Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey

Meizhong Luo, HyeRan R. Kim, David A Kudrna, Nicholas B. Sisneros, So Jeong Lee, Christopher Mueller, Kristi Collura, Andrea Zuccolo, Bryan Buckingham, Suzanne M. Grim, Kazuyo Yanagiya, Hidetoshi Inoko, Takashi Shiina, Martin F. Flajnik, Rod A Wing, Yuko Ohta

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Background: 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. Aims: In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. Results: The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering -4.5 × 1010 bp and thus providing an II-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. Conclusion: We 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.

Original languageEnglish (US)
Article number106
JournalBMC Genomics
Volume7
DOIs
StatePublished - May 3 2006

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Bacterial Artificial Chromosomes
Sharks
Nurses
Genome
Vertebrates
Clone Cells
Genomics
Short Interspersed Nucleotide Elements
Plant Genome
Surveys and Questionnaires
Haploidy
Genes
Libraries
Sequence Analysis
Fishes

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. / Luo, Meizhong; Kim, HyeRan R.; Kudrna, David A; Sisneros, Nicholas B.; Lee, So Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, Bryan; Grim, Suzanne M.; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F.; Wing, Rod A; Ohta, Yuko.

In: BMC Genomics, Vol. 7, 106, 03.05.2006.

Research output: Contribution to journalArticle

Luo, M, Kim, HR, Kudrna, DA, Sisneros, NB, Lee, SJ, Mueller, C, Collura, K, Zuccolo, A, Buckingham, B, Grim, SM, Yanagiya, K, Inoko, H, Shiina, T, Flajnik, MF, Wing, RA & Ohta, Y 2006, 'Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey', BMC Genomics, vol. 7, 106. https://doi.org/10.1186/1471-2164-7-106
Luo, Meizhong ; Kim, HyeRan R. ; Kudrna, David A ; Sisneros, Nicholas B. ; Lee, So Jeong ; Mueller, Christopher ; Collura, Kristi ; Zuccolo, Andrea ; Buckingham, Bryan ; Grim, Suzanne M. ; Yanagiya, Kazuyo ; Inoko, Hidetoshi ; Shiina, Takashi ; Flajnik, Martin F. ; Wing, Rod A ; Ohta, Yuko. / Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. In: BMC Genomics. 2006 ; Vol. 7.
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AU - Sisneros, Nicholas B.

AU - Lee, So Jeong

AU - Mueller, Christopher

AU - Collura, Kristi

AU - Zuccolo, Andrea

AU - Buckingham, Bryan

AU - Grim, Suzanne M.

AU - Yanagiya, Kazuyo

AU - Inoko, Hidetoshi

AU - Shiina, Takashi

AU - Flajnik, Martin F.

AU - Wing, Rod A

AU - Ohta, Yuko

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