title: The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome.
abstract: Pufferfish such as fugu and tetraodon carry the smallest genomes among all vertebrates and are ideal for studying genome evolution. However, comparative genomics using these species is hindered by the poor annotation of their genomes. We performed RNA sequencing during key stages of maternal to zygotic transition of Tetraodon nigroviridis and report its first developmental transcriptome. We assembled 61,033 transcripts (23,837 loci) representing 80% of the annotated gene models and 3816 novel coding transcripts from 2667 loci. We demonstrate the similarities of gene expression profiles between pufferfish and zebrafish during maternal to zygotic transition and annotated 1120 long non-coding RNAs (lncRNAs) many of which differentially expressed during development. The promoters for 60% of the assembled transcripts result validated by CAGE-seq. Despite the extreme compaction of the tetraodon genome and the dramatic loss of transposons, the length of lncRNA exons remain comparable to that of other vertebrates and a small set of lncRNAs appears enriched for transposable elements suggesting a selective pressure acting on lncRNAs length and composition. Finally, a set of lncRNAs are microsyntenic between teleost and vertebrates, which indicates potential regulatory interactions between lncRNAs and their flanking coding genes. Our work provides a fundamental molecular resource for vertebrate comparative genomics and embryogenesis studies.
authors.affiliation: Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples - 80121, Italy.
authors.forename: Swaraj
authors.initials: S
authors.lastname: Basu
authors.affiliation: Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
authors.forename: Yavor
authors.initials: Y
authors.lastname: Hadzhiev
authors.affiliation: Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples - 80121, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Petrosino
authors.affiliation: BRIC - Biotech Research &Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
authors.forename: Chirag
authors.initials: C
authors.lastname: Nepal
authors.affiliation: Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
authors.forename: Jochen
authors.initials: J
authors.lastname: Gehrig
authors.affiliation: Karlsruhe Institute of Technology (KIT), Campus North, Institute of Toxicology and Genetics (ITG), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
authors.forename: Olivier
authors.initials: O
authors.lastname: Armant
authors.affiliation: Karlsruhe Institute of Technology (KIT), Campus North, Institute of Toxicology and Genetics (ITG), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Ferg
authors.affiliation: Karlsruhe Institute of Technology (KIT), Campus North, Institute of Toxicology and Genetics (ITG), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Strahle
authors.affiliation: Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples - 80121, Italy.
authors.forename: Remo
authors.initials: R
authors.lastname: Sanges
authors.affiliation: Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
authors.forename: Ferenc
authors.initials: F
authors.lastname: Müller
mesh_terms: D000818:Animals; D029941:Fish Proteins / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D023281:Genomics; D062085:RNA, Long Noncoding / Q000235:genetics*; D023721:Tetraodontiformes / Q000235:genetics* / Q000254:growth & development; D059467:Transcriptome
chemical_list: D029941:Fish Proteins; D062085:RNA, Long Noncoding