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Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance.

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Haustoria of biotrophic rust fungi are responsible for the uptake of nutrients from their hosts and for the production of secreted proteins, known as effectors, which modulate the host immune system. The identification of the transcriptome of haustoria and an understanding of the functions of expressed genes therefore hold essential keys for the elucidation of fungus-plant interactions and the development of novel fungal control strategies. Here, we purified haustoria from infected leaves and used 454 sequencing to examine the haustorial transcriptomes of Phakopsora pachyrhizi and Uromyces appendiculatus, the causal agents of soybean rust and common bean rust, respectively. These pathogens cause extensive yield losses in their respective legume crop hosts. A series of analyses were used to annotate expressed sequences, including transposable elements and viruses, to predict secreted proteins from the assembled sequences and to identify families of candidate effectors. This work provides a foundation for the comparative analysis of haustorial gene expression with further insights into physiology and effector evolution.

Seven-day-old, etiolated barley (Hordeum vulgare 1. var Post) leaves were fractionated into crude and purified etioplast, microsomal, and plasma membrane (PM) fractions. Protoporphyrinogen oxidase (Protox) specific activities of crude etioplast, purified etio- reduced the Protox activity of all fractions, except that microsomal Protox activity was slightly stimulated by NADPH. Ascorbate, CSH, or a combination of the two reductants enhanced Protox inhibition by AFM, and AFM inhibition of Protox was greatest in all fractions with DTT. NADPH enhanced AFM inhibition significantly only in etioplast fractions. Uroporphyrinogen I (Urogen I) and coproporphyrinogen I (Coprogen I) oxidase activities were found in all fractions; however, etioplast fractions had significantly more substrate specificity for protoporphyrinogen IX (Protogen IX) than the other fractions. Urogen I and Coprogen I oxidase activities were unaffected by AFM in all fractions, and 2 mM DTT almost completely inhibited these activities from all fractions. Diethyldithiocarbamate inhibited PM Protox activity by 62% but had less effect on microsome and little or no effect on etioplast Protox. juglone and duroquinone stimulated microsomal and PM Protox activity, whereas the lesser effect of these quinones on etioplast Protox activity was judged to be due to PM and/or microsomal contaminants. These data indicate that there are microsomal and PM Protogen IX-oxidizing activities that are not the same as those associated with the etioplast and that these activities are not inhibited i n vivo by AFM. In summary, these data support the view that the primary source of high protoporphyrin IX concentrations in AFM-treated plant tissues is from Protogen IX exported by plastids and oxidized by AFM-resistant extraorganellar oxidases.