Basu, S., Hadzhiev, Y., Petrosino, G., Nepal, C., Gehrig, J., Armant, O., Ferg, M., Strahle, U., Sanges, R., & Müller, F. (2016). The Tetraodon nigroviridis reference transcriptome: Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. Scientific Reports, 6, Article 33210. https://doi.org/10.1038/srep33210
The Tetraodon nigroviridis reference transcriptome: Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. / Basu, Swaraj; Hadzhiev, Yavor; Petrosino, Giuseppe et al.
In:
Scientific Reports, Vol. 6, 33210, 15.09.2016.
Research output: Contribution to journal › Journal article › Research › peer-review
Basu, S, Hadzhiev, Y, Petrosino, G, Nepal, C, Gehrig, J, Armant, O, Ferg, M, Strahle, U, Sanges, R & Müller, F 2016, 'The Tetraodon nigroviridis reference transcriptome: Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome', Scientific Reports, vol. 6, 33210. https://doi.org/10.1038/srep33210
Basu S, Hadzhiev Y, Petrosino G, Nepal C, Gehrig J, Armant O et al. The Tetraodon nigroviridis reference transcriptome: Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. Scientific Reports. 2016 Sept 15;6:33210. doi: 10.1038/srep33210
Basu, Swaraj ; Hadzhiev, Yavor ; Petrosino, Giuseppe et al. / The Tetraodon nigroviridis reference transcriptome : Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. In: Scientific Reports. 2016 ; Vol. 6.
@article{df5065ef14774bacbf195d7109845a03,
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.",
author = "Swaraj Basu and Yavor Hadzhiev and Giuseppe Petrosino and Chirag Nepal and Jochen Gehrig and Olivier Armant and Marco Ferg and Uwe Strahle and Remo Sanges and Ferenc M{\"u}ller",
year = "2016",
month = sep,
day = "15",
doi = "10.1038/srep33210",
language = "English",
volume = "6",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "nature publishing group",
}
TY - JOUR
T1 - The Tetraodon nigroviridis reference transcriptome
T2 - Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome
AU - Basu, Swaraj
AU - Hadzhiev, Yavor
AU - Petrosino, Giuseppe
AU - Nepal, Chirag
AU - Gehrig, Jochen
AU - Armant, Olivier
AU - Ferg, Marco
AU - Strahle, Uwe
AU - Sanges, Remo
AU - Müller, Ferenc
PY - 2016/9/15
Y1 - 2016/9/15
N2 - 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.
AB - 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.
U2 - 10.1038/srep33210
DO - 10.1038/srep33210
M3 - Journal article
C2 - 27628538
AN - SCOPUS:84987776711
SN - 2045-2322
VL - 6
JO - Scientific Reports
JF - Scientific Reports
M1 - 33210
ER -
