title: Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.
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.
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Virginia
authors.initials: V
authors.lastname: Savova
authors.affiliation: National Xenopus Resource and Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
authors.forename: Esther J
authors.initials: EJ
authors.lastname: Pearl
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Elvan
authors.initials: E
authors.lastname: Boke
authors.affiliation: Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215, USA.
authors.forename: Anwesha
authors.initials: A
authors.lastname: Nag
authors.affiliation: Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Adzhubei
authors.affiliation: National Xenopus Resource and Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
authors.forename: Marko E
authors.initials: ME
authors.lastname: Horb
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Leonid
authors.initials: L
authors.lastname: Peshkin
mesh_terms: D000818:Animals; D001483:Base Sequence; D003433:Crosses, Genetic; D020440:Gene Duplication; D014644:Genetic Variation; D016678:Genome; D006824:Hybridization, Genetic; D007178:Inbreeding; D013058:Mass Spectrometry; D020125:Mutation, Missense / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*; D029867:Xenopus Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014982:Xenopus laevis / Q000235:genetics*
chemical_list: D029867:Xenopus Proteins