Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa.Peer reviewe

Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing.

11 páginas, 4 figuras, 2 tablas.Transcriptome sequencing with next-generation sequencing technologies has the potential for addressing many longstanding questions about the biology of sponges. Transcriptome sequence quality depends on good cDNA libraries, which requires high-quality mRNA. Standard protocols for preserving and isolating mRNA often require optimization for unusual tissue types. Our aim was assessing the efficiency of two preservation modes, (i) flash freezing with liquid nitrogen (LN2) and (ii) immersion in RNAlater, for the recovery of high-quality mRNA from sponge tissues.We also tested whether the long-term storage of samples at )80 C affects the quantity and quality of mRNA. We extracted mRNA from nine sponge species and analysed the quantity and quality (A260 ⁄ 230 and A260⁄ 280 ratios) of mRNA according to preservation method, storage time, and taxonomy. The quantity and quality of mRNA depended significantly on the preservation method used (LN2 outperforming RNAlater), the sponge species, and the interaction between them.When the preservation was analysed in combination with either storage time or species, the quantity and A260 ⁄ 230 ratio were both significantly higher for LN2-preserved samples. Interestingly, individual comparisons for each preservation method over time indicated that both methods performed equally efficiently during the first month, but RNAlater lost efficiency in storage times longer than 2 months compared with flash-frozen samples. In summary, we find that for long-term preservation of samples, flash freezing is the preferred method. If LN2 is not available, RNAlater can be used, but mRNA extraction during the first month of storage is advisedThis work has been supported by a Marie Curie Fellowship to A.R., a FPI pre-doctoral Fellowship (BES-2008-003009) of the Spanish Ministry of Science and Innovation and a grant included in the project Benthomics (CTM2010-22218-C02-01) to A.R.R.-P., and a Fulbright of the Spanish Ministry of Science and Innovation (EX2009-0128) to S.C. This material is based upon work supported by a grant of the Marie Curie Outgoing Fellowship Program to A.R., by the National Science Foundation under Grant No. DEB #0844881 to G.G, and NSERC Discovery and Ship Time grants to S.P.L.Peer reviewe

Do bipolar distributions exist in marine sponges? Stylocordyla chupachups sp. nv. (Porifera: Hadromerida) from the Weddell Sea (Antarctic), previously reported as S. borealis (Lovén, 1868)

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