Abstract
BackgroundSharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates.AimsIn order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum.ResultsThe BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 × 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6–28 primary positive clones per probe of which 50–90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible.ConclusionWe have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.
Highlights
Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates
Insert size distribution To evaluate the quality of the Bacterial artificial chromosome (BAC) library, we first analyzed the insert sizes of 408 sampling BAC clones with Not I, which liberates the inserts from the BAC vector (Figure 1)
Searching the NSRE2 sequence [GenBank:CZ549534] against the 'htgs' database in GenBank found an average of 3.4 hits/BAC on 8 of the 9 nurse shark BAC draft sequences ranging from a minimum of 1 to a maximum of 5. These results indicate that NSRE1 and NSRE2 are repetitive elements, and NSRE1 is more frequent in the nurse shark genome than NSRE2
Summary
Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Genomic and genetic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates This ancient taxon is of particular interest to us since it is the oldest group of living animals having an adaptive immune system with underlying molecules and mechanisms similar to those of mammals [15]. In this paper we report the construction and characterization of a publicly-available nurse shark BAC library and carry out a preliminary genome survey
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