Abstract
BackgroundGiardia intestinalis is a parasitic unicellular eukaryote with a highly reduced genome, in which only six cis-spliced and four trans-spliced introns have been discovered. However, we anticipate that more cis- and trans-spliced introns likely remain unidentified in genes encoding hypothetical proteins that occupy ca. 2/3 of all of the open reading frames (ORFs) in the Giardia genome. Consequently, comprehensive surveys of introns in ORFs for hypothetical proteins are critical for better understanding of the intron evolution in this organism.ResultsIn this study, we identified two novel cis-spliced introns in the draft genome data of G. intestinalis strain WB, by surveying the conserved sequence motifs shared amongst the previously known introns. G. intestinalis strains can be divided into phylogenetically distinct assemblages A–H, and all the introns identified in past studies are shared among the published genome data from strains WB, DH, GS, and P15 representing assemblages A1, A2, B, and E, respectively. Nevertheless one of the two novel introns identified in this study was found to be absent in strain P15.ConclusionBy considering the organismal relationship among G. intestinalis assemblages A1, A2, B, and E, one of the two introns identified in this study has highly likely been lost after the divergence of the assemblages. On the basis of a sequence comparison between the intron-bearing loci in WB, DH, and GS genomes and the homologous but intron-free locus in P15 genome, we propose that the loss of this particular intron was mediated by integration of the DNA fragment reverse-transcribed from mature mRNAs.
Highlights
Giardia intestinalis is a parasitic unicellular eukaryote with a highly reduced genome, in which only six cis-spliced and four trans-spliced introns have been discovered
Spliceosomal introns, which are excised from pre-mature mRNAs by RNA-protein complexes called spliceosomes [1], are one of the features exclusively found in eukaryotic genomes
Most of introns/splintrons in the Giardia genome were identified principally as non-coding stretches intervening in open reading frames (ORFs) encoding proteins shared amongst phylogenetically diverse eukaryotes
Summary
Giardia intestinalis is a parasitic unicellular eukaryote with a highly reduced genome, in which only six cis-spliced and four trans-spliced introns have been discovered. We anticipate that more cis- and trans-spliced introns likely remain unidentified in genes encoding hypothetical proteins that occupy ca. 2/3 of all of the open reading frames (ORFs) in the Giardia genome. Giardia intestinalis, a unicellular eukaryotic parasite belonging to the Diplomonadida (Excavata) is known to possess a highly reduced genome of only 12 Mbp in length [4]. One of the prominent natures of the Giardia genome is its low intron density—only 6 cis-spliced introns and 4 trans-spliced. Most of introns/splintrons in the Giardia genome were identified principally as non-coding stretches intervening in open reading frames (ORFs) encoding proteins shared amongst phylogenetically diverse eukaryotes. Since unidentified ORFs occupy approximately 2/3 of the ca. 9,000 ORFs encoded in the Giardia genome [4], a large fraction of introns/splintrons in the Giardia genome may have been overlooked by pioneering surveys principally based on sequence similarity
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