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SRX3325616: GSM2830583: Gibeaux201611_XenopusHybrid_TETSs39; Xenopus tropicalis; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 65M spots, 13.1G bases, 5.2Gb downloads

Submitted by: NCBI (GEO)
Study: Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus
show Abstracthide Abstract
Hybridization of eggs and sperm from closely related species can give rise to genetic diversity, or can lead to embryo inviability due to incompatibility. Although central to evolution, the cellular and molecular mechanisms underlying postzygotic barriers that drive reproductive isolation and speciation remain largely unknown. Species of the African Clawed frog Xenopus provide an ideal system to study hybridization and genome evolution. Xenopus laevis is an allotetraploid with 36 chromosomes that arose through interspecific hybridization of diploid progenitors, whereas Xenopus tropicalis is a diploid with 20 chromosomes that diverged from a common ancestor ~48 million years ago. Differences in genome size between the two species are accompanied by organism size differences, and size scaling of the egg and subcellular structures such as nuclei and spindles formed in egg extracts. Nevertheless, early development transcriptional programs, gene expression patterns, and protein sequences are generally conserved. Interestingly, whereas the hybrid produced when X. laevis eggs are fertilized by X. tropicalis sperm (le×ts) is viable, the reverse hybrid (te×ls) dies prior to gastrulation. Here, we applied cell biological tools and high-throughput methods to study the mechanisms underlying hybrid inviability. We reveal that two specific X. laevis chromosomes are incompatible with the X. tropicalis cytoplasm and are mis-segregated during mitosis, leading to unbalanced gene expression at the maternal to zygotic transition, followed by cell-autonomous catastrophic embryo death. Overall design: Collect mRNA from whole embryos; three biological replicates were analyzed
Sample: Gibeaux201611_XenopusHybrid_TETSs39
SAMN07834093 • SRS2629865 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Embryos were homogenize mechanically in TRIzol (Thermo Fisher Scientific, Waltham, MA) using up to a 30-gauge needle and processed according to supplier instructions. After resuspension in nuclease-free H2O, RNAs were cleaned up using RNeasy kit (Qiagen Inc.) with on-column DNA digestion, following supplier protocol. mRNA enrichment was performed on total RNA using polyA selection with the Invitrogen Dynabeads mRNA Direct kit. The library preparation was done on the Apollo324™ with PrepX™ RNAseq Library Prep Kits (WaferGen Biosystems, Fremont, CA), and 13 cycles of PCR amplification was used for index addition and library fragment enrichment.
Experiment attributes:
GEO Accession: GSM2830583
Links:
Runs: 1 run, 65M spots, 13.1G bases, 5.2Gb
Run# of Spots# of BasesSizePublished
SRR621695364,970,15613.1G5.2Gb2017-11-15

ID:
4654353

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