De novo Sequencing and Assembly of Fish Genomes: the Nice One, the Affordable One and their Problems

Shubha Vij^*, Woei Chang Liew^*, Xueyan Shen^*, The Asian Seabass Genome Consortium^**, The Mozambique Tilapia Genome Consortium^*** and László Orbán^*#

 Together with our partners, we have been working on the improvement of food fish lines through marker-assisted selection for over a decade. Recently, we have started to develop advanced platforms for Asian seabass (Lates calcarifer) and Mozambique tilapia (Oreochromis mossambicus)with the aim of developing genomic selection for both species. For that purpose, the genomes of these two species had to be sequenced, assembled and annotated.

 In my presentation, I will describe the two very different approaches we followed in the above two genome projects. The Asian seabass genome
(700 Mb) was sequenced both by the PacBio technology that yielded very long reads (average: 4-8 kb) and the standard Illumina paired-end technology. The assembly was based exclusively on the former, whereas the latter was used for validation only. The genome of the Mozambique tilapia
(1 Gb) was sequenced primarily using the Illumina technology with a low coverage of PacBio added to aid the scaffolding process.

 I will compare the usefulness of these two approaches for generating high quality reference genomes (de novosequencing) from fish. I will also highlight the difficulties and road blocks we have encountered during the process.

 Keywords: seabass, barramundi, tilapia, genome, transcriptome, NGS

 * Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore

** The Asian Seabass Genome Consortium consists of over 40 scientists from the following organizations: Temasek Life Sciences Laboratory, Singapore; Comparative Genome Centre, Murdoch University, Perth, Australia; Georgikon Faculty, University of Pannonia, Keszthely, Hungary; Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, Russia; South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa; Pacific Biosciences, Menlo Park, CA, USA; Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University, St Petersburg, Russia; Genome Research Centre, The Chinese University of Hong Kong, Hong Kong; University of East Anglia, Norwich Research Park, Norwich, UK; The Genome Analysis Centre, Norwich, UK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; James Cook University, Townsville, Australia; Central Institute of Brackishwater Aquaculture, Chennai, India; National Bureau of Fish Genetic Resources, Kochi, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India

 ** The Mozambique Tilapia Genome Consortium consists of seven scientists from Temasek Life Sciences Laboratory, Singapore.

 # Corresponding author. Tel: +65-6872-7413; Email: laszlo@tll.org.sg