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The mangrove rivulus (Kryptolebias marmoratus) is one of two preferentially self-fertilizing hermaphroditic vertebrates. This mode of reproduction makes mangrove rivulus an important model for evolutionary and biomedical studies because long periods of self-fertilization result in naturally homozygous genotypes that can produce isogenic lineages without significant limitations associated with inbreeding depression. Over 400 isogenic lineages currently held in laboratories across the globe show considerable among-lineage variation in physiology, behavior, and life history traits that is maintained under common garden conditions. Temperature mediates the development of primary males and also sex change between hermaphrodites and secondary males, which makes the system ideal for the study of sex determination and sexual plasticity. Mangrove rivulus also exhibit remarkable adaptations to living in extreme environments, and the system has great promise to shed light on the evolution of terrestrial locomotion, aerial respiration, and broad tolerances to hypoxia, salinity, temperature, and environmental pollutants. Genome assembly of the mangrove rivulus allows the study of genes and gene families associated with the traits described above. Here we present a de novo assembled reference genome for the mangrove rivulus, with an approximately 900 Mb genome, including 27,328 annotated, predicted, protein-coding genes. Moreover, we are able to place more than 50% of the assembled genome onto a recently published linkage map. The genome provides an important addition to the linkage map and transcriptomic tools recently developed for this species that together provide critical resources for epigenetic, transcriptomic, and proteomic analyses. Moreover, the genome will serve as the foundation for addressing key questions in behavior, physiology, toxicology, and evolutionary biology.

Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 individuals representing three diverse human populations. We show that rates of indel mutagenesis are highly heterogeneous, with 43%-48% of indels occurring in 4.03% of the genome, whereas in the remaining 96% their prevalence is 16 times lower than SNPs. Polymerase slippage can explain upwards of three-fourths of all indels, with the remainder being mostly simple deletions in complex sequence. However, insertions do occur and are significantly associated with pseudo-palindromic sequence features compatible with the fork stalling and template switching (FoSTeS) mechanism more commonly associated with large structural variations. We introduce a quantitative model of polymerase slippage, which enables us to identify indel-hypermutagenic protein-coding genes, some of which are associated with recurrent mutations leading to disease. Accounting for mutational rate heterogeneity due to sequence context, we find that indels across functional sequence are generally subject to stronger purifying selection than SNPs. We find that indel length modulates selection strength, and that indels affecting multiple functionally constrained nucleotides undergo stronger purifying selection. We further find that indels are enriched in associations with gene expression and find evidence for a contribution of nonsense-mediated decay. Finally, we show that indels can be integrated in existing genome-wide association studies (GWAS); although we do not find direct evidence that potentially causal protein-coding indels are enriched with associations to known disease-associated SNPs, our findings suggest that the causal variant underlying some of these associations may be indels. [ABSTRACT FROM AUTHOR]

Connective tissue growth factor (CTGF) plays a major role in pathways that lead to fibrosis, including fibrosis of major organs, fibroproliferative diseases, and scarring. Tissue hypoxia has been reported to induce the expression and secretion of CTGF in various tissues and organs, such as in renal cortical myofibroblasts, in renal interstitial fibroblasts, and in skin. This implicates CTGF as a mechanism of action for tissue damage caused by hypoxia. Studies have shown that cells deficient in hypoxic inducible factor 1 (HIF-1) were not able to produce CTGF mRNA, suggesting a strong association between the two proteins. In this study fibroblast cells were placed under hypoxic conditions for periods of 2, 24, 48, and 72 hours, and the levels of HIF-1, and CTGF were determined by immunocytochemical techniques. The results show a strong positive response to HIF-1 following hypoxia treatment for periods of 24 hours. By 48 and 72 hours HIF-1 levels are reduced and increases in CTGF cellular staining are noticeable. The results of our study also indicate a strong correlation between HIF-1 and CTGF. Our data also shows that once CTGF is induced, HIF-1 levels decline even though the hypoxic conditions are maintained. Determining the relationship between HIF-1 and CTGF may provide a deeper understanding of the pathogenesis of fibroproliferative disease.