title: Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium.
abstract: BACKGROUND
  Spliceosomal introns are a common feature of eukaryotic genomes. To approach a comprehensive understanding of intron evolution on Earth, studies should look beyond repeatedly studied groups such as animals, plants, and fungi. The slime mold Dictyostelium belongs to a supergroup of eukaryotes not covered in previous studies.
  
  
  RESULTS
  We found 441 precise intron losses in Dictyostelium discoideum and 202 precise intron losses in Dictyostelium purpureum. Consistent with these observations, Dictyostelium discoideum was found to have significantly more copies of reverse transcriptase genes than Dictyostelium purpureum. We also found that the lost introns are significantly further from the 5' end of genes than the conserved introns. Adjacent introns were prone to be lost simultaneously in Dictyostelium discoideum. In both Dictyostelium species, the exonic sequences flanking lost introns were found to have a significantly higher GC content than those flanking conserved introns. Together, these observations support a reverse-transcription model of intron loss in which intron losses were caused by gene conversion between genomic DNA and cDNA reverse transcribed from mature mRNA. We also identified two imprecise intron losses in Dictyostelium discoideum that may have resulted from genomic deletions. Ninety-eight putative intron gains were also observed. Consistent with previous studies of other lineages, the source sequences were found in only a small number of cases, with only two instances of intron gain identified in Dictyostelium discoideum.
  
  
  CONCLUSIONS
  Although they diverged very early from animals and fungi, Dictyostelium species have similar mechanisms of intron loss.
authors.affiliation: MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China. ma_my@outlook.com.|Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China. ma_my@outlook.com.
authors.forename: Ming-Yue
authors.initials: MY
authors.lastname: Ma
authors.affiliation: The High School Affiliated to Renmin University of China, Beijing, 100080, China. 1240704384@qq.com.
authors.forename: Xun-Ru
authors.initials: XR
authors.lastname: Che
authors.affiliation: Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy. aporceddu@uniss.it.
authors.forename: Andrea
authors.initials: A
authors.lastname: Porceddu
authors.affiliation: MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China. dengkeniu@hotmail.com.|Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China. dengkeniu@hotmail.com.
authors.forename: Deng-Ke
authors.initials: DK
authors.lastname: Niu
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004023:Dictyostelium / Q000145:classification* / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D056890:Eukaryota / Q000145:classification / Q000235:genetics; D005091:Exons; D005785:Gene Conversion; D018503:Genome, Protozoan; D007438:Introns; D008969:Molecular Sequence Data; D012194:RNA-Directed DNA Polymerase / Q000235:genetics / Q000378:metabolism; D018626:Retroelements; D017384:Sequence Deletion
chemical_list: D018626:Retroelements; D012194:RNA-Directed DNA Polymerase