Research Article

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins

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Science  05 Jan 2018:
Vol. 359, Issue 6371, pp. 55-61
DOI: 10.1126/science.aao0827
  • Fig. 1 The phylogenetic relationship of Caenorhabditis and comparison of the C. nigoni and C. briggsae genome assemblies.

    (A) Phylogeny of Elegans supergroup Caenorhabditis [adapted from (3)] with outcrossing species producing XX females indicated in blue, and self-fertile lineages with XX hermaphrodites indicated in red. (B) Chromosomal alignments and genomic features over 200-kb chromosomal intervals. Tracks from outside to inside: 1, positions (in Mb) of the six chromosomes of C. nigoni and C. briggsae; 2, gene density heat map (darker shade indicates higher density); 3, repeat frequency; 4, inversion frequencies; 5, percentage of sequence lacking homology in the other assembly (representing either deletions or species-specific gains); 6, DNA sequence synteny.

  • Fig. 2 Size distributions of insertion-deletion variants.

    (A) Size distribution of species-specific sequences in the C. briggsaeC. nigoni whole-genome alignment. Black, sequences present in C. nigoni alone; gray, sequences present in C. briggsae alone. (B) Contribution of different species-specific sequence types to genome size. (C) Regression analysis of total exon and intron lengths for 6404 one-to-one C. briggsaeC. nigoni orthologs on autosomes and 1394 orthologs on the X chromosome. Interspecies differences were insignificant for either exon set (P = 0.378 for autosomes, P = 0.668 for X), but introns on autosomes (P = 1.53 × 10−10) and on the X chromosome (P = 1.2 × 10−5) were significantly larger in C. briggsae (all P values: Wilcoxon rank-sum test with Bonferroni correction).

  • Fig. 3 Comparison of the C. nigoni and C. briggsae proteomes.

    (A) Scatterplot of sizes of OrthoFinder gene families, excluding one-to-one orthologs (table S4). Of 2367 families with unequal numbers of C. nigoni and C. briggsae genes, the majority (1624) were larger in C. nigoni than in C. briggsae (P < 2.2 × 10−16, Wilcoxon signed-rank test). Dotted line indicates equal family sizes. (B) Length distributions of C. nigoni and C. briggsae proteins and of C. nigoni proteins that lack C. briggsae homologs. (C) For genes with sex-biased expression, male bias was seen for 50.9% of 6804 genes with C. briggsae homologs [“C. briggsae (+)”] but was significantly overrepresented (70.9%) among 605 genes lacking C. briggsae homologs [“C. briggsae ()”; P < 0.0001, Fisher exact test; table S9]. (D) Alignment of predicted MSS homologs from outcrossing C. nigoni, C. sinica, C. remanei, and C. brenneri (table S8) (20), with protein domains indicated above. Amino acid abbreviations: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; Y, Tyr. (E) Comparison of mss gene regions in C. nigoni and C. briggsae. Pastel shapes connect homologous sequences. Except for Cni-mss-3, all genes are transcribed from left to right. Genes surrounding the three C. nigoni mss paralogs are conserved in C. briggsae, but only fragments and a pseudogene (Cbr-mss-3-ps) of the mss genes remain. The pseudogene has a lost start codon and a +1 frameshift. CBG26068 has a novel 3′ exon derived from part of the Cni-mss-1 second exon. See fig. S7 and (20) for details.

  • Fig. 4 C. remanei MSS is a male-specific protein localized to the surface of activated sperm.

    (A) Quantitative reverse transcription polymerase chain reaction (for Cre-mss-2) of mixed-sex populations (top) versus larval and adult sex-specific populations (bottom), showing that mss expression is specific to adult males. Data are means ± SEM. Female data are two to three orders of magnitude below male data. (B) Cre-mss-1 transcripts are detected in pachytene-stage primary spermatocytes. (C) Dissected testis expressing HA-tagged Cre-MSS-1, viewed with differential interference contrast (DIC, left) or anti-HA confocal fluorescence (right) microscopy. Cre-HA-MSS-1 is first detectable in spermatocytes (sc) and becomes enriched in spermatids (st). (D) Some Cre-HA-MSS-1 is localized to the plasma membrane of spermatocytes, as indicated by the arrow. Blue fluorescence: Hoechst-stained DNA. (E) Enlarged view of the boxed region in (C), showing complete restriction to membranous organelles (MOs). (F) Cre-HA-MSS-1 remains attached to sperm after activation and transfer to the female. (G) Cre-HA-MSS-1 sperm cells dissected from a female and stained with anti-HA immunohistochemistry, imaged with DIC (top) and confocal (bottom) microscopy. Cre-HA-MSS-1 is visible in the plasma membrane and fused MO remnants.

  • Fig. 5 mss genes are necessary for sperm competitiveness in an outcrossing species, and sufficient to enhance it in a selfing species.

    (A) When mated after a wild-type male (“offense”), C. remanei mss(nmDf1/+) males sire more than twice the progeny of nmDf1/nmDf2 mss-null mutants (N = 16 for both). (B) When allowed to mate first (“defense”), heterozygous C. remanei mss(nmDf1/+) males have a slight advantage over wild-type males; mss-null mutants, in contrast, do not (N = 15 for both). Heterozygote success is assumed to be double the observed nmDf1 frequency in their progeny. For both defense and offense, P < 0.01 (two-sample Kolmogorov-Smirnov test). (C and D) Wild-type young C. briggsae hermaphrodites were mated sequentially (4 hours each) with conspecific males carrying either a C. nigoni mss(+) transgene or a control mCherry::histone reporter (RW0025). Progeny laid 0 to 18 hours and 18 to 42 hours after the second mating were scored for green (MSS+), red (RW0025), or no (self) fluorescent markers. In both offense (C) and defense (D), MSS+ males sire several times as many progeny as control males in the first laying window. *P < 0.001. (E) MSS+ C. briggsae males suppress selfing more effectively than do control AF16 (wild-type) males. Strain JU936 is a second control strain bearing two transcriptional GFP reporters in the AF16 background. *P < 0.001 (Kolmogorov-Smirnov test); ns, not significant. (F) Male frequency in MSS+ and wild-type AF16 C. briggsae populations in which male frequency was artificially elevated to 50% at the start of the experiment. In all panels except (E), error bars denote SD.

Supplementary Materials

  • Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins

    Da Yin, Erich M. Schwarz, Cristel G. Thomas, Rebecca L. Felde, Ian F. Korf, Asher D. Cutter, Caitlin M. Schartner, Edward J. Ralston, Barbara J. Meyer, Eric S. Haag

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S9
    • Tables S1, S2, S6, S7, and S9
    • Captions for tables S3, S4, S5, and S8
    • Captions for datasets S1 to S5
    • References

    Additional Data

    Data S1

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