Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity.

/pdf/the-evolutionary-significance-of-polyploidy-3jfm5py9j7.pdf

The evolutionary significance of polyploidy

The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events—transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.

/pdf/gene-duplication-and-evolution-in-recurring-polyploidization-1tk6fsc37e.pdf

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.

In this protocol, the authors provide a strategy and set of methods to analyze restriction-site-associated DNA-sequencing (RAD-seq) data using Stacks, enabling the genome-wide discovery and genotyping of SNPs across a range of systems. Restriction site-associated DNA sequencing (RAD-seq) allows for the genome-wide discovery and genotyping of single-nucleotide polymorphisms in hundreds of individuals at a time in model and nonmodel species alike. However, converting short-read sequencing data into reliable genotype data remains a nontrivial task, especially as RAD-seq is used in systems that have very diverse genomic properties. Here, we present a protocol to analyze RAD-seq data using the Stacks pipeline. This protocol will be of use in areas such as ecology and population genetics. It covers the assessment and demultiplexing of the sequencing data, read mapping, inference of RAD loci, genotype calling, and filtering of the output data, as well as providing two simple examples of downstream biological analyses. We place special emphasis on checking the soundness of the procedure and choosing the main parameters, given the properties of the data. The procedure can be completed in 1 week, but determining definitive methodological choices will typically take up to 1 month.

Deriving genotypes from RAD-seq short-read data using Stacks

Aquaculture is rapidly growing part of agriculture worldwide. It makes up around 44 percent of total fish production globally. This increased growth of production is achieved despite facing many challenges in the aquaculture environment. Among production limiting challenges, the infectious disease takes the lion share by causing multibillion-dollar loss annually. To reduce the impact of the fish disease, it is necessary to address health constraints based on scientifically proven and recommended ways. This review aims at pointing out some of the best approaches to prevention and control of infectious disease in aquaculture. Among the effective prevention and control strategies, vaccination is one of the key practices. Types of vaccines for use in fish include killed vaccines, attenuated vaccines, DNA vaccines, recombinant technology vaccines, and synthetic peptide vaccines. Administration techniques of vaccines in fish include oral, injection, or immersion methods. Antibiotics are also in use in aquaculture despite their side effects in the development of drug resistance by microorganisms. Biological and chemical disease control strategies such as using probiotics, prebiotics, and medicinal plants are widely in use. Biosecurity measures in aquaculture can keep the safety of a facility from certain disease-causing agents that are absent in particular system. Farm-level biosecurity measures include strict quarantine measures, egg disinfection, traffic control, water treatments, clean feed, and disposal of mortalities. In conclusion, rather than trying to treat every disease case, it advisable to follow a preventive approach before the event of any disease outbreaks.

/pdf/maintenance-of-fish-health-in-aquaculture-review-of-3bjt5wi8de.pdf

Maintenance of Fish Health in Aquaculture: Review of Epidemiological Approaches for Prevention and Control of Infectious Disease of Fish.

Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

/pdf/harnessing-genomics-to-fast-track-genetic-improvement-in-51hi0zp42l.pdf

Harnessing genomics to fast-track genetic improvement in aquaculture.

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

/pdf/the-atlantic-salmon-genome-provides-insights-into-t27j1ulac7.pdf

Yan Hu

Papers

The Atlantic salmon genome provides insights into rediploidization