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Open Access Research article

Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis

Alberto Pallavicini1, Adriana Canapa2*, Marco Barucca2, Jessica Alfőldi5, Maria Assunta Biscotti2, Francesco Buonocore3, Gianluca De Moro1, Federica Di Palma5, Anna Maria Fausto3, Mariko Forconi2, Marco Gerdol1, Daisy Monica Makapedua4, Jason Turner-Meier5, Ettore Olmo2 and Giuseppe Scapigliati3

Author Affiliations

1 Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy

2 Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy

3 Dipartimento per l’Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Viterbo, Italy

4 Faculty of Fisheries and Marine Science, University of Sam Ratulangi, Manado, Indonesia

5 Broad Institute of MIT and Harvard, Cambridge, MA, USA

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BMC Genomics 2013, 14:538  doi:10.1186/1471-2164-14-538

Published: 8 August 2013

Abstract

Background

Latimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species.

Results

The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.

The RNA-seq analysis revealed remarkable differences in the expression profiles between the two tissues, allowing the identification of liver- and testis-specific transcripts which may play a fundamental role in important biological processes carried out by these two organs.

Conclusion

Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.

Keywords:
Coelacanth; Latimeria menadoensis; Transcriptome; de novo assembly; RNA-seq