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RESEARCH PRODUCT

The new era of genome sequencing using high-throughput sequencing technology: generation of the first version of the Atlantic cod genome

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Abstract The genome of Atlantic cod (Gadus morhua L.) published in 2011 was the first example of a teleost genome obtained using a pure high-throughput sequencing (HTS) technology strategy, and the first large vertebrate genome generated by exclusively using Roche/454 sequencing technology. At the start of the sequencing project in 2009, two HTS technologies were available, the Roche/454 and Illumina technologies. Because of the longer read length of the Roche/454 technology and a wider range of suitable software utilizing those data at the time, we chose to use this technology for the first version of the Atlantic cod genome. In this chapter, we describe the process leading to the assembly and annotation of the first Atlantic cod genome. Since the release in 2011, spectacular developments in sequencing technologies and assembly software have allowed for a second, improved version of the Atlantic cod genome—which will be further described in the Atlantic cod genome chapter ( Chapter 3 ). Although rather fragmented according to current standards, our first genome assembly has proven to be an important resource for the community—as illustrated by its extensive use in a wide range of studies and it catalyzing new projects and research funding.