Population genetics of Cobia (Rachycentron canadum): implications for fishery management along the coast of the southeastern United States

Cobia (Rachycentron canadum) is a pelagic, migratory species with a transoceanic distribution in tropical and subtropical waters. Recreational fishing pressure on Cobia in the United States has increased substantially during the last decade, especially in areas of its annual inshore aggregations, making this species potentially susceptible to overfishing. Although Cobia along the Atlantic and Gulf coasts of the southeastern United States are currently managed as a single fishery, the genetic composition of Cobias in these areas is unclear. On the basis of a robust microsatellite data set from collections along the U.S. Atlantic coast (2008–09), offshore groups were genetically homogenous. However, the 2 sampled inshore aggregations (South Carolina and Virginia) were genetically distinct from each other, as well as from the offshore group. The recapture of stocked fish within their release estuary 2 years after release indicates that some degree of estuarine fidelity occurs within these inshore aggregations and supports the detection of their unique genetic structure at the population level. These results complement the observed high site fidelity of Cobias in South Carolina and support a recent study that confirms that Cobia spawn in the inshore aggregations. Our increased understanding of Cobia life history will be beneficial for determining the appropriate scale of fishery management for Cobia.

Sensitivity of Lake Sturgeon population dynamics and genetics to demographic parameters [Powerpoint Slide]

Lake sturgeon Acipenser fulvescens restoration is a priority throughout the Great Lakes basin, where sturgeon have been reduced to less than 1% of historic levels due to habitat degradation, overharvest, and fragmentation of spawning populations. The population parameters most important to long-term lake sturgeon persistence are unknown.

Functional consequences of new exon acquisition in mammalian chromodomain Y-like (CDYL) genes

The origin of new exons is an important mechanism for proteome diversity. Here, we report the recurrent origination of new exons in mammalian chromodomain Y-like (CDYL) genes and the functional consequences associated with the acquisition of the new exons

Evolutionary characteristics of exons expressed at different abundance levels in mammals

With comparative genomics approaches, we evaluated the evolutionary characteristics of conservation of exons which are expressed abundantly, moderately or lowly in mammals. Using non-coding regions and pseudogenes as controls, sequence identity, phastCons

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Report of the NBFGR-BOBLME Indian mackerel genetics harmonisation training workshop, Kochi, India, 20-27 August, 2013

This workshop was held at the National Bureau of Fish Genetic Resources and followed on from the Indian mackerel Working group meeting in Colombo (28-29 May, 2012). Activities included; DNA extraction; PCR (Polymerase Chain Reaction) for microsatellites; genotyping microsatellites; data analysis; emerging technologies; and an action plan