Marine Genomics 18 (2014) 1–2
Contents lists available at ScienceDirect
Marine Genomics Genomics In Aquaculture 2013 Symposium
Editorial
GIA 2013: Genomics in Aquaculture 2013 symposium
The genomics revolution continues, and so does the symposium for Genomics in Aquaculture (GIA). First, please allow me to congratulate the organizers, Drs. Jorge Fernandes and Elena Sarropoulou, for a great success of the GIA 2013! Although I was not able to make it to the conference, from the lectures and the papers to be published, I am so delighted to see the huge progress made in the field. The success of GIA 2013 is marked by a broad spectrum of participants from all over the world, and the shift of subject areas from development of genomic resources to application of genomic resources for aquaculture. As I stated before, having the genome sequences is not the end, nor the beginning of the end, but may be the end of the beginning of genomics research. The real winners of aquaculture genomics will be those who work with the best genetic material, focus on performance traits, and persistently carry the ball to the finish line. Aquaculture genomics is apparently progressing with hugely rapid pace in the right direction. Such progress can be seen clearly through the last three GIA symposiums. In the first GIA symposium held in 2009, the vast majority of seminar and poster presentations were focused on development of primary genomic resources (Fernandes, 2011), such as development of molecular markers (Kuhl et al., 2011; Sarropoulou and Fernandes, 2011), EST resources (Edvardsen et al., 2011; Johansen et al., 2011; Liu, 2011; Sarropoulou and Fernandes, 2011), and microarray technology (Aoki et al., 2011; Krasnov et al., 2011). Two years later, when the second GIA symposium was held in 2011 (Sarropoulou et al., 2012a), the research focus was already shifted on addressing development of advanced technologies for applications of genome information and resources to addressing biological and aquaculture issues of importance. For instance, microarray technology or RNA-Seq technology was used to address biological issues involving reproduction (Minegishi et al., 2012; Piferrer et al., 2012; Sarropoulou et al., 2012b; Viñas et al., 2012), disease defense (Pardo et al., 2012; Kaitetzidou et al., 2012; Sarropoulou and Fernandes, 2011; Díaz-Rosales et al., 2012; Wenger et al., 2012; Micallef et al., 2012), and growth. In this GIA 2013, two aspects of advances are apparent: first, the use of advanced genome technologies in aquaculture is prominent as evidenced by the application of next generation sequencing, RNA-Seq and microarrays (Louro et al., 2014; Edvardsen et al., 2014). Second, the research focus has shifted to important aquaculture performance traits such as embryonic development, survival, disease resistance, reproduction, and muscle growth (Rise et al., 2014; Lazado et al., 2014; Richardson et al., 2014; Kulkarni et al., 2014). In addition, aquaculture genomics research also extends into non-coding RNAs as well as epigenetics control mechanisms in aquaculture species (Kulkarni et al., 2014; Zhang et al., 2014). Clearly, advanced genome technologies are being used in aquaculture not only to map the genes
http://dx.doi.org/10.1016/j.margen.2014.10.005 1874-7787/© 2014 Elsevier B.V. All rights reserved.
for performance traits, but also to reveal the molecular mechanisms controlling expression of the genome in determination of the phenome. While this Special Issue publishes only some examples of the research papers presented at GIA 2013, the symposium was clearly a tremendous success. Unlike many genomics meetings that cover so many different species and topics, GIA symposium provides a platform specifically for aquaculture genomicists, geneticists, bioinformaticians and the like to interact, discuss and establish collaborations. I would like to thank the sponsors, organizers, invited speakers and all participants for the great success of GIA 2013. In particular, I acknowledge the University of Nordland (227854/030) and the BIOTEK21 programme of the Research Council of Norway for funding this project (Ref. 227854/030). I would also like to express my gratitude to Marine Genomics and the editorial team (Cinzia Verde, Frank Glöckner, Jorge Fernandes, Elena Sarropoulou, Igor Babiak and Kiron Viswanath) for publishing this Special Issue. References Aoki, T., Hirono, I., Kondo, H., Hikima, J.-i., Jung, T.S., 2011. Microarray technology is an effective tool for identifying genes related to the aquacultural improvement of Japanese flounder, Paralichthys olivaceus. Comp. Biochem. Physiol. D 6, 39–43. Díaz-Rosales, P., Romero, A., Balseiro, P., Dios, S., Novoa, B., Figueras, A., 2012. Microarraybased identification of differentially expressed genes in families of turbot (Scophthalmus maximus) after infection with viral haemorrhagic septicaemia virus (VHSV). Mar. Biotechnol. (NY) 14 (5), 515–529. Edvardsen, R.B., Dalvin, S., Furmanek, T., Malde, K., Mæhle, S., Kvamme, B.O., Skern-Mauritzen, R., 2014. Gene expression in five salmon louse (Lepeophtheirus salmonis, Krøyer 1837) tissues. Mar. Genomics 18, 39–44. Edvardsen, R.B., Malde, K., Mittelholzer, C., Taranger, G.L., Nilsen, F., 2011. EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua). Comp. Biochem. Physiol. D 6, 23–30. Fernandes, J., 2011. Genomics in Aquaculture (GIA) 2009 symposium. Comp. Biochem. Physiol. D Genomics Proteomics 6, 9–10. Johansen, S.D., Karlsen, B.O., Furmanek, T., Andreassen, M., Jørgensen, T.E., Bizuayehu, T.T., Breines, R., Emblem, Å., Kettunen, P., Luukko, K., Edvardsen, R.B., Nordeide, J.T., Coucheron, D.H., Moum, T., 2011. RNA deep sequencing of the Atlantic cod transcriptome. Comp. Biochem. Physiol. D 6, 18–22. Kaitetzidou, E., Crespo, D., Vraskou, Y., Antonopoulou, E., Planas, J.V., 2012. Transcriptomic response of skeletal muscle to lipopolysaccharide in the gilthead seabream (Sparus aurata). Mar. Biotechnol. (NY) 14 (5), 605–619. Krasnov, A., Timmerhaus, G., Afanasyev, S., Jørgensen, S.M., 2011. Development and assessment of oligonucleotide microarrays for Atlantic salmon (Salmo salar L.). Comp. Biochem. Physiol. D 6, 31–38. Kuhl, H., Tine, M., Hecht, J., Knaust, F., Reinhardt, R., 2011. Analysis of single nucleotide polymorphisms in three chromosomes of European sea bass Dicentrarchus labrax. Comp. Biochem. Physiol. D 6, 70–75. Kulkarni, A.D., Caipang, C.M.A., Kiron, V., Rombout, J.H.W.M., Fernandes, J.M.O., Brinchmann, M.F., 2014. Evaluation of immune and apoptosis related gene responses using an RNAi approach in vaccinated Penaeus monodon during oral WSSV infection. Mar. Genomics 18, 55–65. Lazado, C.C., Nagasawa, K., Babiak, I., Kumaratunga, H.P., Fernandes, J.M., 2014. Circadian rhythmicity and photic plasticity of myosin gene transcription in fast skeletal muscle of Atlantic cod (Gadus morhua). Mar. Genomics 18, 21–29.
2
Editorial
Liu, Z., 2011. Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome. Comp. Biochem. Physiol. D 6, 11–17. Louro, B., Power, D.M., Canario, A.V., 2014. Advances in European sea bass genomics and future perspectives. Mar. Genomics 18, 71–75. Micallef, G., Bickerdike, R., Reiff, C., Fernandes, J.M., Bowman, A.S., Martin, S.A., 2012. Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ. Mar. Biotechnol. (NY) 14 (5), 559–569. Minegishi, Y., Henkel, C.V., Dirks, R.P., van den Thillart, G.E., 2012. Genomics in eels— towards aquaculture and biology. Mar. Biotechnol. (NY) 14 (5), 583–590. Pardo, B.G., Millán, A., Gómez-Tato, A., Fernández, C., Bouza, C., Alvarez-Dios, J.A., Cabaleiro, S., Lamas, J., Leiro, J.M., Martínez, P., 2012. Gene expression profiles of spleen, liver, and head kidney in turbot (Scophthalmus maximus) along the infection process with Philasterides dicentrarchi using an immune-enriched oligo-microarray. Mar. Biotechnol. (NY) 14 (5), 570–582. Piferrer, F., Ribas, L., Díaz, N., 2012. Genomic approaches to study genetic and environmental influences on fish sex determination and differentiation. Mar. Biotechnol. (NY) 14 (5), 591–604. Richardson, C.J., Bernier, N.J., Danzmann, R.G., Ferguson, M.M., 2014. Phenotypic and QTL allelic associations among embryonic developmental rate, body size, and precocious maturation in male rainbow trout. Mar. Genomics 18, 31–38. Rise, M.L., Nash, G.W., Hall, J.R., Booman, M., Hori, T.S., Trippel, E.A., Gamperl, A.K., 2014. Variation in embryonic mortality and maternal transcript expression among Atlantic cod (Gadus morhua) broodstock: A functional genomics study. Mar. Genomics 18, 3–20. Sarropoulou, E., Fernandes, J., Liu, Z.J., 2012a. GIA 2011: Genomics in Aquaculture 2011 symposium. Mar. Biotechnol. (NY) 14 (5), 513–514.
Sarropoulou, E., Galindo-Villegas, J., García-Alcázar, A., Kasapidis, P., Mulero, V., 2012b. Characterization of European sea bass transcripts by RNA SEQ after oral vaccine against V. anguillarum. Mar. Biotechnol. (NY) 14 (5), 634–642. Sarropoulou, E., Fernandes, J.M.O., 2011. Comparative genomics in teleost species: knowledge transfer by linking the genomes of model and non-model fish species. Comp. Biochem. Physiol. D. 6, 92–102. Viñas, A., Taboada, X., Vale, L., Robledo, D., Hermida, M., Vera, M., Martínez, P., 2012. Mapping of DNA sex-specific markers and genes related to sex differentiation in turbot (Scophthalmus maximus). Mar. Biotechnol. (NY) 14 (5), 655–663. Wenger, M., Krasnov, A., Skugor, S., Goldschmidt-Clermont, E., Sattler, U., Afanasyev, S., Segner, H., 2012. Estrogen modulates hepatic gene expression and survival of rainbow trout infected with pathogenic bacteria Yersinia ruckeri. Mar. Biotechnol. (NY) 14 (5), 530–543. Zhang, L., Liu, W., Shao, C., Zhang, N., Li, H., Liu, K., Dong, Z., Qi, Q., Zhao, W., Chen, S., 2014. Cloning, expression and methylation analysis of piwil2 in half-smooth tongue sole (Cynoglossus semilaevis). Mar. Genomics 18, 45–54.
Zhanjiang Liu School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA E-mail address: [email protected].
Contents lists available at ScienceDirect
Marine Genomics Genomics In Aquaculture 2013 Symposium
Editorial
GIA 2013: Genomics in Aquaculture 2013 symposium
The genomics revolution continues, and so does the symposium for Genomics in Aquaculture (GIA). First, please allow me to congratulate the organizers, Drs. Jorge Fernandes and Elena Sarropoulou, for a great success of the GIA 2013! Although I was not able to make it to the conference, from the lectures and the papers to be published, I am so delighted to see the huge progress made in the field. The success of GIA 2013 is marked by a broad spectrum of participants from all over the world, and the shift of subject areas from development of genomic resources to application of genomic resources for aquaculture. As I stated before, having the genome sequences is not the end, nor the beginning of the end, but may be the end of the beginning of genomics research. The real winners of aquaculture genomics will be those who work with the best genetic material, focus on performance traits, and persistently carry the ball to the finish line. Aquaculture genomics is apparently progressing with hugely rapid pace in the right direction. Such progress can be seen clearly through the last three GIA symposiums. In the first GIA symposium held in 2009, the vast majority of seminar and poster presentations were focused on development of primary genomic resources (Fernandes, 2011), such as development of molecular markers (Kuhl et al., 2011; Sarropoulou and Fernandes, 2011), EST resources (Edvardsen et al., 2011; Johansen et al., 2011; Liu, 2011; Sarropoulou and Fernandes, 2011), and microarray technology (Aoki et al., 2011; Krasnov et al., 2011). Two years later, when the second GIA symposium was held in 2011 (Sarropoulou et al., 2012a), the research focus was already shifted on addressing development of advanced technologies for applications of genome information and resources to addressing biological and aquaculture issues of importance. For instance, microarray technology or RNA-Seq technology was used to address biological issues involving reproduction (Minegishi et al., 2012; Piferrer et al., 2012; Sarropoulou et al., 2012b; Viñas et al., 2012), disease defense (Pardo et al., 2012; Kaitetzidou et al., 2012; Sarropoulou and Fernandes, 2011; Díaz-Rosales et al., 2012; Wenger et al., 2012; Micallef et al., 2012), and growth. In this GIA 2013, two aspects of advances are apparent: first, the use of advanced genome technologies in aquaculture is prominent as evidenced by the application of next generation sequencing, RNA-Seq and microarrays (Louro et al., 2014; Edvardsen et al., 2014). Second, the research focus has shifted to important aquaculture performance traits such as embryonic development, survival, disease resistance, reproduction, and muscle growth (Rise et al., 2014; Lazado et al., 2014; Richardson et al., 2014; Kulkarni et al., 2014). In addition, aquaculture genomics research also extends into non-coding RNAs as well as epigenetics control mechanisms in aquaculture species (Kulkarni et al., 2014; Zhang et al., 2014). Clearly, advanced genome technologies are being used in aquaculture not only to map the genes
http://dx.doi.org/10.1016/j.margen.2014.10.005 1874-7787/© 2014 Elsevier B.V. All rights reserved.
for performance traits, but also to reveal the molecular mechanisms controlling expression of the genome in determination of the phenome. While this Special Issue publishes only some examples of the research papers presented at GIA 2013, the symposium was clearly a tremendous success. Unlike many genomics meetings that cover so many different species and topics, GIA symposium provides a platform specifically for aquaculture genomicists, geneticists, bioinformaticians and the like to interact, discuss and establish collaborations. I would like to thank the sponsors, organizers, invited speakers and all participants for the great success of GIA 2013. In particular, I acknowledge the University of Nordland (227854/030) and the BIOTEK21 programme of the Research Council of Norway for funding this project (Ref. 227854/030). I would also like to express my gratitude to Marine Genomics and the editorial team (Cinzia Verde, Frank Glöckner, Jorge Fernandes, Elena Sarropoulou, Igor Babiak and Kiron Viswanath) for publishing this Special Issue. References Aoki, T., Hirono, I., Kondo, H., Hikima, J.-i., Jung, T.S., 2011. Microarray technology is an effective tool for identifying genes related to the aquacultural improvement of Japanese flounder, Paralichthys olivaceus. Comp. Biochem. Physiol. D 6, 39–43. Díaz-Rosales, P., Romero, A., Balseiro, P., Dios, S., Novoa, B., Figueras, A., 2012. Microarraybased identification of differentially expressed genes in families of turbot (Scophthalmus maximus) after infection with viral haemorrhagic septicaemia virus (VHSV). Mar. Biotechnol. (NY) 14 (5), 515–529. Edvardsen, R.B., Dalvin, S., Furmanek, T., Malde, K., Mæhle, S., Kvamme, B.O., Skern-Mauritzen, R., 2014. Gene expression in five salmon louse (Lepeophtheirus salmonis, Krøyer 1837) tissues. Mar. Genomics 18, 39–44. Edvardsen, R.B., Malde, K., Mittelholzer, C., Taranger, G.L., Nilsen, F., 2011. EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua). Comp. Biochem. Physiol. D 6, 23–30. Fernandes, J., 2011. Genomics in Aquaculture (GIA) 2009 symposium. Comp. Biochem. Physiol. D Genomics Proteomics 6, 9–10. Johansen, S.D., Karlsen, B.O., Furmanek, T., Andreassen, M., Jørgensen, T.E., Bizuayehu, T.T., Breines, R., Emblem, Å., Kettunen, P., Luukko, K., Edvardsen, R.B., Nordeide, J.T., Coucheron, D.H., Moum, T., 2011. RNA deep sequencing of the Atlantic cod transcriptome. Comp. Biochem. Physiol. D 6, 18–22. Kaitetzidou, E., Crespo, D., Vraskou, Y., Antonopoulou, E., Planas, J.V., 2012. Transcriptomic response of skeletal muscle to lipopolysaccharide in the gilthead seabream (Sparus aurata). Mar. Biotechnol. (NY) 14 (5), 605–619. Krasnov, A., Timmerhaus, G., Afanasyev, S., Jørgensen, S.M., 2011. Development and assessment of oligonucleotide microarrays for Atlantic salmon (Salmo salar L.). Comp. Biochem. Physiol. D 6, 31–38. Kuhl, H., Tine, M., Hecht, J., Knaust, F., Reinhardt, R., 2011. Analysis of single nucleotide polymorphisms in three chromosomes of European sea bass Dicentrarchus labrax. Comp. Biochem. Physiol. D 6, 70–75. Kulkarni, A.D., Caipang, C.M.A., Kiron, V., Rombout, J.H.W.M., Fernandes, J.M.O., Brinchmann, M.F., 2014. Evaluation of immune and apoptosis related gene responses using an RNAi approach in vaccinated Penaeus monodon during oral WSSV infection. Mar. Genomics 18, 55–65. Lazado, C.C., Nagasawa, K., Babiak, I., Kumaratunga, H.P., Fernandes, J.M., 2014. Circadian rhythmicity and photic plasticity of myosin gene transcription in fast skeletal muscle of Atlantic cod (Gadus morhua). Mar. Genomics 18, 21–29.
2
Editorial
Liu, Z., 2011. Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome. Comp. Biochem. Physiol. D 6, 11–17. Louro, B., Power, D.M., Canario, A.V., 2014. Advances in European sea bass genomics and future perspectives. Mar. Genomics 18, 71–75. Micallef, G., Bickerdike, R., Reiff, C., Fernandes, J.M., Bowman, A.S., Martin, S.A., 2012. Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ. Mar. Biotechnol. (NY) 14 (5), 559–569. Minegishi, Y., Henkel, C.V., Dirks, R.P., van den Thillart, G.E., 2012. Genomics in eels— towards aquaculture and biology. Mar. Biotechnol. (NY) 14 (5), 583–590. Pardo, B.G., Millán, A., Gómez-Tato, A., Fernández, C., Bouza, C., Alvarez-Dios, J.A., Cabaleiro, S., Lamas, J., Leiro, J.M., Martínez, P., 2012. Gene expression profiles of spleen, liver, and head kidney in turbot (Scophthalmus maximus) along the infection process with Philasterides dicentrarchi using an immune-enriched oligo-microarray. Mar. Biotechnol. (NY) 14 (5), 570–582. Piferrer, F., Ribas, L., Díaz, N., 2012. Genomic approaches to study genetic and environmental influences on fish sex determination and differentiation. Mar. Biotechnol. (NY) 14 (5), 591–604. Richardson, C.J., Bernier, N.J., Danzmann, R.G., Ferguson, M.M., 2014. Phenotypic and QTL allelic associations among embryonic developmental rate, body size, and precocious maturation in male rainbow trout. Mar. Genomics 18, 31–38. Rise, M.L., Nash, G.W., Hall, J.R., Booman, M., Hori, T.S., Trippel, E.A., Gamperl, A.K., 2014. Variation in embryonic mortality and maternal transcript expression among Atlantic cod (Gadus morhua) broodstock: A functional genomics study. Mar. Genomics 18, 3–20. Sarropoulou, E., Fernandes, J., Liu, Z.J., 2012a. GIA 2011: Genomics in Aquaculture 2011 symposium. Mar. Biotechnol. (NY) 14 (5), 513–514.
Sarropoulou, E., Galindo-Villegas, J., García-Alcázar, A., Kasapidis, P., Mulero, V., 2012b. Characterization of European sea bass transcripts by RNA SEQ after oral vaccine against V. anguillarum. Mar. Biotechnol. (NY) 14 (5), 634–642. Sarropoulou, E., Fernandes, J.M.O., 2011. Comparative genomics in teleost species: knowledge transfer by linking the genomes of model and non-model fish species. Comp. Biochem. Physiol. D. 6, 92–102. Viñas, A., Taboada, X., Vale, L., Robledo, D., Hermida, M., Vera, M., Martínez, P., 2012. Mapping of DNA sex-specific markers and genes related to sex differentiation in turbot (Scophthalmus maximus). Mar. Biotechnol. (NY) 14 (5), 655–663. Wenger, M., Krasnov, A., Skugor, S., Goldschmidt-Clermont, E., Sattler, U., Afanasyev, S., Segner, H., 2012. Estrogen modulates hepatic gene expression and survival of rainbow trout infected with pathogenic bacteria Yersinia ruckeri. Mar. Biotechnol. (NY) 14 (5), 530–543. Zhang, L., Liu, W., Shao, C., Zhang, N., Li, H., Liu, K., Dong, Z., Qi, Q., Zhao, W., Chen, S., 2014. Cloning, expression and methylation analysis of piwil2 in half-smooth tongue sole (Cynoglossus semilaevis). Mar. Genomics 18, 45–54.
Zhanjiang Liu School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA E-mail address: [email protected].
