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Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes . We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ∼18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid  to a massive algal chloroplast , including gnetophytes  and cycads . The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and rapid discovery of informative candidate regions.
Reference-Free Comparative Genomics of 174 Chloroplasts
Chai-Shian Kua, 1 , 2 Jue Ruan, 3 John Harting, 4 Cheng-Xi Ye, 5 Matthew R. Helmus, 1 , 6 Jun Yu, 3 and Charles H. Cannon 1 , 4 , * Jianwei Zhang, Editor
Three new species of the genus Plato from caves in the states of Para and Minas Gerais, Brazil, are described. P. novalima sp. n., from Minas Gerais, is the first record of the genus in the southeastern region of Brazil. P. ferriferus sp. n. and P. striatus sp. n., from Carajas, Para, north of Brazil, are also described. The former is an extremely abundant species, whereas the latter has only one known male specimen. Cuacuba gen. n. is proposed and represented by two new species, C. mariana sp. n. (type species) and C. morrodopilar sp. n., both from the state of Minas Gerais. Morphology of genitalia in Cuacuba gen. n. is similar to other Theridiosomatidae genera and is herein discussed. None of the proposed species presents troglomorphic adaptations. They are widespread, abundant inside caves in different and large karst areas, and each genus prefers different lithologies.
biospeleology, Neotropical region, taxonomy
Three new species of the spider genus Plato and the new genus Cuacuba from caves of the states of Para and Minas Gerais, Brazil (Araneae, Theridiosomatidae)
Pedro H. Prete,1 Igor Cizauskas,1 and Antonio D. Brescovit1
The regulation of liver apolipoprotein (apo) A-I gene expression by fibrates was studied in human apo A-I transgenic mice containing a human genomic DNA fragment driving apo A-I expression in liver. Treatment with fenofibrate (0.5% wt/wt) for 7 d increased plasma human apo A-I levels up to 750% and HDL-cholesterol levels up to 200% with a shift to larger particles. The increase in human apo A-I plasma levels was time and dose dependent and was already evident after 3 d at the highest dose (0.5% wt/wt) of fenofibrate. In contrast, plasma mouse apo A-I concentration was decreased after fenofibrate in nontransgenic mice. The increase in plasma human apo A-I levels after fenofibrate treatment was associated with a 97% increase in hepatic human apo A-I mRNA, whereas mouse apo A-I mRNA levels decreased to 51%. In nontransgenic mice, a similar down-regulation of hepatic apo A-I mRNA levels was observed. Nuclear run-on experiments demonstrated that the increase in human apo A-I and the decrease in mouse apo A-I gene expression after fenofibrate occurred at the transcriptional level. Since part of the effects of fibrates are mediated through the nuclear receptor PPAR (peroxisome proliferator-activated receptor), the expression of the acyl CoA oxidase (ACO) gene was measured as a control of PPAR activation. Both in transgenic and nontransgenic mice, fenofibrate induced ACO mRNA levels up to sixfold. When transgenic mice were treated with gemfibrozil (0.5% wt/wt) plasma human apo A-I and HDL-cholesterol levels increased 32 and 73%, respectively, above control levels. The weaker effect of this compound on human apo A-I and HDL-cholesterol levels correlated with a less pronounced impact on ACO mRNA levels (a threefold increase) suggesting that the level of induction of human apo A-I gene is related to the PPAR activating potency of the fibrate used. Treatment of human primary hepatocytes with fenofibric acid (500 microM) provoked an 83 and 50% increase in apo A-I secretion and mRNA levels, respectively, supporting that a direct action of fibrates on liver human apo A-I production leads to the observed increase in plasma apo A4 and HDL-cholesterol.
Opposite regulation of human versus mouse apolipoprotein A-I by fibrates in human apolipoprotein A-I transgenic mice.
L Berthou, N Duverger, F Emmanuel, S Langouët, J Auwerx, A Guillouzo, J C Fruchart, E Rubin, P Denefle, B Staels, and D Branellec
1996 Jun 1