Abstract
The red snapper Lutjanus campechanus is an exploited reef fish of major economic importance in the Gulf of Mexico region. Studies of genome wide genetic variation are needed to understand the structure of wild populations and develop breeding programs for aquaculture but interpretation of these genome scans is limited by the absence of reference genome. In this work, the first draft of a reference genome was developed and characterized for the red snapper. P-454 and Illumina sequencing were conducted to produce paired-end reads that were assembled into reference contigs and scaffolds. The current assembly spans over 770 Mb, representing an estimated 69% of the red snapper genome in 67,254 scaffolds (N50 = 16,803 bp). The genome contigs were applied to map double digest Restriction-Site Associated DNA Tags and characterize Single Nucleotide Polymorphisms (SNPs) in five outbred full-sib families. The identified SNPs and 97 microsatellite loci were used to generate a high-density linkage map that includes 7,420 markers distributed across 24 linkage groups and spans 1,346.64 cM with an average inter–marker distance of 0.18 cM. Sex-specific maps revealed a 1.10:1 female to male map length ratio. A total of 4,422 genome contigs (10.5% of the assembly) were anchored to the map and used in a comparative genomic analysis of the red snapper and two model teleosts. Red snapper showed a high degree of chromosome level syntenic conservation with both medaka and spotted green puffer and a near one to one correspondence between the 24 red snapper linkage groups and corresponding medaka chromosomes was observed. This work established the first draft of a reference genome for a lutjanid fish. The obtained genomic resources will serve as a framework for the interpretation of genome scans during studies of wild populations and captive breeding programs.
Highlights
Studies of the genetic architecture of population adaptations or of the genetic basis of complex characters in non-model species have been limited by the high costs and efforts involved in generating reliable reference genomes [1]
Polymorphisms identified and surveyed during these studies can be mapped on genome contigs which allows positioning them on linkage groups and inferring their degree of linkage
The objective of this work was to initiate the development of genomic resources for the red snapper (Lutjanus campechanus), a marine reef-associated fish belonging to the Lutjanidae family
Summary
Studies of the genetic architecture of population adaptations or of the genetic basis of complex characters in non-model species have been limited by the high costs and efforts involved in generating reliable reference genomes [1]. The production of a fully assembled reference genome still requires a considerable investment of resources in species with large genomes, but partial genome assemblies with relatively high coverage can be attained at a reasonable cost using high-throughput sequencing technologies. These partial sequences are often fragmented and can contain misassembled regions [2], making their direct application to applied genomic studies challenging. Mapped contigs can be applied in comparisons of genome organization among species [5] [6] [7] Another potential application of the integrated map and genome sequence is in the interpretation of high density genomic scans during population genomic surveys. Mapped genome contigs can be used in Quantitative Trait Loci (QTL) mapping studies aiming to locate loci impacting phenotypic characters affecting fitness or traits of importance to commercial production in aquaculture species, further contributing to the comprehensive characterization of the genetic basis of these traits [11]
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