Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome

Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element–like and long interspersed element–like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes

VEGF and Angiopoietin-1 Exert Opposing Effects on Cell Junctions by Regulating the Rho GEF Syx

Vascular endothelial growth factor (VEGF) and Ang1 (Angiopoietin-1) have opposing effects on vascular permeability, but the molecular basis of these effects is not fully known. We report in this paper that VEGF and Ang1 regulate endothelial cell (EC) junctions by determining the localization of the RhoA-specific guanine nucleotide exchange factor Syx. Syx was recruited to junctions by members of the Crumbs polarity complex and promoted junction integrity by activating Diaphanous. VEGF caused translocation of Syx from cell junctions, promoting junction disassembly, whereas Ang1 maintained Syx at the junctions, inducing junction stabilization. The VEGF-induced translocation of Syx from EC junctions was caused by PKD1 (protein kinase D1)-mediated phosphorylation of Syx at Ser806, which reduced Syx association to its junctional anchors. In support of the pivotal role of Syx in regulating EC junctions, syx−/− mice had defective junctions, resulting in vascular leakiness, edema, and impaired heart function

Single-male paternity in coelacanths

Latimeria chalumnae, a ‘living fossil,’ is of great scientific interest, as it is closely related to the aquatic ancestors of land-living tetrapods. Latimeria show internal fertilization and bear live young, but their reproductive behaviour is poorly known. Here we present for the first time a paternity analysis of the only available material from gravid females and their offspring. We genotype two L. chalumnae females and their unborn brood for 14 microsatellite loci. We find that the embryos are closely related to each other and never show more than three different alleles per locus, providing evidence for a single father siring all of the offspring. We reconstruct the father’s genotype but cannot identify it in the population. These data suggest that coelacanths have a monogamous mating system and that individual relatedness is not important for mate choice

Mining functional information from cereal genomes–the utility of expressed sequence tags

The vast number of expressed sequence tags (ESTs) generated from cereals with large genome size is an important complement method to the whole genome sequencing projects. As technology-driven revolution sweeps through, we are submerged in an avalanche of new information about genes and their function. To accomplish functional roles to the available ESTs, proper annotation of EST data is crucial, which could be achieved through the employment of tools of bioinformatics generated in the recent past. In this review, the critical steps involved in EST-based gene discovery and the employment of available web-based bioinformatic tools for annotation of ESTs is discussed. The current status of application of EST clones in the development of molecular markers in cereal species and utilizing ESTs as a resource for the construction of arrays is summarized as well. We also focus on large-scale gene expression data analysis methods and the challenges for computational biologists to extract functional information from such large-scale gene expression data