Focus has been devoted the development of a suite of molecular tools, predominantly based on transcriptomic analysis.
A combination of predicted gene models and transcripts, RNA-sequencing followed by transcriptome assembly, and use of available expressed sequence tags (ESTs) have enabled the development of a suite of microarrays for marine and freshwater invertebrates and fish.
Chlamydomonas reinhardtii: C. reinhardtii, a single celled green chlorophyte alga inhabitating different freshwater environments world-wide, is commonly used in biological and toxicological research. A microarray designed on basis of predicted genes from the C. reinhardtii v.5.3.1 genome and Augustus annotation update u11.6 (http://www.phytozome.net/chlamy.php) have been produced. The current assembly include about 20k predicted protein-coding transcripts, whereof approx. 13k stable gene and transcript identifiers.
Phaeodactylum tricornutum: P. tricornutum, a pennate unicellular diatom found in the eastern and western North Atlantic Ocean, has gained popularity as a versatile test species for ecotoxicological testing. A microarray designed on basis of predicted genes from the P. tricornutum v.2 genome with annotations performed by the JGI Genome Annotation Pipeline (http://genome.jgi-psf.org/Phatr2/Phatr2.info.html) has been used for construction of a custom microarray. The current assembly includes about 11k predicted genes, whereof approximately 9k of these supported by ESTs.
Daphnia magna microarray: D. magna, a cladoceran freshwater water flea inhabiting North America, Eurasia and some regions of Africa, have been extensive used in ecotoxicological research due to its small size, rapid lifespan, and availability of standardized test protocols. RNA-sequencing followed by de-novo assembly of the D. magnatranscriptome is currently being performed for future development of a genome-wide microarray. The 1th version of the array is expected finalized by end of 2013.
Calanus finmarchicus microarray: C. finmarchicus, a planktonic copepod found in the Sub-Arctic to Arctic regions of the Atlantic Ocean, is a key component in the North Atlantic food web. A 60k high density microarray has been designed on basis of de-novo assembly of the C. finmarchicus trancriptome, complemented by available ESTs from NCBI. The current version of the array is based on 58k transcripts, whereof 55 k contigs and 3k single reads. About 50% of the transcripts have been annotated towards different databases.
Acartia tonsa microarray: A. tonsa, an estuarine Calanoid copepod in temperate and subtropical coastal waters, is commonly used in field and laboratory experiments due to well characterized behavior, ecology, reproductive biology, and availability of standardized ecotoxicological test guidelines. RNA-sequencing followed by de-novo assembly of the A. tonsa transcriptome has been carried out for the development of a genome-wide microarray. Current version of the array is based on the assembly of 60k unigenes, whereof 48k with predicted protein coding regions and about 60% of the transcripts have been annotated.
Tisbe battagliai: T. battagliai, a marine harpacticoid copepod with wide geographic distribution, is a suitable organism for environmental monitoring and ecotoxicological hazard/ risk assessment. RNA-sequencing followed by de-novo assembly of the T. battagliai transcriptome has been carried out for the development of a genome-wide microarray. Current version of the array is based on the assembly of 55k unigenes, whereof 42k transcripts with predicted protein coding regions and about 32k of the transcripts have been annotated.
Polar cod (Boreogadus saida): Polar cod, a codfish found in Arctic regions north of Russia, Alaska, Canada, Grenland and Norway, is a keystone species in the arctic food web. RNA-sequencing followed by de-novo assembly of the Polar cod transcriptome has been carried out for the development of a genome-wide microarray. Current version of the array is based on the assembly of 83k unigenes, whereof 50k transcripts with predicted protein coding regions and 54k transcripts that have been annotated.