ArticleDevelopmental biology2017
Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.
Article in Developmental biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics.eLife · 2025Article
- Differentiation success of reprogrammed cells is heterogeneous in vivo and modulated by somatic cell identity memory.Stem cell reports · 2025Article
- Enhanced Loss of Retinoic Acid Network Genes inCells · 2022Article
- Retinoic Acid Fluctuation Activates an Uneven, Direction-Dependent Network-Wide Robustness Response in Early Embryogenesis.Frontiers in cell and developmental biology · 2021Article
- Natural size variation among embryos leads to the corresponding scaling in gene expression.Developmental biology · 2020Article
- Genomics Methods forCold Spring Harbor protocols · 2020Article
- The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.Science (New York, N.Y.) · 2018Article
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Authors and funding
7 authors.
Funding
Abstract
We characterize the genetic diversity of Xenopus laevis strains using RNA-seq data and allele-specific analysis. This data provides a catalogue of coding variation, which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). Further, we specifically compare the variation in the progeny of four crosses: inbred genomic (J)-strain, outbred albino (B)-strain, and two hybrid crosses of J and B strains. We identify a subset of mutations specific to the B strain, which allows us to investigate the selection pressures affecting duplicated genes in this allotetraploid. From these crosses we find the ratio of non-synonymous to synonymous mutations is lower in duplicated genes, which suggests that they are under greater purifying selection. Surprisingly, we also find that function-altering ("damaging") mutations constitute a greater fraction of the non-synonymous variants in this group, which suggests a role for subfunctionalization in coding variation affecting duplicated genes.
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