title: Reverse transcriptase and intron number evolution.
abstract: BACKGROUND
  Introns are universal in eukaryotic genomes and play important roles in transcriptional regulation, mRNA export to the cytoplasm, nonsense-mediated decay as both a regulatory and a splicing quality control mechanism, R-loop avoidance, alternative splicing, chromatin structure, and evolution by exon-shuffling.
  
  
  METHODS
  Sixteen complete fungal genomes were used 13 of which were sequenced and annotated by JGI. Ustilago maydis, Cryptococcus neoformans, and Coprinus cinereus (also named Coprinopsis cinerea) were from the Broad Institute. Gene models from JGI-annotated genomes were taken from the GeneCatalog track that contained the best representative gene models. Varying fractions of the GeneCatalog were manually curated by external users. For clarity, we used the JGI unique database identifier.
  
  
  RESULTS
  The last common ancestor of eukaryotes (LECA) has an estimated 6.4 coding exons per gene (EPG) and evolved into the diverse eukaryotic life forms, which is recapitulated by the development of a stem cell. We found a parallel between the simulated reverse transcriptase (RT)-mediated intron loss and the comparative analysis of 16 fungal genomes that spanned a wide range of intron density. Although footprints of RT (RTF) were dynamic, relative intron location (RIL) to the 5'-end of mRNA faithfully traced RT-mediated intron loss and revealed 7.7 EPG for LECA. The mode of exon length distribution was conserved in simulated intron loss, which was exemplified by the shared mode of 75 nt between fungal and Chlamydomonas genomes. The dominant ancient exon length was corroborated by the average exon length of the most intron-rich genes in fungal genomes and consistent with ancient protein modules being ~25 aa. Combined with the conservation of a protein length of 400 aa, the earliest ancestor of eukaryotes could have 16 EPG. During earlier evolution, Ascomycota's ancestor had significantly more 3'-biased RT-mediated intron loss that was followed by dramatic RTF loss. There was a down trend of EPG from more conserved to less conserved genes. Moreover, species-specific genes have higher exon-densities, shorter exons, and longer introns when compared to genes conserved at the phylum level. However, intron length in species-specific genes became shorter than that of genes conserved in all species after genomes experiencing drastic intron loss. The estimated EPG from the most frequent exon length is more than double that from the RIL method.
  
  
  CONCLUSIONS
  This implies significant intron loss during the very early period of eukaryotic evolution. De novo gene-birth contributes to shorter exons, longer introns, and higher exon-density in species-specific genes relative to conserved genes.
authors.affiliation: 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Kemin
authors.initials: K
authors.lastname: Zhou
authors.affiliation: 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Kuo
authors.affiliation: 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
keywords: Intron gain and loss; fungal ancestor; genome size; reverse transcriptase (RT)