Sismicità all’Etna dal 1989 al 2010: evidenze sull’evoluzione spazio-temporale dell’attività sismica

Il Monte Etna, uno dei più attivi vulcani basaltici tra i più monitorati al mondo, è sede di una notevole attività sismica e vulcanica. Esso è ubicato in Sicilia orientale in un complesso quadro geodinamico, dove le principali strutture tettoniche regionali giocano un ruolo chiave nei processi dinamici del vulcano. La sismicità dell’Etna si manifesta con un elevato rate di terremoti di bassa e moderata energia che, a volte, a causa dell’estrema superficialità della sorgente, provocano danni ai centri abitati prossimi all’area epicentrale. Il monitoraggio sistematico dell’attività sismica etnea è effettuato sin dal 1989, mediante una rete sismica locale permanente che nel tempo è stata oggetto di importanti miglioramenti. La prima configurazione di rete era costituita da circa 10 stazioni analogiche con sensori a corto periodo gestita dall’Istituto Internazionale di Vulcanologia (IIV-CNR). Nel 1994, una rete sismica costituita da circa 40 stazioni (analogiche con sensori a corto periodo) fu installata sull’Etna nell’ambito del Progetto Poseidon. Nel 2001, le reti gestite dall’IIV-CNR e dal Progetto Poseidon confluirono nell’Istituto Nazionale di Geofisica e Vulcanologia (INGV); attualmente la rete sismica, costituita da circa 50 stazioni digitali equipaggiate con sismometri broadband a tre componenti, è gestita dalla Sezione di Catania dell’INGV. Nel periodo 1989-1999, il catalogo dei terremoti risulta costituito da circa 2000 eventi con soglia di completezza per magnitudo pari a 2.0; dal 1999 ad oggi contiene circa 6000 terremoti con soglia di completezza per magnitudo 1.5. La capacità di detezione della rete è migliorata nel tempo permettendo di registrare e localizzare anche gli eventi meno energetici (M≥1.0). In questo lavoro, vengono presentati i caratteri predominanti della sismicità etnea negli ultimi 20 anni, con un maggiore dettaglio della distribuzione spazio-temporale della sismicità verificatasi dal 1999. L’analisi della attività sismica rappresenta un utile strumento per l’interpretazione delle dinamiche che hanno contraddistinto numerose ed importanti eruzioni (2001, 2002-03, 2004, 2006, 2008-09). In particolare, la variazione del rilascio energetico della sismicità ha contribuito in maniera significativa ad identificare i probabili processi geodinamici legati alla ricarica del sistema magmatico del vulcano. La distribuzione spaziale della sismicità ha consentito di evidenziare inoltre l’esistenza di diverse aree sismogenetiche caratterizzate da un differente rate sismico, profondità focali e cinematica delle strutture associate. Infine, osservando le caratteristiche della sismicità nel lungo periodo, differenti settori del vulcano sono risultati maggiormente attivi in relazione ai più importanti recenti eventi eruttivi

Transcriptomics approaches to identify genes and markers for production traits in giant freshwater prawn Macrobrachium rosenbergii

This study used next generation sequencing technologies to investigate growth in a cultured crustacean. The objective was to identify and characterise specific gene loci that contribute important phenotypic variation to growth as well as to develop a large set of SNP markers in candidate genes for assessing correlations between specific mutations and individual growth performance. The genomic dataset generated provides a fundamental resource for application in future crustacean stock improvement programs. Ultimately, the data can be applied to development of culture lines with improved growth performance

Development of type I genetic markers from expressed sequence tags in highly polymorphic species

Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: - 1) priming site polymorphism in the template leads to inferior or erratic amplification; - 2) introns in the target amplicon are too large and/or numerous to allow effective amplification under standard screening conditions, and; - 3) at least occasionally, a PCR primer straddles an exon–intron junction and is unable to bind to genomic DNA template. The first is only a minor issue for species or strains with low heterozygosity but becomes a significant problem for species with high genomic variation, such as marine organisms with extremely large effective population sizes. Problems arising from unanticipated introns are unavoidable but are most pronounced in intron-rich species, such as vertebrates and lophotrochozoans. We present an approach to marker development in the Pacific oyster Crassostrea gigas, a highly polymorphic and intron-rich species, which minimizes these problems, and should be applicable to other non-model species for which EST databases are available. Placement of PCR primers in the 3′ end of coding sequence and 3′ UTR improved PCR success rate from 51% to 97%. Almost all (37 of 39) markers developed for the Pacific oyster were polymorphic in a small test panel of wild and domesticated oysters

Transferability of cupped oyster EST (Expressed Sequence Tag)-derived SNP (Single Nucleotide Polymorphism) markers to related crassostrea and ostrea species

Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa

Phan tich he gen chuc nang tu mo than ca tra (pangasianodon hypophthalmus) nuoi o dieu kien man: Lap rap, chu giai, phan tich chi thi snp (A transcriptomic analysis of the kidney tissue of tra catfish (Pangasianodon hypophthalmus) reared in saline condition: de novo assembly, annotation, snp discovery)

Pangasianodon hypophthalmus is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The current study using Ion Torrent technology generated EST resources from the kidney for Tra catfish reared at a salinity level of 9 ppt. We obtained 2,623,929 reads after trimming and processing with an average length of 104 bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 29,940 contigs, and allowing identification of 5,710 putative genes when comppared with NCBI non-redundant database. A large number of single nucleotide polymorphisms (SNPs) were also detected. The sequence collection generated in our study represents the most comprehensive transcriptomic resource for P. hypophthalmus available to date

Genes and growth performance in crustacean species : a review of relevant genomic studies in crustaceans and other taxa

Global aquaculture has expanded rapidly to address the increasing demand for aquatic protein needs and an uncertain future for wild fisheries. To date, however, most farmed aquatic stocks are essentially wild and little is known about their genomes or the genes that affect important economic traits in culture. Biologists have recognized that recent technological advances including next generation sequencing (NGS) have opened up the possibility of generating genome wide sequence data sets rapidly from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', understanding gene function and genetic effects on expressed quantitative trait locus phenotypes will be fundamental to future knowledge development. Many factors can influence the individual growth rate in target species but of particular importance in agriculture and aquaculture will be the identification and characterization of the specific gene loci that contribute important phenotypic variation to growth because the information can be applied to speed up genetic improvement programmes and to increase productivity via marker-assisted selection (MAS). While currently there is only limited genomic information available for any crustacean species, a number of putative candidate genes have been identified or implicated in growth and muscle development in some species. In an effort to stimulate increased research on the identification of growth-related genes in crustacean species, here we review the available information on: \ud \ud (i) associations between genes and growth reported in crustaceans, \ud (ii) growth-related genes involved with moulting, \ud (iii) muscle development and degradation genes involved in moulting, and; \ud (iv) correlations between DNA sequences that have confirmed growth trait effects in farmed animal species used in terrestrial agriculture and related sequences in crustacean species. \ud \ud The information in concert can provide a foundation for increasing the rate at which knowledge about key genes affecting growth traits in crustacean species is gained

Evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypophthalmus) using an RNA-Seq approach

Increasing salinity levels in freshwater and coastal environments caused by sea level rise linked to climate change is now recognized to be a major factor that can impact fish growth negatively, especially for freshwater teleost species. Striped catfish (Pangasianodon hypophthalmus) is an important freshwater teleost that is now widely farmed across the Mekong River Delta in Vietnam. Understanding the basis for tolerance and adaptation to raised environmental salinity conditions can assist the regional culture industry to mitigate predicted impacts of climate change across this region. Attempt of next generation sequencing using the ion proton platform results in more than 174 million raw reads from three tissue libraries (gill, kidney and intestine). Reads were filtered and de novo assembled using a variety of assemblers and then clustered together to generate a combined reference transcriptome. Downstream analysis resulted in a final reference transcriptome that contained 60,585 transcripts with an N50 of 683 bp. This resource was further annotated using a variety of bioinformatics databases, followed by differential gene expression analysis that resulted in 3062 transcripts that were differentially expressed in catfish samples raised under two experimental conditions (0 and 15 ppt). A number of transcripts with a potential role in salinity tolerance were then classified into six different functional gene categories based on their gene ontology assignments. These included; energy metabolism, ion transportation, detoxification, signal transduction, structural organization and detoxification. Finally, we combined the data on functional salinity tolerance genes into a hypothetical schematic model that attempted to describe potential relationships and interactions among target genes to explain the molecular pathways that control adaptive salinity responses in P. hypophthalmus. Our results indicate that P. hypophthalmus exhibit predictable plastic regulatory responses to elevated salinity by means of characteristic gene expression patterns, providing numerous candidate genes for future investigations

A genome survey sequence (GSS) analysis and microsatellite marker development for Indian mackerel, Rastrelliger kanagurta, using Ion Torrent technology

A next generation sequencing platform (Ion Torrent PGM™) was used to generate a partial genome survey sequence (GSS) dataset to develop microsatellite markers from R. kanagurta genomic DNA. Data generated included a total of 399,794 sequence reads (81.29 Mbp) with 16,209 sequence reads successfully assembled. This produced 327 contigs averaging 677 bp in length in addition to the SSR markers. Results based on GSS BLASTx and BLASTn possessed significant similarity (E value −6) with available data in public databases, with the majority matching well to previously reported fish sequences. A total of 7891 SSR-containing motif repeats of which 1688 qualified for primer design were generated. After optimization and testing for reproducibility and polymorphism, eight microsatellite markers were deemed suitable for future population genetic analysis in the target species

Comparative Evaluation of Genome Assemblers from Long-Read Sequencing for Plants and Crops

The availability of recent state-of-the-art long-read sequencing technologies has significantly increased the ease and speed of producing high-quality plant genome assemblies. A wide variety of genome-related software tools are now available and they are typically benchmarked using microbial or model eukaryotic genomes such as Arabidopsis and rice. However, many plant species have much larger and more complex genomes than these, and the choice of tools, parameters, and/or strategies that can be used is not always obvious. Thus, we have compared the metrics of assemblies generated by various pipelines to discuss how assembly quality can be affected by two different assembly strategies. First, we focused on optimizing read preprocessing and assembler variables using eight different de novo assemblers on five different Pacific Biosciences long-read datasets of diploid and tetraploid species. Then, we examined a single scaffolding tool (quickmerge) that has been employed for the postprocessing step. We then merged the outputs from multiple assemblies to produce a higher quality consensus assembly. Then, we benchmarked the assemblies for completeness and accuracy (assembly metrics and BUSCO), computer memory, and CPU times. Two lightweight assemblers, Miniasm/Minimap/Racon and WTDBG, were deemed good for novice users because they involved smaller required learning curves and light computational resources. However, two heavyweight tools, CANU and Flye, should be the first choice when the goal is to achieve accurate and complete assemblies. Our results will provide valuable guidance in future plant genome projects and beyond. </p