title: LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.
abstract: RNA-seq is becoming a preferred tool for genomics studies of model and non-model organisms. However, DNA-based analysis of organisms lacking sequenced genomes cannot rely on RNA-seq data alone to isolate most genes of interest, as DNA codes both exons and introns. With this in mind, we designed a novel tool, LEMONS, that exploits the evolutionary conservation of both exon/intron boundary positions and splice junction recognition signals to produce high throughput splice-junction predictions in the absence of a reference genome. When tested on multiple annotated vertebrate mRNA data, LEMONS accurately identified 87% (average) of the splice-junctions. LEMONS was then applied to our updated Mediterranean chameleon transcriptome, which lacks a reference genome, and predicted a total of 90,820 exon-exon junctions. We experimentally verified these splice-junction predictions by amplifying and sequencing twenty randomly selected genes from chameleon DNA templates. Exons and introns were detected in 19 of 20 of the positions predicted by LEMONS. To the best of our knowledge, LEMONS is currently the only experimentally verified tool that can accurately predict splice-junctions in organisms that lack a reference genome.
authors.affiliation: Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
authors.forename: Liron
authors.initials: L
authors.lastname: Levin
authors.affiliation: Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
authors.forename: Dan
authors.initials: D
authors.lastname: Bar-Yaacov
authors.affiliation: Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
authors.forename: Amos
authors.initials: A
authors.lastname: Bouskila
authors.affiliation: Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.|School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
authors.forename: Michal
authors.initials: M
authors.lastname: Chorev
authors.affiliation: Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
authors.forename: Liran
authors.initials: L
authors.lastname: Carmel
authors.affiliation: Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
authors.forename: Dan
authors.initials: D
authors.lastname: Mishmar
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005091:Exons; D023281:Genomics / Q000379:methods; D007438:Introns; D059372:Nucleotide Motifs; D022821:RNA Splice Sites; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D012984:Software; D059467:Transcriptome
chemical_list: D022821:RNA Splice Sites; D012333:RNA, Messenger