Elsevier

Genomics

Volume 86, Issue 4, October 2005, Pages 396-404
Genomics

A physical map of the genome of Atlantic salmon, Salmo salar

https://doi.org/10.1016/j.ygeno.2005.06.001Get rights and content

Abstract

A physical map of the Atlantic salmon (Salmo salar) genome was generated based on HindIII fingerprints of a publicly available BAC (bacterial artificial chromosome) library constructed from DNA isolated from a Norwegian male. Approximately 11.5 haploid genome equivalents (185,938 clones) were successfully fingerprinted. Contigs were first assembled via FPC using high-stringency (1e−16), and then end-to-end joins yielded 4354 contigs and 37,285 singletons. The accuracy of the contig assembly was verified by hybridization and PCR analysis using genetic markers. A subset of the BACs in the library contained few or no HindIII recognition sites in their insert DNA. BglI digestion fragment patterns of these BACs allowed us to identify three classes: (1) BACs containing histone genes, (2) BACs containing rDNA-repeating units, and (3) those that do not have BglI recognition sites. End-sequence analysis of selected BACs representing these three classes confirmed the identification of the first two classes and suggested that the third class contained highly repetitive DNA corresponding to tRNAs and related sequences.

Introduction

Salmonids (salmon, trout, and charr) are economically important and of scientific interest. These fish are used extensively in aquaculture, with world production of Atlantic salmon alone almost 900,000 metric tons in 2000, with a value of US $2.75 billion [1]. There are also significant commercial harvests of wild salmonids and lucrative sports fisheries for Atlantic salmon, Pacific salmon, rainbow trout, brown trout, and Arctic charr in several countries. The common ancestor of salmonids experienced a genome duplication event between 20 and 120 million years ago [2], and the extant species may be considered pseudo-tetraploid as they are in the process of reverting to a stable diploid state, by losing segments of the genome, by gene silencing, or by divergence such that duplicated genes have different patterns of expression [3]. This makes them ideal organisms for examining genome evolution and specifically the fate of duplicated genomic segments [4]. The salmonids are also used extensively in the study of physiology, comparative immunology, toxicology, and ecology [5].

Linkage maps have been constructed for Atlantic salmon [6], [7], rainbow trout [8], [9], and Arctic charr [10]. These maps and the associated genetic markers have enabled the identification of quantitative trait loci (QTL) for growth [11], upper temperature tolerance [12], [13], spawning time [11], and a comparison of the sex-determining regions in salmonid genomes [14]. Large EST databases are publicly available for rainbow trout [15] and Atlantic salmon [16]. A cDNA microarray has been developed that can be used to examine expression patterns in all salmonids tested to date [16], and it has recently been used to investigate the Atlantic salmon’s response to a bacterial pathogen [17] and the expression of genes during development [18]. The karyotypes of several salmonid species have been described, and they reveal that many chromosomal rearrangements have occurred along the different lineages since the genome duplication occurred [19], [20].

Physical maps enable the integration of linkage maps and karyotypes, and are essential tools for comprehensive comparative genomic studies. In addition, the existence of a well-characterized physical map makes it more feasible to undertake a whole genome sequencing project. BAC libraries have been constructed for rainbow trout [21], [22], [23] and Atlantic salmon [24]. The CHORI-214 Atlantic salmon BAC library and corresponding arrayed filters are publicly available (http://bacpac.chori.org/salmon214.htm). Here we report the production of a physical map for Atlantic salmon based on HindIII BAC fingerprint analysis.

Section snippets

Generation of a BAC fingerprint map

We carried out HindIII fingerprinting (see Methods) on the first 200,640 clones of the CHORI-214 Atlantic salmon BAC library [24]. After discounting clones that failed to grow, were nonrecombinant, or those with low-complexity restriction fragment patterns that were rejected by the automated band calling software, BandLeader [25], 185,938 (93%) successful fingerprints were obtained. There were on average 40 restriction fragments produced per BAC. The average size of the inserts was 186,000 bp,

BAC clone fingerprinting

Clones for the BAC-based physical map were fingerprinted using an agarose gel-based methodology and the restriction enzyme HindIII [43], [44]. Fingerprints were derived from clones sampled from the first and second segments of the CHORI-214 library [24]. Briefly, the BAC clones were cultured overnight in 96-well blocks and bacterial pellets collected by centrifugation. BAC DNA was isolated using an alkaline lysis purification, the DNA was digested with the restriction enzyme HindIII, and the

Acknowledgments

Funding for this work was provided by Genome Canada, Genome BC, and the Province of British Columbia as well as from the Norwegian Salmon Genome Project. We thank the technical staff at the BC Cancer Agency Genome Sciences Centre who worked on fingerprinting the Atlantic salmon BACs.

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    Sequence data for this article have been deposited with the EMBL/GenBank Data Libraries under Accession Nos.

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