact on the horse. In this thesis, 328 Fjord horses underwent a GWAS for white markings based on 67k SNPchip data. Of these 328 horses, 19 had white markings on the head or body. This GWAS identified 2 regions on chromosome 23 with significant association to white markings. Following this, 16 horses, evenly split between cases and controls, underwent resequencing culminating in variant calling using the GATK and FreeBayes. Further analysis was carried out on the peaks identified in the GWAS, as well as regions containing known white marking genes. This further analysis comprised of differences in allele frequency, Weir and Cockerham’s Fst and variant annotation. No clear mutations were identified in a protein coding gene, however an association with U6 spliceosomal RNA were indicated following filtering on variant annotation.EM-AB