Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America

Roundup(®) in Zebrafish: Effects on Oxidative Status and Gene Expression

The objective of the present study was to determine the effects of Roundup on oxidative status in adult Danio rerio liver and gills. Reactive oxygen species (ROS) and antioxidant capacity (ACAP) were measured in fish after exposure to Roundup (5 and 10 mg/L) for 24, 48, 72, and 96 h. Furthermore, gene expression related to antioxidant response was evaluated after 24 and 96 h. In gills, an increase in ACAP was observed after 96 h in the highest concentration. In the liver, a reduction in ROS and ACAP was observed after 24 h, whereas an increase in ACAP was observed after 48 h in the highest concentration. Exposure to the lowest concentration caused a reduction in ROS after 72 and 96 h. Regarding gene expression, a reduction in superoxide dismutase 2 (sod2) and glutathione S-transferase (gstπ) was observed. An increase in uncoupling protein 1 (ucp1) expression was observed in gills of animals exposed to the highest concentration after 24 h. Glutathione peroxidase (gpx) gene expression was reduced in the gills of animals exposed to the lowest concentration; however, it was induced in liver tissue after 96 h of exposure to the highest concentration. These results indicate that zebrafish exposure to Roundup alters oxidative status and causes a response in terms of antioxidant defense system gene expression.

Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns

Group I introns are highly dynamic and mobile, featuring extensive presence-absence variation and widespread horizontal transfer. Group I introns can invade intron-lacking alleles via intron homing powered by their own encoded homing endonuclease gene (HEG) after horizontal transfer or via reverse splicing through an RNA intermediate. After successful invasion, the intron and HEG are subject to degeneration and sequential loss. It remains unclear whether these mechanisms can fully address the high dynamics and mobility of group I introns. Here, we found that HEGs undergo a fast gain-and-loss turnover comparable with introns in the yeast mitochondrial 21S-rRNA gene, which is unexpected, as the intron and HEG are generally believed to move together as a unit. We further observed extensively mosaic sequences in both the introns and HEGs, and evidence of gene conversion between HEG-containing and HEG-lacking introns. Our findings suggest horizontal transfer and gene conversion can accelerate HEG/intron degeneration and loss, or rescue and propagate HEG/introns, and ultimately result in high HEG/intron turnover rate. Given that up to 25% of the yeast mitochondrial genome is composed of introns and most mitochondrial introns are group I introns, horizontal transfer and gene conversion could have served as an important mechanism in introducing mitochondrial intron diversity, promoting intron mobility and consequently shaping mitochondrial genome architecture.

A SURVEY OF BANGIALES (RHODOPHYTA) BASED ON MULTIPLE MOLECULAR MARKERS REVEALS CRYPTIC DIVERSITY(1)

The Bangiales is a diverse order consisting of 28 species in Canada. Morphological simplicity and similarity among species has led to taxonomic confusion and the need for molecular techniques for species identification. This study is the first to employ the standardized DNA barcode marker COI-5P in a broad floristic survey of the Bangiales in Canadian marine waters. A total of 37 species were ultimately sequenced, 29 of which occurred in Canada. Molecular results led to the synonymization of Wildemania cuneiformis with W. amplissima, as well as the description of two new species: Porphyra corallicola sp. nov. and Pyropia peggicovensis sp. nov., and discovery of another five putative new species. Comparison of the performance of COI-5P as a species identification tool relative to rbcL (large subunit of ribulose-1,5-bisphosphate carboxylase oxygenase) and the UPA (universal plastid amplicon) revealed that, although each marker had strengths and weaknesses, the COI-5P showed the highest species-discriminatory power due to its high level of interspecific variation. The rbcL was further used to place the new species into a phylogenetic context, whereas UPA was not recommended for species identification in the Bangiales owing to within-individual heterogeneity between the two copies present in the plastid genomes in some lineages.

Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture

In photosynthetic eukaryotes, relative silent-site nucleotide substitution rates (which can be used to approximate relative mutation rates) among mitochondrial, plastid, and nuclear genomes (mtDNAs, ptDNAs, and nucDNAs) are estimated to be 1:3:10 respectively for seed plants and roughly equal for green algae. These estimates correlate with certain genome characteristics, such as size and coding density, and have therefore been taken to support a relationship between mutation rate and genome architecture. Plants and green algae, however, represent a small fraction of the major eukaryotic plastid-bearing lineages. Here, we investigate relative rates of mutation within the model red algal genus Porphyra. In contrast to plants, we find that the levels of silent-site divergence between the Porphyra purpurea and Porphyra umbilicalis mtDNAs are three times that of their ptDNAs and five times that of their nucDNAs. Moreover, relative mutation rates do not correlate with genome architecture: despite an estimated three-fold difference in their mutation rate, the mitochondrial and plastid genome coding densities are equivalent - an observation that extends to organisms with secondary red algal plastids. These findings are supported by within-species silent-site polymorphism data from P. purpurea.