Sampling the skin transcriptome of the North Atlantic right whale

Graduate Program of Marine Biology, College of Charleston, 205 Fort Johnson Rd, Charleston, SC 29412, USA.
Comparative Biochemistry and Physiology Part D Genomics and Proteomics (Impact Factor: 2.06). 09/2009; 4(3):154-8. DOI: 10.1016/j.cbd.2009.01.004
Source: PubMed


As an initial step in defining the transcriptome of the North Atlantic right whale (Eubalaena glacialis) and developing functional genomic tools to study right whale health at the molecular physiological level, a cDNA library has been constructed from a skin biopsy. 2496 randomly selected clones (expressed sequence tags, ESTs) have been sequenced, and genes identified as important in the response to stress and immune challenges have been cloned by targeted RT-PCR from skin cDNA. The analysis of the EST collection (archived at and GenBank) showed a 34.79% redundancy, yielding 1578 unigenes and 27 potential microsatellite markers. 96 genes were cloned by targeted PCR; moreover, 52 of these genes are stress and immune function related. A Gene Ontology analysis of the unigene collection indicates that the skin is a rich source of expressed genes with diverse functions, suggesting an important role in multiple physiological processes including those related to immunity and stress response.

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Available from: Annalaura Mancia, Mar 02, 2015
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    • "For HSP70 primers, we used the cDNA sequence reported for a north Atlantic Right whale [GenBank: ES556841.1] [35] (see Additional file 1). Sequences were aligned using the free Multiple Alignment software ClustalW ( Primer pairs were designed within conserved regions (see Additional file 1), ideally spanning two exons to avoid DNA amplification. "
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    Full-text · Article · Jul 2013 · BMC Research Notes
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    • "Unfortunately, many marine mammal populations are also severely depleted due to a combination of historical exploitation [14] and contemporary threats including bycatch and other fisheries interactions [15] and climate change [16]. These factors may explain why only two marine mammal EST libraries, in both cases developed from either skin or blood, have been published to date [17,18]. Nevertheless, marine mammals are strong candidates for generating transcriptomes from tissues collected post mortem, since colonially breeding pinnipeds tend to suffer from high mortality rates and occasional mass mortality events [19,20], while many cetacean species are routinely stranded ashore en masse[21]. "
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    ABSTRACT: Background Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissue-specific expression patterns, developing a complete transcriptome usually requires a 'discovery pool' of individuals to be sacrificed in order to harvest mRNA from as many different types of tissue as possible. This hinders transcriptome development in large, charismatic and endangered species, many of which stand the most to gain from such approaches. To circumvent this problem in a model pinniped species, we 454 sequenced cDNA from testis, heart, spleen, intestine, kidney and lung tissues obtained from nine adult male Antarctic fur seals (Arctocephalus gazella) that died of natural causes at Bird Island, South Georgia. Results After applying stringent quality control criteria based on length and annotation, we obtained 12,397 contigs which, in combination with 454 data previously obtained from skin, gave a total of 23,096 unique contigs. Homology was found to 77.0% of dog (Canis lupus familiaris) transcripts, suggesting that the combined assembly represents a substantial proportion of this species' transcriptome. Moreover, only 0.5% of transcripts revealed sequence similarity to bacteria, implying minimal contamination, and the percentage of transcripts involved in cell death was low at 2.6%. Transcripts with immune-related annotations were almost five-fold enriched relative to skin and represented 13.2% of all spleen-specific contigs. By reference to the dog, we also identified transcripts revealing homology to five class I, ten class II and three class III genes of the Major Histocompatibility Complex and derived the putative genomic distribution of 17,121 contigs, 2,119 in silico mined microsatellites and 9,382 single nucleotide polymorphisms. Conclusions Our findings suggest that transcriptome development based on samples collected post mortem may greatly facilitate genomic studies, not only of marine mammals but also more generally of species that are of conservation concern.
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    • "have utilized multiple types of tissue (e.g. Ierardi et al. 2009; Schwarz et al. 2009; Wang et al. 2010). "
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