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, 62 (5), 679-87

Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array

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Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array

Gregory S Mendez et al. J Eukaryot Microbiol.

Abstract

Dinoflagellates are one of the last major lineages of eukaryotes for which little is known about genome structure and organization. We report here the sequence and gene structure of a clone isolated from a cosmid library which, to our knowledge, represents the largest contiguously sequenced, dinoflagellate genomic, tandem gene array. These data, combined with information from a large transcriptomic library, allowed a high level of confidence of every base pair call. This degree of confidence is not possible with PCR-based contigs. The sequence contains an intron-rich set of five highly expressed gene repeats arranged in tandem. One of the tandem repeat gene members contains an intron 26,372 bp long. This study characterizes a splice site consensus sequence for dinoflagellate introns. Two to nine base pairs around the 3' splice site are repeated by an identical two to nine base pairs around the 5' splice site. The 5' and 3' splice sites are in the same locations within each repeat so that the repeat is found only once in the mature mRNA. This identically repeated intron boundary sequence might be useful in gene modeling and annotation of genomes.

Keywords: Alternative splicing; Crypthecodinium; identically repeated intron boundary; intron; splicing.

Figures

Figure 1
Figure 1
Schematic of alcohol dehydrogenase (ADH) cosmid insert. The exons, poly‐adenylation signals, splice leader acceptor sites, and start and stop codons are all indicated. The transcripts as they align to genomic sequences are indicated. Exactly 24,000 bp from the middle of the eighth intron of member ADH‐C has been removed for illustrative purposes.
Figure 2
Figure 2
Nucleotide sequences surrounding the intron splice sites of alcohol dehydrogenase (ADH) from Crypthecodinium cohnii as well as previously published genes of various dinoflagellates. A. Genomic and mRNA sequences of the intron splice sites of ADH‐B intron 1 indicating the identical repeated intron boundary (IRIB) sequence is present at either end of the intron twice, but is present in the mRNA only once. B. Sequence logos, generated by WebLogo, using the intron splice sites from all introns present in the ADH cosmid sequence. C. Intron splice sites of ADH‐B and previously published dinoflagellate genomic sequences indicating the IRIB sequence and the size of the IRIB. Each IRIB sequence is indicated in bold and their corresponding sizes are listed at right. Portions of each internal intron sequence have been replaced by ellipses as shown.

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