The Tetraodon nigroviridis reference transcriptome: Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome

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 noncoding
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. ... mehrFinally, 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.