ORIGINAL ARTICLE Expressed Sequences and Polymorphisms in Rohu Carp (Labeo rohita, Hamilton) Revealed by mRNA-seq Nicholas Robinson & Pramoda K. Sahoo & Matthew Baranski & Kanta Das Mahapatra & Jatindra N. Saha & Sweta Das & Yashowant Mishra & Paramananda Das & Hirak K. Barman & Ambekar E. Eknath Received: 27 October 2011 / Accepted: 23 December 2011 / Published online: 2 February 2012 # Springer Science+Business Media, LLC 2012 Abstract Expressed genes and polymorphisms were identified in lines of rohu Labeo rohita selected for resistance or susceptibility to Aeromonas hydrophila, an important bacterial pathogen causing aeromoniasis. All animals were grown in a common environment and RNA from ten individuals from each line pooled for Illumina mRNA-seq. De novo transcriptome assembly produced 137,629 contigs with 40× average coverage. Forty-four percent of the assembled sequences were annotated with gene names and ontology terms. Of these, 3,419 were assigned biological process terms related to “stress response” and 1,939 “immune system”. Twenty-six contigs containing 38 single nucleotide polymorphisms (SNPs) were found to map to the Cyprinus carpio mitochondrial genome and over 26,000 putative SNPs and 1,700 microsatellite loci were detected. Seventeen percent of the 100 transcripts with coverage data most indicative of higher-fold expression (>5.6 fold) in the resistant line pool showed homology to major histocompatibility (MH), heat shock proteins (HSP) 30, 70 and 90, glycoproteins or serum lectin genes with putative functions affecting immune response. Forty-one percent of these 100 transcripts showed no or low homology to known genes. Of the SNPs identified, 96 showing the highest allele frequency differences between susceptible and Electronic supplementary material The online version of this article (doi:10.1007/s10126-012-9433-8) contains supplementary material, which is available to authorized users. N. Robinson : M. Baranski Nofima, PO Box 5010, 1432 Ås, Norway M. Baranski e-mail: matthew.baranski@nofima.no P. K. Sahoo : K. D. Mahapatra : J. N. Saha : S. Das : Y. Mishra : P. Das : H. K. Barman : A. E. Eknath Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751 002, India P. K. Sahoo e-mail: pksahoo1@hotmail.com K. D. Mahapatra e-mail: kdmahapatra@yahoo.co.in J. N. Saha e-mail: jnsaha2000@yahoo.co.in S. Das e-mail: swetabt@gmail.com Y. Mishra e-mail: yashowant@gmail.com P. Das e-mail: pdas77@hotmail.com H. K. Barman e-mail: hkbarman68@hotmail.com A. E. Eknath e-mail: ambekar.eknath@yahoo.co.in N. Robinson Flinders University, Sturt Road, Bedford Park, Adelaide, SA 5042, Australia N. Robinson (*) 31 Hutchinson Avenue, Warrandyte, Melbourne VIC 3113, Australia e-mail: nick.robinson@nofima.no Mar Biotechnol (2012) 14:620–633 DOI 10.1007/s10126-012-9433-8